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Xia Y, Chen K, Yang Q, Chen Z, Jin L, Zhang L, Yu X, Wang L, Xie C, Zhao Y, Shen Y, Tong J. Methylation in cornea and corneal diseases: a systematic review. Cell Death Discov 2024; 10:169. [PMID: 38589350 PMCID: PMC11002037 DOI: 10.1038/s41420-024-01935-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 04/10/2024] Open
Abstract
Corneal diseases are among the primary causes of blindness and vision loss worldwide. However, the pathogenesis of corneal diseases remains elusive, and diagnostic and therapeutic tools are limited. Thus, identifying new targets for the diagnosis and treatment of corneal diseases has gained great interest. Methylation, a type of epigenetic modification, modulates various cellular processes at both nucleic acid and protein levels. Growing evidence shows that methylation is a key regulator in the pathogenesis of corneal diseases, including inflammation, fibrosis, and neovascularization, making it an attractive potential therapeutic target. In this review, we discuss the major alterations of methylation and demethylation at the DNA, RNA, and protein levels in corneal diseases and how these dynamics contribute to the pathogenesis of corneal diseases. Also, we provide insights into identifying potential biomarkers of methylation that may improve the diagnosis and treatment of corneal diseases.
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Affiliation(s)
- Yutong Xia
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Kuangqi Chen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Qianjie Yang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Zhitong Chen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Le Jin
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Liyue Zhang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Xin Yu
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Liyin Wang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Chen Xie
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Yuan Zhao
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Ye Shen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China.
| | - Jianping Tong
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China.
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2
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Damiani F, Cornuti S, Tognini P. The gut-brain connection: Exploring the influence of the gut microbiota on neuroplasticity and neurodevelopmental disorders. Neuropharmacology 2023; 231:109491. [PMID: 36924923 DOI: 10.1016/j.neuropharm.2023.109491] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/22/2023] [Accepted: 03/05/2023] [Indexed: 03/17/2023]
Abstract
Neuroplasticity refers to the ability of brain circuits to reorganize and change the properties of the network, resulting in alterations in brain function and behavior. It is traditionally believed that neuroplasticity is influenced by external stimuli, learning, and experience. Intriguingly, there is new evidence suggesting that endogenous signals from the body's periphery may play a role. The gut microbiota, a diverse community of microorganisms living in harmony with their host, may be able to influence plasticity through its modulation of the gut-brain axis. Interestingly, the maturation of the gut microbiota coincides with critical periods of neurodevelopment, during which neural circuits are highly plastic and potentially vulnerable. As such, dysbiosis (an imbalance in the gut microbiota composition) during early life may contribute to the disruption of normal developmental trajectories, leading to neurodevelopmental disorders. This review aims to examine the ways in which the gut microbiota can affect neuroplasticity. It will also discuss recent research linking gastrointestinal issues and bacterial dysbiosis to various neurodevelopmental disorders and their potential impact on neurological outcomes.
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Affiliation(s)
| | - Sara Cornuti
- Laboratory of Biology, Scuola Normale Superiore, Pisa, Italy
| | - Paola Tognini
- Laboratory of Biology, Scuola Normale Superiore, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy.
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3
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Shang A, Bieszczad KM. Epigenetic mechanisms regulate cue memory underlying discriminative behavior. Neurosci Biobehav Rev 2022; 141:104811. [PMID: 35961385 DOI: 10.1016/j.neubiorev.2022.104811] [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: 03/31/2022] [Revised: 06/15/2022] [Accepted: 08/01/2022] [Indexed: 12/01/2022]
Abstract
The burgeoning field of neuroepigenetics has introduced chromatin modification as an important interface between experience and brain function. For example, epigenetic mechanisms like histone acetylation and DNA methylation operate throughout a lifetime to powerfully regulate gene expression in the brain that is required for experiences to be transformed into long-term memories. This review highlights emerging evidence from sensory models of memory that converge on the premise that epigenetic regulation of activity-dependent transcription in the sensory brain facilitates highly precise memory recall. Chromatin modifications may be key for neurophysiological responses to transient sensory cue features experienced in the "here and now" to be recapitulated over the long term. We conclude that the function of epigenetic control of sensory system neuroplasticity is to regulate the amount and type of sensory information retained in long-term memories by regulating neural representations of behaviorally relevant cues that guide behavior. This is of broad importance in the neuroscience field because there are few circumstances in which behavioral acts are devoid of an initiating sensory experience.
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Affiliation(s)
- Andrea Shang
- Dept. of Psychology - Behavioral and Systems Neuroscience, Rutgers University - New Brunswick, 152 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Kasia M Bieszczad
- Dept. of Psychology - Behavioral and Systems Neuroscience, Rutgers University - New Brunswick, 152 Frelinghuysen Road, Piscataway, NJ 08854, USA; Rutgers Center for Cognitive Science (RuCCS), Rutgers University, Piscataway, NJ 08854, USA; Department of Otolaryngology - Head and Neck Surgery, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08854, USA.
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4
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Gibel-Russo R, Benacom D, Di Nardo AA. Non-Cell-Autonomous Factors Implicated in Parvalbumin Interneuron Maturation and Critical Periods. Front Neural Circuits 2022; 16:875873. [PMID: 35601531 PMCID: PMC9115720 DOI: 10.3389/fncir.2022.875873] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/04/2022] [Indexed: 02/04/2023] Open
Abstract
From birth to adolescence, the brain adapts to its environmental stimuli through structural and functional remodeling of neural circuits during critical periods of heightened plasticity. They occur across modalities for proper sensory, motor, linguistic, and cognitive development. If they are disrupted by early-life adverse experiences or genetic deficiencies, lasting consequences include behavioral changes, physiological and cognitive deficits, or psychiatric illness. Critical period timing is orchestrated not only by appropriate neural activity but also by a multitude of signals that participate in the maturation of fast-spiking parvalbumin interneurons and the consolidation of neural circuits. In this review, we describe the various signaling factors that initiate critical period onset, such as BDNF, SPARCL1, or OTX2, which originate either from local neurons or glial cells or from extracortical sources such as the choroid plexus. Critical period closure is established by signals that modulate extracellular matrix and myelination, while timing and plasticity can also be influenced by circadian rhythms and by hormones and corticosteroids that affect brain oxidative stress levels or immune response. Molecular outcomes include lasting epigenetic changes which themselves can be considered signals that shape downstream cross-modal critical periods. Comprehensive knowledge of how these signals and signaling factors interplay to influence neural mechanisms will help provide an inclusive perspective on the effects of early adversity and developmental defects that permanently change perception and behavior.
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5
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Epigenetic MRI: Noninvasive imaging of DNA methylation in the brain. Proc Natl Acad Sci U S A 2022; 119:e2119891119. [PMID: 35235458 PMCID: PMC8915962 DOI: 10.1073/pnas.2119891119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Dynamic epigenetic activity is a fundamental mechanism underpinning how the brain changes its function during development and aging and in response to environmental and disease stimuli. We developed a technology called epigenetic MRI (eMRI) that enables noninvasive imaging of DNA methylation in the brain, a major epigenetic mechanism. eMRI reveals strong regional differences in global DNA methylation in pig brains, a model with stronger resemblance to human brains than are rodents. Given the noninvasive nature of eMRI, our results pave the way for a DNA-methylation imaging paradigm for living human brains. We expect eMRI to enable many studies to unravel the molecular control of brain function and disease. Both neuronal and genetic mechanisms regulate brain function. While there are excellent methods to study neuronal activity in vivo, there are no nondestructive methods to measure global gene expression in living brains. Here, we present a method, epigenetic MRI (eMRI), that overcomes this limitation via direct imaging of DNA methylation, a major gene-expression regulator. eMRI exploits the methionine metabolic pathways for DNA methylation to label genomic DNA through 13C-enriched diets. A 13C magnetic resonance spectroscopic imaging method then maps the spatial distribution of labeled DNA. We validated eMRI using pigs, whose brains have stronger similarity to humans in volume and anatomy than rodents, and confirmed efficient 13C-labeling of brain DNA. We also discovered strong regional differences in global DNA methylation. Just as functional MRI measurements of regional neuronal activity have had a transformational effect on neuroscience, we expect that the eMRI signal, both as a measure of regional epigenetic activity and as a possible surrogate for regional gene expression, will enable many new investigations of human brain function, behavior, and disease.
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6
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Rodríguez-Campuzano AG, Hernández-Kelly LC, Ortega A. DNA Methylation-Dependent Gene Expression Regulation of Glutamate Transporters in Cultured Radial Glial Cells. Mol Neurobiol 2022; 59:1912-1924. [PMID: 35032319 DOI: 10.1007/s12035-022-02746-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 01/11/2022] [Indexed: 11/26/2022]
Abstract
Exposure to xenobiotics has a significant impact in brain physiology that could be liked to an excitotoxic process induced by a massive release of the main excitatory neurotransmitter, L-glutamate. Overstimulation of extra-synaptic glutamate receptors, mainly of the N-methyl-D-aspartate subtype leads to a disturbance of intracellular calcium homeostasis that is critically involved in neuronal death. Hence, glutamate extracellular levels are tightly regulated through its uptake by glial glutamate transporters. It has been observed that glutamate regulates its own removal, both in the short-time frame via a transporter-mediated decrease in the uptake, and in the long-term through the transcriptional control of its gene expression, a process mediated by glutamate receptors that involves the Ca2+/diacylglycerol-dependent protein kinase and the transcription factor Ying Yang 1. Taking into consideration that this transcription factor is a member of the Polycomb complex and thus, part of repressive and activating chromatin remodeling factors, it might direct the interaction of DNA methyltransferases or dioxygenases of methylated cytosines to their target sequences. Here we explored the role of dynamic DNA methylation in the expression and function of glial glutamate transporters. To this end, we used the well-characterized models of primary cultures of chick cerebellar Bergmann glia cells and a human retina-derived Müller glia cell line. A time and dose-dependent increase in global DNA methylation was evident upon glutamate exposure. Under hypomethylation conditions, the glial glutamate transporter protein levels and uptake activity were increased. These results favor the notion that a dynamic DNA methylation program triggered by glutamate in glial cells modulates one of its major functions: glutamate removal.
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Affiliation(s)
- Ada G Rodríguez-Campuzano
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, Zacatenco Ciudad de México, 07360, México
| | - Luisa C Hernández-Kelly
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, Zacatenco Ciudad de México, 07360, México
| | - Arturo Ortega
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, Zacatenco Ciudad de México, 07360, México.
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7
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Thomas KT, Zakharenko SS. MicroRNAs in the Onset of Schizophrenia. Cells 2021; 10:2679. [PMID: 34685659 PMCID: PMC8534348 DOI: 10.3390/cells10102679] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/30/2021] [Accepted: 10/02/2021] [Indexed: 12/14/2022] Open
Abstract
Mounting evidence implicates microRNAs (miRNAs) in the pathology of schizophrenia. These small noncoding RNAs bind to mRNAs containing complementary sequences and promote their degradation and/or inhibit protein synthesis. A single miRNA may have hundreds of targets, and miRNA targets are overrepresented among schizophrenia-risk genes. Although schizophrenia is a neurodevelopmental disorder, symptoms usually do not appear until adolescence, and most patients do not receive a schizophrenia diagnosis until late adolescence or early adulthood. However, few studies have examined miRNAs during this critical period. First, we examine evidence that the miRNA pathway is dynamic throughout adolescence and adulthood and that miRNAs regulate processes critical to late neurodevelopment that are aberrant in patients with schizophrenia. Next, we examine evidence implicating miRNAs in the conversion to psychosis, including a schizophrenia-associated single nucleotide polymorphism in MIR137HG that is among the strongest known predictors of age of onset in patients with schizophrenia. Finally, we examine how hemizygosity for DGCR8, which encodes an obligate component of the complex that synthesizes miRNA precursors, may contribute to the onset of psychosis in patients with 22q11.2 microdeletions and how animal models of this disorder can help us understand the many roles of miRNAs in the onset of schizophrenia.
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Affiliation(s)
- Kristen T. Thomas
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Stanislav S. Zakharenko
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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8
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Kasamatsu T, Imamura K. Ocular dominance plasticity: Molecular mechanisms revisited. J Comp Neurol 2020; 528:3039-3074. [PMID: 32737874 DOI: 10.1002/cne.25001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022]
Abstract
Ocular dominance plasticity (ODP) is a type of cortical plasticity operating in visual cortex of mammals that are endowed with binocular vision based on the competition-driven disparity. Earlier, a molecular mechanism was proposed that catecholamines play an important role in the maintenance of ODP in kittens. Having survived the initial test, the hypothesis was further advanced to identify noradrenaline (NA) as a key factor that regulates ODP in the immature cortex. Later, the ODP-promoting effect of NA is extended to the adult with age-related limitations. Following the enhanced NA availability, the chain events downstream lead to the β-adrenoreceptor-induced cAMP accumulation, which in turn activates the protein kinase A. Eventually, the protein kinase translocates to the cell nucleus to activate cAMP responsive element binding protein (CREB). CREB is a cellular transcription factor that controls the transcription of various genes, underpinning neuronal plasticity and long-term memory. In the advent of molecular genetics in that various types of new tools have become available with relative ease, ODP research has lightly adopted in the rodent model the original concepts and methodologies. Here, after briefly tracing the strategic maturation of our quest, the review moves to the later development of the field, with the emphasis placed around the following issues: (a) Are we testing ODP per se? (b) What does monocular deprivation deprive of the immature cortex? (c) The critical importance of binocular competition, (d) What is the adult plasticity? (e) Excitation-Inhibition balance in local circuits, and (f) Species differences in the animal models.
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Affiliation(s)
- Takuji Kasamatsu
- Smith-Kettlewell Eye Research Institute, San Francisco, California, USA
| | - Kazuyuki Imamura
- Department of Systems Life Engineering, Maebashi Institute of Technology, Maebashi-shi, Gunma, Japan
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9
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Baroncelli L, Lunghi C. Neuroplasticity of the visual cortex: in sickness and in health. Exp Neurol 2020; 335:113515. [PMID: 33132181 DOI: 10.1016/j.expneurol.2020.113515] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/14/2020] [Accepted: 10/21/2020] [Indexed: 01/18/2023]
Abstract
Brain plasticity refers to the ability of synaptic connections to adapt their function and structure in response to experience, including environmental changes, sensory deprivation and injuries. Plasticity is a distinctive, but not exclusive, property of the developing nervous system. This review introduces the concept of neuroplasticity and describes classic paradigms to illustrate cellular and molecular mechanisms underlying synapse modifiability. Then, we summarize a growing number of studies showing that the adult cerebral cortex retains a significant degree of plasticity highlighting how the identification of strategies to enhance the plastic potential of the adult brain could pave the way for the development of novel therapeutic approaches aimed at treating amblyopia and other neurodevelopmental disorders. Finally, we analyze how the visual system adjusts to neurodegenerative conditions leading to blindness and we discuss the crucial role of spared plasticity in the visual system for sight recovery.
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Affiliation(s)
- Laura Baroncelli
- Institute of Neuroscience, National Research Council (CNR), I-56124 Pisa, Italy; Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, I-56128 Pisa, Italy.
| | - Claudia Lunghi
- Laboratoire des systèmes perceptifs, Département d'études cognitives, École normale supérieure, PSL University, CNRS, 75005 Paris, France
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10
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Napoli D, Lupori L, Mazziotti R, Sagona G, Bagnoli S, Samad M, Sacramento EK, Kirkpartick J, Putignano E, Chen S, Terzibasi Tozzini E, Tognini P, Baldi P, Kwok JC, Cellerino A, Pizzorusso T. MiR-29 coordinates age-dependent plasticity brakes in the adult visual cortex. EMBO Rep 2020; 21:e50431. [PMID: 33026181 DOI: 10.15252/embr.202050431] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 09/04/2020] [Accepted: 09/08/2020] [Indexed: 12/15/2022] Open
Abstract
Visual cortical circuits show profound plasticity during early life and are later stabilized by molecular "brakes" limiting excessive rewiring beyond a critical period. The mechanisms coordinating the expression of these factors during the transition from development to adulthood remain unknown. We found that miR-29a expression in the visual cortex dramatically increases with age, but it is not experience-dependent. Precocious high levels of miR-29a blocked ocular dominance plasticity and caused an early appearance of perineuronal nets. Conversely, inhibition of miR-29a in adult mice using LNA antagomirs activated ocular dominance plasticity, reduced perineuronal nets, and restored their juvenile chemical composition. Activated adult plasticity had the typical functional and proteomic signature of critical period plasticity. Transcriptomic and proteomic studies indicated that miR-29a manipulation regulates the expression of plasticity brakes in specific cortical circuits. These data indicate that miR-29a is a regulator of the plasticity brakes promoting age-dependent stabilization of visual cortical connections.
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Affiliation(s)
- Debora Napoli
- BIO@SNS Lab, Scuola Normale Superiore, Pisa, Italy.,Institute of Neuroscience, National Research Council, Pisa, Italy
| | | | - Raffaele Mazziotti
- Department of Neuroscience, Psychology, Drug Research and Child Health, NEUROFARBA University of Florence, Florence, Italy
| | - Giulia Sagona
- Department of Neuroscience, Psychology, Drug Research and Child Health, NEUROFARBA University of Florence, Florence, Italy.,Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Sara Bagnoli
- BIO@SNS Lab, Scuola Normale Superiore, Pisa, Italy
| | - Muntaha Samad
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, CA, USA
| | | | - Joanna Kirkpartick
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Elena Putignano
- Institute of Neuroscience, National Research Council, Pisa, Italy
| | - Siwei Chen
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, CA, USA
| | | | - Paola Tognini
- BIO@SNS Lab, Scuola Normale Superiore, Pisa, Italy.,Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Pierre Baldi
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, CA, USA
| | - Jessica Cf Kwok
- School of Biomedical Sciences, University of Leeds, Leeds, UK.,Institute of Experimental Medicine, Czech Academy of Science, Prague, Czech Republic
| | - Alessandro Cellerino
- BIO@SNS Lab, Scuola Normale Superiore, Pisa, Italy.,Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Tommaso Pizzorusso
- BIO@SNS Lab, Scuola Normale Superiore, Pisa, Italy.,Institute of Neuroscience, National Research Council, Pisa, Italy.,Department of Neuroscience, Psychology, Drug Research and Child Health, NEUROFARBA University of Florence, Florence, Italy
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11
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Apulei J, Kim N, Testa D, Ribot J, Morizet D, Bernard C, Jourdren L, Blugeon C, Di Nardo AA, Prochiantz A. Non-cell Autonomous OTX2 Homeoprotein Regulates Visual Cortex Plasticity Through Gadd45b/g. Cereb Cortex 2020; 29:2384-2395. [PMID: 29771284 DOI: 10.1093/cercor/bhy108] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 04/19/2018] [Indexed: 11/14/2022] Open
Abstract
The non-cell autonomous transfer of OTX2 homeoprotein transcription factor into juvenile mouse cerebral cortex regulates parvalbumin interneuron maturation and critical period timing. By analyzing gene expression in primary visual cortex of wild-type and Otx2+/GFP mice at plastic and nonplastic ages, we identified several putative genes implicated in Otx2-dependent visual cortex plasticity for ocular dominance. Cortical OTX2 infusion in juvenile mice induced Gadd45b/g expression through direct regulation of transcription. Intriguingly, a reverse effect was found in the adult, where reducing cortical OTX2 resulted in Gadd45b/g upregulation. Viral expression of Gadd45b in adult visual cortex directly induced ocular dominance plasticity with concomitant changes in MeCP2 foci within parvalbumin interneurons and in methylation states of several plasticity gene promoters, suggesting epigenetic regulation. This interaction provides a molecular mechanism for OTX2 to trigger critical period plasticity yet suppress adult plasticity.
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Affiliation(s)
- Jessica Apulei
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U1050, PSL University, Labex MemoLife, Paris, France
| | - Namsuk Kim
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U1050, PSL University, Labex MemoLife, Paris, France
| | - Damien Testa
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U1050, PSL University, Labex MemoLife, Paris, France
| | - Jérôme Ribot
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U1050, PSL University, Labex MemoLife, Paris, France
| | - David Morizet
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U1050, PSL University, Labex MemoLife, Paris, France
| | - Clémence Bernard
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U1050, PSL University, Labex MemoLife, Paris, France
| | - Laurent Jourdren
- Genomic Core Facility, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, Paris, France
| | - Corinne Blugeon
- Genomic Core Facility, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, Paris, France
| | - Ariel A Di Nardo
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U1050, PSL University, Labex MemoLife, Paris, France
| | - Alain Prochiantz
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U1050, PSL University, Labex MemoLife, Paris, France
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12
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Schwartz BA, Wang W, Bao S. Pharmacological DNA Demethylation Weakens Inhibitory Synapses in the Auditory Cortex and Re-opens the Critical Period for Frequency Map Plasticity. Neuroscience 2020; 440:239-248. [PMID: 32512139 DOI: 10.1016/j.neuroscience.2020.05.056] [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: 12/11/2019] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 10/24/2022]
Abstract
The critical period is a time of maximal plasticity within the cortex. The progression of the critical period is marked by experience-dependent transcriptional alterations in cortical neurons, which in turn shifts the excitatory-inhibitory balance in the brain, and accordingly reduces plasticity. Epigenetic mechanisms, such as DNA methylation, control the transcriptional state of neurons, and have been shown to be dynamically regulated during the critical period. Here we show that adult animals have a significantly higher concentration of DNA methylation than critical period animals. Pharmacological reduction of DNA methylation in adult animals re-establishes critical period auditory map plasticity. Furthermore, the reduction of DNA methylation in adult animals, reverted intrinsic characteristics of inhibitory synapses to an immature state. Our data suggest that accumulation of DNA methylation during the critical period confers a mature phenotype to cortical neurons, which in turn, facilitates the reduction in plasticity seen after the critical period.
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Affiliation(s)
- Benjamin A Schwartz
- Neuroscience Program, University of Arizona, Tucson, AZ 85724, United States
| | - Weihua Wang
- Departments of Physiology, University of Arizona, Tucson, AZ 85724, United States
| | - Shaowen Bao
- Neuroscience Program, University of Arizona, Tucson, AZ 85724, United States; Departments of Physiology, University of Arizona, Tucson, AZ 85724, United States.
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13
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Interplay between Metabolism, Nutrition and Epigenetics in Shaping Brain DNA Methylation, Neural Function and Behavior. Genes (Basel) 2020; 11:genes11070742. [PMID: 32635190 PMCID: PMC7397264 DOI: 10.3390/genes11070742] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/25/2020] [Accepted: 07/02/2020] [Indexed: 12/14/2022] Open
Abstract
Gene expression in the brain is dramatically regulated by a variety of stimuli. While the role of neural activity has been extensively studied, less is known about the effects of metabolism and nutrition on transcriptional control mechanisms in the brain. Extracellular signals are integrated at the chromatin level through dynamic modifications of epigenetic marks, which in turn fine-tune gene transcription. In the last twenty years, it has become clear that epigenetics plays a crucial role in modulating central nervous system functions and finally behavior. Here, we will focus on the effect of metabolic signals in shaping brain DNA methylation, both during development and adulthood. We will provide an overview of maternal nutrition effects on brain methylation and behavior in offspring. In addition, the impact of different diet challenges on cytosine methylation dynamics in the adult brain will be discussed. Finally, the possible role played by the metabolic status in modulating DNA hydroxymethylation, which is particularly abundant in neural tissue, will be considered.
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14
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He J, Xu X, Monavarfeshani A, Banerjee S, Fox MA, Xie H. Retinal-input-induced epigenetic dynamics in the developing mouse dorsal lateral geniculate nucleus. Epigenetics Chromatin 2019; 12:13. [PMID: 30764861 PMCID: PMC6374911 DOI: 10.1186/s13072-019-0257-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 02/05/2019] [Indexed: 12/28/2022] Open
Abstract
DNA methylation plays important roles in the regulation of nervous system development and in cellular responses to environmental stimuli such as light-derived signals. Despite great efforts in understanding the maturation and refinement of visual circuits, we lack a clear understanding of how changes in DNA methylation correlate with visual activity in the developing subcortical visual system, such as in the dorsal lateral geniculate nucleus (dLGN), the main retino-recipient region in the dorsal thalamus. Here, we explored epigenetic dynamics underlying dLGN development at ages before and after eye opening in wild-type mice and mutant mice in which retinal ganglion cells fail to form. We observed that development-related epigenetic changes tend to co-localize together on functional genomic regions critical for regulating gene expression, while retinal-input-induced epigenetic changes are enriched on repetitive elements. Enhancers identified in neurons are prone to methylation dynamics during development, and activity-induced enhancers are associated with retinal-input-induced epigenetic changes. Intriguingly, the binding motifs of activity-dependent transcription factors, including EGR1 and members of MEF2 family, are enriched in the genomic regions with epigenetic aberrations in dLGN tissues of mutant mice lacking retinal inputs. Overall, our study sheds new light on the epigenetic regulatory mechanisms underlying the role of retinal inputs on the development of mouse dLGN.
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Affiliation(s)
- Jianlin He
- Biocomplexity Institute of Virginia Tech, Blacksburg, VA, 24061, USA
| | - Xiguang Xu
- Biocomplexity Institute of Virginia Tech, Blacksburg, VA, 24061, USA.,Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Aboozar Monavarfeshani
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.,Developmental and Translational Neurobiology Center, Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA, 24016, USA
| | - Sharmi Banerjee
- Biocomplexity Institute of Virginia Tech, Blacksburg, VA, 24061, USA.,Bradley Department of Electrical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Michael A Fox
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA. .,Developmental and Translational Neurobiology Center, Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, VA, 24016, USA. .,Department of Pediatrics, Virginia Tech Carilion School of Medicine, Roanoke, VA, 24016, USA.
| | - Hehuang Xie
- Biocomplexity Institute of Virginia Tech, Blacksburg, VA, 24061, USA. .,Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA. .,Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, 24061, USA.
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15
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Hsu CL, Chou CH, Huang SC, Lin CY, Lin MY, Tung CC, Lin CY, Lai IP, Zou YF, Youngson NA, Lin SP, Yang CH, Chen SK, Gau SSF, Huang HS. Analysis of experience-regulated transcriptome and imprintome during critical periods of mouse visual system development reveals spatiotemporal dynamics. Hum Mol Genet 2019; 27:1039-1054. [PMID: 29346572 DOI: 10.1093/hmg/ddy023] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/09/2018] [Indexed: 12/15/2022] Open
Abstract
Visual system development is light-experience dependent, which strongly implicates epigenetic mechanisms in light-regulated maturation. Among many epigenetic processes, genomic imprinting is an epigenetic mechanism through which monoallelic gene expression occurs in a parent-of-origin-specific manner. It is unknown if genomic imprinting contributes to visual system development. We profiled the transcriptome and imprintome during critical periods of mouse visual system development under normal- and dark-rearing conditions using B6/CAST F1 hybrid mice. We identified experience-regulated, isoform-specific and brain-region-specific imprinted genes. We also found imprinted microRNAs were predominantly clustered into the Dlk1-Dio3 imprinted locus with light experience affecting some imprinted miRNA expression. Our findings provide the first comprehensive analysis of light-experience regulation of the transcriptome and imprintome during critical periods of visual system development. Our results may contribute to therapeutic strategies for visual impairments and circadian rhythm disorders resulting from a dysfunctional imprintome.
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Affiliation(s)
- Chi-Lin Hsu
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Chih-Hsuan Chou
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Shih-Chuan Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Chia-Yi Lin
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Meng-Ying Lin
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Chun-Che Tung
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Chun-Yen Lin
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan.,Department of Pediatrics, Yong-He Cardinal Tien Hospital, Taipei 234, Taiwan
| | - Ivan Pochou Lai
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Yan-Fang Zou
- Department of Life Science, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Neil A Youngson
- Department of Pharmacology, School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Shau-Ping Lin
- Institute of Biotechnology, College of Bio-Resources & Agriculture, National Taiwan University, Taipei 106, Taiwan
| | - Chang-Hao Yang
- Department of Ophthalmology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Shih-Kuo Chen
- Department of Life Science, College of Life Science, National Taiwan University, Taipei 106, Taiwan.,Neurodevelopment Club in Taiwan, Taipei 10051, Taiwan
| | - Susan Shur-Fen Gau
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan.,Department of Psychiatry, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Hsien-Sung Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan.,Neurodevelopment Club in Taiwan, Taipei 10051, Taiwan
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16
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Sakai A, Sugiyama S. Experience-dependent transcriptional regulation in juvenile brain development. Dev Growth Differ 2019; 60:473-482. [PMID: 30368782 DOI: 10.1111/dgd.12571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 09/21/2018] [Accepted: 09/21/2018] [Indexed: 12/26/2022]
Abstract
During brain development, once primary neural networks are formed, they are largely sculpted by environmental stimuli. The juvenile brain has a unique time window termed the critical period, in which neuronal circuits are remodeled by experience. Accumulating evidence indicates that abnormal rewiring of circuits in early life contributes to various neurodevelopmental disorders at later stages of life. Recent studies implicate two important aspects for activation of the critical period, both of which are experience-dependent: (a) proper excitatory/inhibitory (E/I) balance of neural circuit achieved during developmental trajectory of inhibitory interneurons, and (b) epigenetic regulation allowing flexible gene expression for neuronal plasticity. In this review, we discuss the molecular mechanisms of juvenile brain plasticity from the viewpoints of transcriptional and chromatin regulation, with a focus on Otx2 homeoprotein. Depending on experience, Otx2 is transported into cortical parvalbumin-positive interneurons (PV cells), where it induces PV cell maturation to activate the critical period. Understanding the unique behavior and function of Otx2 as a "messenger" of experience should therefore provide insights into mechanisms of juvenile brain development. Recently identified downstream targets of Otx2 suggest novel roles of Otx2 in homeostasis of PV cells, and, moreover, in regulation of chromatin state, which is important for neuronal plasticity. We further discuss epigenetic changes during postnatal brain development spanning the critical period. Different aspects of chromatin regulation may underlie experience-dependent neuronal development and plasticity.
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Affiliation(s)
- Akiko Sakai
- Laboratory of Neuronal Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Sayaka Sugiyama
- Laboratory of Neuronal Development, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
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17
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Jawaid A, Roszkowski M, Mansuy IM. Transgenerational Epigenetics of Traumatic Stress. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 158:273-298. [PMID: 30072057 DOI: 10.1016/bs.pmbts.2018.03.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Traumatic stress is a type of environmental experience that can modify behavior, cognition and physiological functions such as metabolism, in mammals. Many of the effects of traumatic stress can be transmitted to subsequent generations even when individuals from these generations are not exposed to any traumatic stressor. This book chapter discusses the concept of epigenetic/non-genomic inheritance of such traits involving the germline in mammals. It includes a comprehensive review of animal and human studies on inter- and transgenerational inheritance of the effects of traumatic stress, some of the epigenetic changes in the germline currently known to be associated with traumatic stress, and possible mechanisms for their induction and maintenance during development and adulthood. We also describe some experimental interventions that attempted to prevent the transmission of these effects, and consider the evolutionary importance of transgenerational inheritance and future outlook of the field.
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Affiliation(s)
- Ali Jawaid
- Laboratory of Neuroepigenetics, Medical Faculty of the University of Zurich and Department of Health Science and Technology of the Swiss Federal Institute of Technology, Neuroscience Center Zurich, Zurich, Switzerland
| | - Martin Roszkowski
- Laboratory of Neuroepigenetics, Medical Faculty of the University of Zurich and Department of Health Science and Technology of the Swiss Federal Institute of Technology, Neuroscience Center Zurich, Zurich, Switzerland
| | - Isabelle M Mansuy
- Laboratory of Neuroepigenetics, Medical Faculty of the University of Zurich and Department of Health Science and Technology of the Swiss Federal Institute of Technology, Neuroscience Center Zurich, Zurich, Switzerland.
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18
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The Stress-Induced Transcription Factor NR4A1 Adjusts Mitochondrial Function and Synapse Number in Prefrontal Cortex. J Neurosci 2018; 38:1335-1350. [PMID: 29295823 PMCID: PMC5815341 DOI: 10.1523/jneurosci.2793-17.2017] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/10/2017] [Accepted: 12/08/2017] [Indexed: 12/28/2022] Open
Abstract
The energetic costs of behavioral chronic stress are unlikely to be sustainable without neuronal plasticity. Mitochondria have the capacity to handle synaptic activity up to a limit before energetic depletion occurs. Protective mechanisms driven by the induction of neuronal genes likely evolved to buffer the consequences of chronic stress on excitatory neurons in prefrontal cortex (PFC), as this circuitry is vulnerable to excitotoxic insults. Little is known about the genes involved in mitochondrial adaptation to the buildup of chronic stress. Using combinations of genetic manipulations and stress for analyzing structural, transcriptional, mitochondrial, and behavioral outcomes, we characterized NR4A1 as a stress-inducible modifier of mitochondrial energetic competence and dendritic spine number in PFC. NR4A1 acted as a transcription factor for changing the expression of target genes previously involved in mitochondrial uncoupling, AMP-activated protein kinase activation, and synaptic growth. Maintenance of NR4A1 activity by chronic stress played a critical role in the regressive synaptic organization in PFC of mouse models of stress (male only). Knockdown, dominant-negative approach, and knockout of Nr4a1 in mice and rats (male only) protected pyramidal neurons against the adverse effects of chronic stress. In human PFC tissues of men and women, high levels of the transcriptionally active NR4A1 correlated with measures of synaptic loss and cognitive impairment. In the context of chronic stress, prolonged expression and activity of NR4A1 may lead to responses of mitochondria and synaptic connectivity that do not match environmental demand, resulting in circuit malfunction between PFC and other brain regions, constituting a pathological feature across disorders. SIGNIFICANCE STATEMENT The bioenergetic cost of chronic stress is too high to be sustainable by pyramidal prefrontal neurons. Cellular checkpoints have evolved to adjust the responses of mitochondria and synapses to the buildup of chronic stress. NR4A1 plays such a role by controlling the energetic competence of mitochondria with respect to synapse number. As an immediate-early gene, Nr4a1 promotes neuronal plasticity, but sustained expression or activity can be detrimental. NR4A1 expression and activity is sustained by chronic stress in animal models and in human studies of neuropathologies sensitive to the buildup of chronic stress. Therefore, antagonism of NR4A1 is a promising avenue for preventing the regressive synaptic reorganization in cortical systems in the context of chronic stress.
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19
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A Systematic Look at Environmental Modulation and Its Impact in Brain Development. Trends Neurosci 2018; 41:4-17. [DOI: 10.1016/j.tins.2017.10.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/11/2017] [Accepted: 10/18/2017] [Indexed: 11/19/2022]
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20
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Schmitz J, Metz GA, Güntürkün O, Ocklenburg S. Beyond the genome—Towards an epigenetic understanding of handedness ontogenesis. Prog Neurobiol 2017; 159:69-89. [DOI: 10.1016/j.pneurobio.2017.10.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 09/18/2017] [Accepted: 10/26/2017] [Indexed: 12/13/2022]
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21
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Impey S, Jopson T, Pelz C, Tafessu A, Fareh F, Zuloaga D, Marzulla T, Riparip LK, Stewart B, Rosi S, Turker MS, Raber J. Bi-directional and shared epigenomic signatures following proton and 56Fe irradiation. Sci Rep 2017; 7:10227. [PMID: 28860502 PMCID: PMC5579159 DOI: 10.1038/s41598-017-09191-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 07/24/2017] [Indexed: 12/04/2022] Open
Abstract
The brain’s response to radiation exposure is an important concern for patients undergoing cancer therapy and astronauts on long missions in deep space. We assessed whether this response is specific and prolonged and is linked to epigenetic mechanisms. We focused on the response of the hippocampus at early (2-weeks) and late (20-week) time points following whole body proton irradiation. We examined two forms of DNA methylation, cytosine methylation (5mC) and hydroxymethylation (5hmC). Impairments in object recognition, spatial memory retention, and network stability following proton irradiation were observed at the two-week time point and correlated with altered gene expression and 5hmC profiles that mapped to specific gene ontology pathways. Significant overlap was observed between DNA methylation changes at the 2 and 20-week time points demonstrating specificity and retention of changes in response to radiation. Moreover, a novel class of DNA methylation change was observed following an environmental challenge (i.e. space irradiation), characterized by both increased and decreased 5hmC levels along the entire gene body. These changes were mapped to genes encoding neuronal functions including postsynaptic gene ontology categories. Thus, the brain’s response to proton irradiation is both specific and prolonged and involves novel remodeling of non-random regions of the epigenome.
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Affiliation(s)
- Soren Impey
- Oregon Stem Cell Center and Department of Pediatrics, Oregon Health and Science University, Portland, OR, 97239, USA. .,Department of Cell and Developmental Biology, Oregon Health and Science University, Portland, OR, 97239, USA.
| | - Timothy Jopson
- Brain and Spinal Injury Center, Departments of Neurological Surgery and Physical Therapy and Rehabilitation Science, University of California, San Francisco, San Francisco, CA, 94110, USA
| | - Carl Pelz
- Oregon Stem Cell Center and Department of Pediatrics, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Amanuel Tafessu
- Oregon Stem Cell Center and Department of Pediatrics, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Fatema Fareh
- Oregon Stem Cell Center and Department of Pediatrics, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Damian Zuloaga
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Tessa Marzulla
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Lara-Kirstie Riparip
- Brain and Spinal Injury Center, Departments of Neurological Surgery and Physical Therapy and Rehabilitation Science, University of California, San Francisco, San Francisco, CA, 94110, USA
| | - Blair Stewart
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Susanna Rosi
- Brain and Spinal Injury Center, Departments of Neurological Surgery and Physical Therapy and Rehabilitation Science, University of California, San Francisco, San Francisco, CA, 94110, USA
| | - Mitchell S Turker
- Oregon Institute of Occupational Health Sciences and Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, 97239, USA
| | - Jacob Raber
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, 97239, USA. .,Departments of Neurology and Radiation Medicine, Division of Neuroscience ONPRC, Oregon Health and Science University, Portland, OR, 97239, USA.
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22
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Gupta T, Morgan HR, Andrews JC, Brewer ER, Certel SJ. Methyl-CpG binding domain proteins inhibit interspecies courtship and promote aggression in Drosophila. Sci Rep 2017; 7:5420. [PMID: 28710457 PMCID: PMC5511146 DOI: 10.1038/s41598-017-05844-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 06/05/2017] [Indexed: 11/10/2022] Open
Abstract
Reproductive isolation and speciation are driven by the convergence of environmental and genetic variation. The integration of these variation sources is thought to occur through epigenetic marks including DNA methylation. Proteins containing a methyl-CpG-binding domain (MBD) bind methylated DNA and interpret epigenetic marks, providing a dynamic yet evolutionarily adapted cellular output. Here, we report the Drosophila MBD-containing proteins, dMBD-R2 and dMBD2/3, contribute to reproductive isolation and survival behavioral strategies. Drosophila melanogaster males with a reduction in dMBD-R2 specifically in octopamine (OA) neurons exhibit courtship toward divergent interspecies D. virilis and D. yakuba females and a decrease in conspecific mating success. Conspecific male-male courtship is increased between dMBD-R2-deficient males while aggression is reduced. These changes in adaptive behavior are separable as males with a hypermethylated OA neuronal genome exhibited a decrease in aggression without altering male-male courtship. These results suggest Drosophila MBD-containing proteins are required within the OA neural circuitry to inhibit interspecies and conspecific male-male courtship and indicate that the genetically hard-wired neural mechanisms enforcing behavioral reproductive isolation include the interpretation of the epigenome.
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Affiliation(s)
- Tarun Gupta
- Neuroscience Graduate Program, The University of Montana, Missoula, MT, United States
| | - Hannah R Morgan
- Division of Biological Sciences, The University of Montana, Missoula, MT, United States
| | - Jonathan C Andrews
- Division of Biological Sciences, The University of Montana, Missoula, MT, United States
| | - Edmond R Brewer
- Division of Biological Sciences, The University of Montana, Missoula, MT, United States
| | - Sarah J Certel
- Neuroscience Graduate Program, The University of Montana, Missoula, MT, United States. .,Division of Biological Sciences, The University of Montana, Missoula, MT, United States.
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23
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Torres RF, Hidalgo C, Kerr B. Mecp2 Mediates Experience-Dependent Transcriptional Upregulation of Ryanodine Receptor Type-3. Front Mol Neurosci 2017; 10:188. [PMID: 28659760 PMCID: PMC5468404 DOI: 10.3389/fnmol.2017.00188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 05/29/2017] [Indexed: 12/03/2022] Open
Abstract
Mecp2 is a DNA methylation reader that plays a critical role in experience-dependent plasticity. Increasing evidence supports a role for epigenetic modifications in activity-induced gene expression. Hence, candidate genes related to such phenomena are of great interest. Ryanodine receptors are intracellular calcium channels that contribute to hippocampal synaptic plasticity, dendritic spine remodeling, and participate in learning and memory processes. Here we exposed mice to the enriched environment (EE) paradigm, which through increased stimulation induces experience dependent-plasticity, to explore a role for methyl-cytosines, and Mecp2 in directing Ryanodine receptor 3 (Ryr3) transcriptional activity. EE induced a hippocampal-specific increase in the methylation of discrete cytosines located at a Ryr3 isoform promoter; chromatin immunoprecipitation experiments revealed that EE increased Mecp2 binding to this Ryr3 isoform promoter. Interestingly, the experimental paradigm induced robust Ryr3 upregulation, accompanied by miR132-dependent suppression of p250GAP, a pathway driving synaptogenesis. In contrast to WT mice, Mecp2-null mice showed diminished levels of Ryr3 and displayed impaired EE-induced Ryr3 upregulation, compromising miR132 dependent suppression of p250GAP and experience-dependent structural plasticity. Based on these results, we propose that Mecp2 acts as a transcriptional activator of Ryr3, contributing to experience-dependent plasticity.
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Affiliation(s)
- Rodrigo F Torres
- Laboratory of Biology, Centro de Estudios CientíficosValdivia, Chile
| | - Cecilia Hidalgo
- Biomedical Neuroscience Institute, Centro de Estudios Moleculares de la Célula, Department of Neuroscience and Physiology and Biophysics Program, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de ChileSantiago, Chile
| | - Bredford Kerr
- Laboratory of Biology, Centro de Estudios CientíficosValdivia, Chile
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24
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Vivian CJ, Brinker AE, Graw S, Koestler DC, Legendre C, Gooden GC, Salhia B, Welch DR. Mitochondrial Genomic Backgrounds Affect Nuclear DNA Methylation and Gene Expression. Cancer Res 2017; 77:6202-6214. [PMID: 28663334 DOI: 10.1158/0008-5472.can-17-1473] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 06/14/2017] [Accepted: 06/15/2017] [Indexed: 12/19/2022]
Abstract
Mitochondrial DNA (mtDNA) mutations and polymorphisms contribute to many complex diseases, including cancer. Using a unique mouse model that contains nDNA from one mouse strain and homoplasmic mitochondrial haplotypes from different mouse strain(s)-designated Mitochondrial Nuclear Exchange (MNX)-we showed that mtDNA could alter mammary tumor metastasis. Because retrograde and anterograde communication exists between the nuclear and mitochondrial genomes, we hypothesized that there are differential mtDNA-driven changes in nuclear (n)DNA expression and DNA methylation. Genome-wide nDNA methylation and gene expression were measured in harvested brain tissue from paired wild-type and MNX mice. Selective differential DNA methylation and gene expression were observed between strains having identical nDNA, but different mtDNA. These observations provide insights into how mtDNA could be altering epigenetic regulation and thereby contribute to the pathogenesis of metastasis. Cancer Res; 77(22); 6202-14. ©2017 AACR.
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Affiliation(s)
- Carolyn J Vivian
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas.,Heartland Center for Mitochondrial Medicine, Phoenix, Arizona
| | - Amanda E Brinker
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas.,Heartland Center for Mitochondrial Medicine, Phoenix, Arizona.,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas
| | - Stefan Graw
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas
| | - Devin C Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas.,The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, Kansas
| | | | | | - Bodour Salhia
- Translational Genomics Research Institute, Phoenix, Arizona
| | - Danny R Welch
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas. .,Heartland Center for Mitochondrial Medicine, Phoenix, Arizona.,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas.,The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, Kansas
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25
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Miyata S, Kitagawa H. Formation and remodeling of the brain extracellular matrix in neural plasticity: Roles of chondroitin sulfate and hyaluronan. Biochim Biophys Acta Gen Subj 2017. [PMID: 28625420 DOI: 10.1016/j.bbagen.2017.06.010] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND The extracellular matrix (ECM) of the brain is rich in glycosaminoglycans such as chondroitin sulfate (CS) and hyaluronan. These glycosaminoglycans are organized into either diffuse or condensed ECM. Diffuse ECM is distributed throughout the brain and fills perisynaptic spaces, whereas condensed ECM selectively surrounds parvalbumin-expressing inhibitory neurons (PV cells) in mesh-like structures called perineuronal nets (PNNs). The brain ECM acts as a non-specific physical barrier that modulates neural plasticity and axon regeneration. SCOPE OF REVIEW Here, we review recent progress in understanding of the molecular basis of organization and remodeling of the brain ECM, and the involvement of several types of experience-dependent neural plasticity, with a particular focus on the mechanism that regulates PV cell function through specific interactions between CS chains and their binding partners. We also discuss how the barrier function of the brain ECM restricts dendritic spine dynamics and limits axon regeneration after injury. MAJOR CONCLUSIONS The brain ECM not only forms physical barriers that modulate neural plasticity and axon regeneration, but also forms molecular brakes that actively controls maturation of PV cells and synapse plasticity in which sulfation patterns of CS chains play a key role. Structural remodeling of the brain ECM modulates neural function during development and pathogenesis. GENERAL SIGNIFICANCE Genetic or enzymatic manipulation of the brain ECM may restore neural plasticity and enhance recovery from nerve injury. This article is part of a Special Issue entitled Neuro-glycoscience, edited by Kenji Kadomatsu and Hiroshi Kitagawa.
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Affiliation(s)
- Shinji Miyata
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Nagoya 464-8601, Japan
| | - Hiroshi Kitagawa
- Department of Biochemistry, Kobe Pharmaceutical University, 4-19-1 Motoyamakita-machi, Kobe 658-8558, Japan.
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26
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Duke CG, Kennedy AJ, Gavin CF, Day JJ, Sweatt JD. Experience-dependent epigenomic reorganization in the hippocampus. ACTA ACUST UNITED AC 2017; 24:278-288. [PMID: 28620075 PMCID: PMC5473107 DOI: 10.1101/lm.045112.117] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/12/2017] [Indexed: 11/24/2022]
Abstract
Using a hippocampus-dependent contextual threat learning and memory task, we report widespread, coordinated DNA methylation changes in CA1 hippocampus of Sprague-Dawley rats specific to threat learning at genes involved in synaptic transmission. Experience-dependent alternations in gene expression and DNA methylation were observed as early as 1 h following memory acquisition and became more pronounced after 24 h. Gene ontology analysis revealed significant enrichment of functional categories related to synaptic transmission in genes that were hypomethylated at 24 h following threat learning. Integration of these data sets with previously characterized epigenetic and transcriptional changes in brain disease states suggested significant overlap between genes regulated by memory formation and genes altered in memory-related neurological and neuropsychiatric diseases. These findings provide a comprehensive resource to aid in the identification of memory-relevant therapeutic targets. Our results shed new light on the gene expression and DNA methylation changes involved in memory formation, confirming that these processes are dynamic and experience-dependent. Finally, this work provides a roadmap for future studies to identify linkage of memory-associated genes to altered disease states.
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Affiliation(s)
- Corey G Duke
- Department of Neurobiology, Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Andrew J Kennedy
- Department of Chemistry, Bates College, Lewiston, Maine 04240, USA
| | - Cristin F Gavin
- Department of Neurobiology, Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Jeremy J Day
- Department of Neurobiology, Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - J David Sweatt
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37235, USA
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27
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Abstract
In mammals, DNA methylation in the form of 5-methylcytosine (5mC) can be actively reversed to unmodified cytosine (C) through TET dioxygenase-mediated oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), followed by replication-dependent dilution or thymine DNA glycosylase (TDG)-dependent base excision repair. In the past few years, biochemical and structural studies have revealed mechanistic insights into how TET and TDG mediate active DNA demethylation. Additionally, many regulatory mechanisms of this process have been identified. Technological advances in mapping and tracing the oxidized forms of 5mC allow further dissection of their functions. Furthermore, the biological functions of active DNA demethylation in various biological contexts have also been revealed. In this Review, we summarize the recent advances and highlight key unanswered questions.
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Mazziotti R, Baroncelli L, Ceglia N, Chelini G, Sala GD, Magnan C, Napoli D, Putignano E, Silingardi D, Tola J, Tognini P, Arthur JSC, Baldi P, Pizzorusso T. Mir-132/212 is required for maturation of binocular matching of orientation preference and depth perception. Nat Commun 2017; 8:15488. [PMID: 28534484 PMCID: PMC5457514 DOI: 10.1038/ncomms15488] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 04/03/2017] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) are known to mediate post-transcriptional gene regulation, but their role in postnatal brain development is still poorly explored. We show that the expression of many miRNAs is dramatically regulated during functional maturation of the mouse visual cortex with miR-132/212 family being one of the top upregulated miRNAs. Age-downregulated transcripts are significantly enriched in miR-132/miR-212 putative targets and in genes upregulated in miR-132/212 null mice. At a functional level, miR-132/212 deletion affects development of receptive fields of cortical neurons determining a specific impairment of binocular matching of orientation preference, but leaving orientation and direction selectivity unaltered. This deficit is associated with reduced depth perception in the visual cliff test. Deletion of miR-132/212 from forebrain excitatory neurons replicates the binocular matching deficits. Thus, miR-132/212 family shapes the age-dependent transcriptome of the visual cortex during a specific developmental window resulting in maturation of binocular cortical cells and depth perception.
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Affiliation(s)
- Raffaele Mazziotti
- Department of Neuroscience, Psychology, Drug Research and Child Health NEUROFARBA University of Florence, Area San Salvi—Pad. 26, 50135 Florence, Italy
| | - Laura Baroncelli
- Institute of Neuroscience, National Research Council, Via Moruzzi, 1 56124 Pisa, Italy
| | - Nicholas Ceglia
- Department of Computer Science, University of California, Irvine, Irvine, California 92697, USA
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California 92697, USA
| | - Gabriele Chelini
- Department of Neuroscience, Psychology, Drug Research and Child Health NEUROFARBA University of Florence, Area San Salvi—Pad. 26, 50135 Florence, Italy
| | - Grazia Della Sala
- Department of Neuroscience, Psychology, Drug Research and Child Health NEUROFARBA University of Florence, Area San Salvi—Pad. 26, 50135 Florence, Italy
| | - Christophe Magnan
- Department of Computer Science, University of California, Irvine, Irvine, California 92697, USA
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California 92697, USA
| | - Debora Napoli
- BIO@SNS lab, Scuola Normale Superiore via Moruzzi, 1 56124 Pisa, Italy
| | - Elena Putignano
- Institute of Neuroscience, National Research Council, Via Moruzzi, 1 56124 Pisa, Italy
| | - Davide Silingardi
- Department of Neuroscience, Psychology, Drug Research and Child Health NEUROFARBA University of Florence, Area San Salvi—Pad. 26, 50135 Florence, Italy
| | - Jonida Tola
- Institute of Neuroscience, National Research Council, Via Moruzzi, 1 56124 Pisa, Italy
| | - Paola Tognini
- BIO@SNS lab, Scuola Normale Superiore via Moruzzi, 1 56124 Pisa, Italy
- Department of Biological Chemistry, University of California, Irvine, Irvine, California 92697, USA
- Center for Epigenetics and Metabolism, University of California, Irvine, Irvine, California 92697, USA
| | - J. Simon C. Arthur
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Pierre Baldi
- Department of Computer Science, University of California, Irvine, Irvine, California 92697, USA
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California 92697, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, California 92697, USA
- Center for Epigenetics and Metabolism, University of California, Irvine, Irvine, California 92697, USA
| | - Tommaso Pizzorusso
- Department of Neuroscience, Psychology, Drug Research and Child Health NEUROFARBA University of Florence, Area San Salvi—Pad. 26, 50135 Florence, Italy
- Institute of Neuroscience, National Research Council, Via Moruzzi, 1 56124 Pisa, Italy
- BIO@SNS lab, Scuola Normale Superiore via Moruzzi, 1 56124 Pisa, Italy
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Eleftheriou C, Cesca F, Maragliano L, Benfenati F, Maya-Vetencourt JF. Optogenetic Modulation of Intracellular Signalling and Transcription: Focus on Neuronal Plasticity. J Exp Neurosci 2017; 11:1179069517703354. [PMID: 28579827 PMCID: PMC5415353 DOI: 10.1177/1179069517703354] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 03/02/2017] [Indexed: 12/17/2022] Open
Abstract
Several fields in neuroscience have been revolutionized by the advent of optogenetics, a technique that offers the possibility to modulate neuronal physiology in response to light stimulation. This innovative and far-reaching tool provided unprecedented spatial and temporal resolution to explore the activity of neural circuits underlying cognition and behaviour. With an exponential growth in the discovery and synthesis of new photosensitive actuators capable of modulating neuronal networks function, other fields in biology are experiencing a similar re-evolution. Here, we review the various optogenetic toolboxes developed to influence cellular physiology as well as the diverse ways in which these can be engineered to precisely modulate intracellular signalling and transcription. We also explore the processes required to successfully express and stimulate these photo-actuators in vivo before discussing how such tools can enlighten our understanding of neuronal plasticity at the systems level.
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Affiliation(s)
- Cyril Eleftheriou
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - Fabrizia Cesca
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy.,Department of Experimental Medicine, University of Genova, Genova, Italy
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Abstract
While some autoimmune disorders remain extremely rare, others largely predominate the epidemiology of human autoimmunity. Notably, these include psoriasis, diabetes, vitiligo, thyroiditis, rheumatoid arthritis and multiple sclerosis. Thus, despite the quasi-infinite number of "self" antigens that could theoretically trigger autoimmune responses, only a limited set of antigens, referred here as superautoantigens, induce pathogenic adaptive responses. Several lines of evidence reviewed in this paper indicate that, irrespective of the targeted organ (e.g. thyroid, pancreas, joints, brain or skin), a significant proportion of superautoantigens are highly expressed in the synaptic compartment of the central nervous system (CNS). Such an observation applies notably for GAD65, AchR, ribonucleoproteins, heat shock proteins, collagen IV, laminin, tyrosine hydroxylase and the acetylcholinesterase domain of thyroglobulin. It is also argued that cognitive alterations have been described in a number of autoimmune disorders, including psoriasis, rheumatoid arthritis, lupus, Crohn's disease and autoimmune thyroiditis. Finally, the present paper points out that a great majority of the "incidental" autoimmune conditions notably triggered by neoplasms, vaccinations or microbial infections are targeting the synaptic or myelin compartments. On this basis, the concept of an immunological homunculus, proposed by Irun Cohen more than 25 years ago, is extended here in a model where physiological autoimmunity against brain superautoantigens confers both: i) a crucial evolutionary-determined advantage via cognition-promoting autoimmunity; and ii) a major evolutionary-determined vulnerability, leading to the emergence of autoimmune disorders in Homo sapiens. Moreover, in this theoretical framework, the so called co-development/co-evolution model, both the development (at the scale of an individual) and evolution (at the scale of species) of the antibody and T-cell repertoires are coupled to those of the neural repertoires (i.e. the distinct neuronal populations and synaptic circuits supporting cognitive and sensorimotor functions). Clinical implications and future experimental insights are also presented and discussed.
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Affiliation(s)
- Serge Nataf
- Bank of Tissues and Cells, Lyon University Hospital (Hospices Civils de Lyon), CarMeN Laboratory, INSERM 1060, INRA 1397, INSA Lyon, Université Claude Bernard Lyon-1, Lyon, F-69000, France
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31
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Pan Y, Daito T, Sasaki Y, Chung YH, Xing X, Pondugula S, Swamidass SJ, Wang T, Kim AH, Yano H. Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity. Sci Rep 2016; 6:31022. [PMID: 27516062 PMCID: PMC4981892 DOI: 10.1038/srep31022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 07/13/2016] [Indexed: 02/06/2023] Open
Abstract
Although epigenetic abnormalities have been described in Huntington's disease (HD), the causal epigenetic mechanisms driving neurodegeneration in HD cortex and striatum remain undefined. Using an epigenetic pathway-targeted drug screen, we report that inhibitors of DNA methyltransferases (DNMTs), decitabine and FdCyd, block mutant huntingtin (Htt)-induced toxicity in primary cortical and striatal neurons. In addition, knockdown of DNMT3A or DNMT1 protected neurons against mutant Htt-induced toxicity, together demonstrating a requirement for DNMTs in mutant Htt-triggered neuronal death and suggesting a neurodegenerative mechanism based on DNA methylation-mediated transcriptional repression. Inhibition of DNMTs in HD model primary cortical or striatal neurons restored the expression of several key genes, including Bdnf, an important neurotrophic factor implicated in HD. Accordingly, the Bdnf promoter exhibited aberrant cytosine methylation in mutant Htt-expressing cortical neurons. In vivo, pharmacological inhibition of DNMTs in HD mouse brains restored the mRNA levels of key striatal genes known to be downregulated in HD. Thus, disturbances in DNA methylation play a critical role in mutant Htt-induced neuronal dysfunction and death, raising the possibility that epigenetic strategies targeting abnormal DNA methylation may have therapeutic utility in HD.
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Affiliation(s)
- Yanchun Pan
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Takuji Daito
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yo Sasaki
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yong Hee Chung
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Santhi Pondugula
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - S. Joshua Swamidass
- Department of Immunology and Pathology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Albert H. Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hiroko Yano
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders Washington University School of Medicine, St. Louis, MO 63110, USA
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Vogel Ciernia A, LaSalle J. The landscape of DNA methylation amid a perfect storm of autism aetiologies. Nat Rev Neurosci 2016; 17:411-23. [PMID: 27150399 PMCID: PMC4966286 DOI: 10.1038/nrn.2016.41] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Increasing evidence points to a complex interplay between genes and the environment in autism spectrum disorder (ASD), including rare de novo mutations in chromatin genes such as methyl-CpG binding protein 2 (MECP2) in Rett syndrome. Epigenetic mechanisms such as DNA methylation act at this interface, reflecting the plasticity in metabolic and neurodevelopmentally regulated gene pathways. Genome-wide studies of gene sequences, gene pathways and DNA methylation are providing valuable mechanistic insights into ASD. The dynamic developmental landscape of DNA methylation is vulnerable to numerous genetic and environmental insults: therefore, understanding pathways that are central to this 'perfect storm' will be crucial to improving the diagnosis and treatment of ASD.
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Affiliation(s)
- Annie Vogel Ciernia
- Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, California 95616, USA
| | - Janine LaSalle
- Medical Microbiology and Immunology, MIND Institute, Genome Center, University of California, Davis, California 95616, USA
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Bernard C, Vincent C, Testa D, Bertini E, Ribot J, Di Nardo AA, Volovitch M, Prochiantz A. A Mouse Model for Conditional Secretion of Specific Single-Chain Antibodies Provides Genetic Evidence for Regulation of Cortical Plasticity by a Non-cell Autonomous Homeoprotein Transcription Factor. PLoS Genet 2016; 12:e1006035. [PMID: 27171438 PMCID: PMC4865174 DOI: 10.1371/journal.pgen.1006035] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 04/18/2016] [Indexed: 11/19/2022] Open
Abstract
During postnatal life the cerebral cortex passes through critical periods of plasticity allowing its physiological adaptation to the environment. In the visual cortex, critical period onset and closure are influenced by the non-cell autonomous activity of the Otx2 homeoprotein transcription factor, which regulates the maturation of parvalbumin-expressing inhibitory interneurons (PV cells). In adult mice, the maintenance of a non-plastic adult state requires continuous Otx2 import by PV cells. An important source of extra-cortical Otx2 is the choroid plexus, which secretes Otx2 into the cerebrospinal fluid. Otx2 secretion and internalization requires two small peptidic domains that are part of the DNA-binding domain. Thus, mutating these “transfer” sequences also modifies cell autonomous transcription, precluding this approach to obtain a cell autonomous-only mouse. Here, we develop a mouse model with inducible secretion of an anti-Otx2 single-chain antibody to trap Otx2 in the extracellular milieu. Postnatal secretion of this single-chain antibody by PV cells delays PV maturation and reduces plasticity gene expression. Induced adult expression of this single-chain antibody in cerebrospinal fluid decreases Otx2 internalization by PV cells, strongly induces plasticity gene expression and reopens physiological plasticity. We provide the first mammalian genetic evidence for a signaling mechanism involving intercellular transfer of a homeoprotein transcription factor. Our single-chain antibody mouse model is a valid strategy for extracellular neutralization that could be applied to other homeoproteins and signaling molecules within and beyond the nervous system. Classically, cell signaling is based on the secretion of molecules that bind cell surface receptors. Lipophilic agents can do without cell-surface receptors due to their ability to diffuse through the plasma membrane, but this is normally not the case for proteins, which cannot pass the membrane barrier. However, homeoprotein transcription factors represent an exception as they are secreted and internalized by live cells owing to two peptidic domains. An important illustration of this novel signaling mechanism is provided by Otx2, a homeoprotein that travels from the choroid plexus to specific inhibitory neurons in the cerebral cortex, where it regulates physiological plasticity throughout life. Because the two transfer peptides are in the DNA-binding domain of Otx2, it is impossible to mutate them without altering both cell signaling and cell-autonomous functions. We have therefore developed a mouse in which a secreted anti-Otx2 single-chain antibody can be induced to trap extracellular Otx2 while leaving its cell autonomous function untouched. We show that neutralizing extracellular Otx2 modifies the expression of plasticity genes in the visual cortex, thus providing the first genetic demonstration for homeoprotein signaling in a mammal.
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Affiliation(s)
- Clémence Bernard
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241/INSERM U1050, PSL Research University, Paris, France
| | - Clémentine Vincent
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241/INSERM U1050, PSL Research University, Paris, France
| | - Damien Testa
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241/INSERM U1050, PSL Research University, Paris, France
| | - Eva Bertini
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241/INSERM U1050, PSL Research University, Paris, France
| | - Jérôme Ribot
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241/INSERM U1050, PSL Research University, Paris, France
| | - Ariel A. Di Nardo
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241/INSERM U1050, PSL Research University, Paris, France
| | - Michel Volovitch
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241/INSERM U1050, PSL Research University, Paris, France
| | - Alain Prochiantz
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241/INSERM U1050, PSL Research University, Paris, France
- * E-mail:
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34
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Abstract
Over the past decade, since epigenetic mechanisms were first implicated in memory formation and synaptic plasticity, dynamic DNA methylation reactions have been identified as integral to long-term memory formation, maintenance, and recall. This review incorporates various new findings that DNA methylation mechanisms are important regulators of non-Hebbian plasticity mechanisms, suggesting that these epigenetic mechanisms are a fundamental link between synaptic plasticity and metaplasticity. Because the field of neuroepigenetics is so young and the biochemical tools necessary to probe gene-specific questions are just now being developed and used, this review also speculates about the direction and potential of therapeutics that target epigenetic mechanisms in the central nervous system and the unique pharmacokinetic and pharmacodynamic properties that epigenetic therapies may possess. Mapping the dynamics of the epigenome in response to experiential learning, even a single epigenetic mark in isolation, remains a significant technical and bioinformatic hurdle facing the field, but will be necessary to identify changes to the methylome that govern memory-associated gene expression and effectively drug the epigenome.
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Affiliation(s)
- Andrew J Kennedy
- a Department of Neurobiology , University of Alabama at Birmingham , Birmingham , AL , USA
| | - J David Sweatt
- a Department of Neurobiology , University of Alabama at Birmingham , Birmingham , AL , USA
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35
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Otx2-PNN Interaction to Regulate Cortical Plasticity. Neural Plast 2016; 2016:7931693. [PMID: 26881132 PMCID: PMC4736602 DOI: 10.1155/2016/7931693] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 07/13/2015] [Indexed: 01/31/2023] Open
Abstract
The ability of the environment to shape cortical function is at its highest during critical periods of postnatal development. In the visual cortex, critical period onset is triggered by the maturation of parvalbumin inhibitory interneurons, which gradually become surrounded by a specialized glycosaminoglycan-rich extracellular matrix: the perineuronal nets. Among the identified factors regulating cortical plasticity in the visual cortex, extracortical homeoprotein Otx2 is transferred specifically into parvalbumin interneurons and this transfer regulates both the onset and the closure of the critical period of plasticity for binocular vision. Here, we review the interaction between the complex sugars of the perineuronal nets and homeoprotein Otx2 and how this interaction regulates cortical plasticity during critical period and in adulthood.
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36
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Abstract
Two recent papers center on the emerging intersection of DNA methylation and homeostatic plasticity. To better appreciate the context of these studies, we first briefly review the mechanistic connections between DNA methylation and plasticity before delving into the ways in which these two papers fortify the connection between synapse and nucleus but also highlight the need for studies with a broader perspective.
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Affiliation(s)
- Erin A Clark
- Department of Biology and Center for Behavioral Genomics, Brandeis University, Waltham, MA 02454, USA
| | - Sacha B Nelson
- Department of Biology and Center for Behavioral Genomics, Brandeis University, Waltham, MA 02454, USA.
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37
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Tognini P, Napoli D, Pizzorusso T. Dynamic DNA methylation in the brain: a new epigenetic mark for experience-dependent plasticity. Front Cell Neurosci 2015; 9:331. [PMID: 26379502 PMCID: PMC4548453 DOI: 10.3389/fncel.2015.00331] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/10/2015] [Indexed: 02/04/2023] Open
Abstract
Experience-dependent plasticity is the ability of brain circuits to undergo molecular, structural and functional changes as a function of neural activity. Neural activity continuously shapes our brain during all the stages of our life, from infancy through adulthood and beyond. Epigenetic modifications of histone proteins and DNA seem to be a leading molecular mechanism to modulate the transcriptional changes underlying the fine-tuning of synaptic connections and circuitry rewiring during activity-dependent plasticity. The recent discovery that cytosine methylation is an epigenetic mark particularly dynamic in brain cells has strongly increased the interest of neuroscientists in understanding the role of covalent modifications of DNA in activity-induced remodeling of neuronal circuits. Here, we provide an overview of the role of DNA methylation and hydroxylmethylation in brain plasticity both during adulthood, with emphasis on learning and memory related processes, and during postnatal development, focusing specifically on experience-dependent plasticity in the visual cortex.
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Affiliation(s)
- Paola Tognini
- Department of Biological Chemistry, University of California, Irvine Irvine, CA, USA
| | - Debora Napoli
- BioSNS laboratory, Scuola Normale Superiore di Pisa Pisa, Italy
| | - Tommaso Pizzorusso
- Institute of Neuroscience CNR Pisa, Italy ; Department of Neuroscience, Psychology, Drug Research and Child Health Neurofarba, University of Florence Florence, Italy
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