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Di Bella DJ, Domínguez-Iturza N, Brown JR, Arlotta P. Making Ramón y Cajal proud: Development of cell identity and diversity in the cerebral cortex. Neuron 2024; 112:2091-2111. [PMID: 38754415 DOI: 10.1016/j.neuron.2024.04.021] [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: 12/15/2023] [Revised: 03/28/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024]
Abstract
Since the beautiful images of Santiago Ramón y Cajal provided a first glimpse into the immense diversity and complexity of cell types found in the cerebral cortex, neuroscience has been challenged and inspired to understand how these diverse cells are generated and how they interact with each other to orchestrate the development of this remarkable tissue. Some fundamental questions drive the field's quest to understand cortical development: what are the mechanistic principles that govern the emergence of neuronal diversity? How do extrinsic and intrinsic signals integrate with physical forces and activity to shape cell identity? How do the diverse populations of neurons and glia influence each other during development to guarantee proper integration and function? The advent of powerful new technologies to profile and perturb cortical development at unprecedented resolution and across a variety of modalities has offered a new opportunity to integrate past knowledge with brand new data. Here, we review some of this progress using cortical excitatory projection neurons as a system to draw out general principles of cell diversification and the role of cell-cell interactions during cortical development.
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Affiliation(s)
- Daniela J Di Bella
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Nuria Domínguez-Iturza
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Juliana R Brown
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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2
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Luo X, Xu M, Guo W. Adult neurogenesis research in China. Dev Growth Differ 2023; 65:534-545. [PMID: 37899611 DOI: 10.1111/dgd.12900] [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: 09/16/2023] [Revised: 10/22/2023] [Accepted: 10/25/2023] [Indexed: 10/31/2023]
Abstract
Neural stem cells are multipotent stem cells that generate functional newborn neurons through a process called neurogenesis. Neurogenesis in the adult brain is tightly regulated and plays a pivotal role in the maintenance of brain function. Disruption of adult neurogenesis impairs cognitive function and is correlated with numerous neurologic disorders. Deciphering the mechanisms underlying adult neurogenesis not only advances our understanding of how the brain functions, but also offers new insight into neurologic diseases and potentially contributes to the development of effective treatments. The field of adult neurogenesis is experiencing significant growth in China. Chinese researchers have demonstrated a multitude of factors governing adult neurogenesis and revealed the underlying mechanisms of and correlations between adult neurogenesis and neurologic disorders. Here, we provide an overview of recent advancements in the field of adult neurogenesis due to Chinese scientists.
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Affiliation(s)
- Xing Luo
- State Key Laboratory for Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Graduate School, University of Chinese Academy of Sciences, Beijing, China
| | - Mingyue Xu
- State Key Laboratory for Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Graduate School, University of Chinese Academy of Sciences, Beijing, China
| | - Weixiang Guo
- State Key Laboratory for Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Graduate School, University of Chinese Academy of Sciences, Beijing, China
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3
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Yan L, Geng Q, Cao Z, Liu B, Li L, Lu P, Lin L, Wei L, Tan Y, He X, Li L, Zhao N, Lu C. Insights into DNMT1 and programmed cell death in diseases. Biomed Pharmacother 2023; 168:115753. [PMID: 37871559 DOI: 10.1016/j.biopha.2023.115753] [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: 08/07/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023] Open
Abstract
DNMT1 (DNA methyltransferase 1) is the predominant member of the DNMT family and the most abundant DNMT in various cell types. It functions as a maintenance DNMT and is involved in various diseases, including cancer and nervous system diseases. Programmed cell death (PCD) is a fundamental mechanism that regulates cell proliferation and maintains the development and homeostasis of multicellular organisms. DNMT1 plays a regulatory role in various types of PCD, including apoptosis, autophagy, necroptosis, ferroptosis, and others. DNMT1 is closely associated with the development of various diseases by regulating key genes and pathways involved in PCD, including caspase 3/7 activities in apoptosis, Beclin 1, LC3, and some autophagy-related proteins in autophagy, glutathione peroxidase 4 (GPX4) and nuclear receptor coactivator 4 (NCOA4) in ferroptosis, and receptor-interacting protein kinase 1-receptor-interacting protein kinase 3-mixed lineage kinase domain-like protein (RIPK1-RIPK3-MLKL) in necroptosis. Our study summarizes the regulatory relationship between DNMT1 and different types of PCD in various diseases and discusses the potential of DNMT1 as a common regulatory hub in multiple types of PCD, offering a perspective for therapeutic approaches in disease.
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Affiliation(s)
- Lan Yan
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qi Geng
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhiwen Cao
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Bin Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Li Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Peipei Lu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lin Lin
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lini Wei
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yong Tan
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaojuan He
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Li Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ning Zhao
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Cheng Lu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China.
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4
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Mir FA, Amanullah A, Jain BP, Hyderi Z, Gautam A. Neuroepigenetics of ageing and neurodegeneration-associated dementia: An updated review. Ageing Res Rev 2023; 91:102067. [PMID: 37689143 DOI: 10.1016/j.arr.2023.102067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023]
Abstract
Gene expression is tremendously altered in the brain during memory acquisition, recall, and forgetfulness. However, non-genetic factors, including environmental elements, epigenetic changes, and lifestyle, have grabbed significant attention in recent years regarding the etiology of neurodegenerative diseases (NDD) and age-associated dementia. Epigenetic modifications are essential in regulating gene expression in all living organisms in a DNA sequence-independent manner. The genes implicated in ageing and NDD-related memory disorders are epigenetically regulated by processes such as DNA methylation, histone acetylation as well as messenger RNA editing machinery. The physiological and optimal state of the epigenome, especially within the CNS of humans, plays an intricate role in helping us adjust to the changing environment, and alterations in it cause many brain disorders, but the mechanisms behind it still need to be well understood. When fully understood, these epigenetic landscapes could act as vital targets for pharmacogenetic rescue strategies for treating several diseases, including neurodegeneration- and age-induced dementia. Keeping this objective in mind, this updated review summarises the epigenetic changes associated with age and neurodegeneration-associated dementia.
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Affiliation(s)
- Fayaz Ahmad Mir
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Zeeshan Hyderi
- Department of Biotechnology, Alagappa University, Karaikudi, India
| | - Akash Gautam
- Centre for Neural and Cognitive Sciences, University of Hyderabad, Hyderabad, India.
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5
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Davis KN, Qu PP, Ma S, Lin L, Plastini M, Dahl N, Plazzi G, Pizza F, O’Hara R, Wong WH, Hallmayer J, Mignot E, Zhang X, Urban AE. Mutations in human DNA methyltransferase DNMT1 induce specific genome-wide epigenomic and transcriptomic changes in neurodevelopment. Hum Mol Genet 2023; 32:3105-3120. [PMID: 37584462 PMCID: PMC10586194 DOI: 10.1093/hmg/ddad123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 08/17/2023] Open
Abstract
DNA methyltransferase type 1 (DNMT1) is a major enzyme involved in maintaining the methylation pattern after DNA replication. Mutations in DNMT1 have been associated with autosomal dominant cerebellar ataxia, deafness and narcolepsy (ADCA-DN). We used fibroblasts, induced pluripotent stem cells (iPSCs) and induced neurons (iNs) generated from patients with ADCA-DN and controls, to explore the epigenomic and transcriptomic effects of mutations in DNMT1. We show cell type-specific changes in gene expression and DNA methylation patterns. DNA methylation and gene expression changes were negatively correlated in iPSCs and iNs. In addition, we identified a group of genes associated with clinical phenotypes of ADCA-DN, including PDGFB and PRDM8 for cerebellar ataxia, psychosis and dementia and NR2F1 for deafness and optic atrophy. Furthermore, ZFP57, which is required to maintain gene imprinting through DNA methylation during early development, was hypomethylated in promoters and exhibited upregulated expression in patients with ADCA-DN in both iPSC and iNs. Our results provide insight into the functions of DNMT1 and the molecular changes associated with ADCA-DN, with potential implications for genes associated with related phenotypes.
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Affiliation(s)
- Kasey N Davis
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
| | - Ping-Ping Qu
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
| | - Shining Ma
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Ling Lin
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Center for Narcolepsy, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Melanie Plastini
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology Sciences for Life Laboratory, Uppsala University BMC, Uppsala 75122, Sweden
| | - Giuseppe Plazzi
- IRCCS—Istituto delle Scienze Neurologiche di Bologna, Bologna 40139, Italy
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Fabio Pizza
- IRCCS—Istituto delle Scienze Neurologiche di Bologna, Bologna 40139, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40126, Italy
| | - Ruth O’Hara
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Wing Hung Wong
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Joachim Hallmayer
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Emmanuel Mignot
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Center for Narcolepsy, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Xianglong Zhang
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
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6
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Hosaka T, Tsuji H, Kwak S. Roles of Aging, Circular RNAs, and RNA Editing in the Pathogenesis of Amyotrophic Lateral Sclerosis: Potential Biomarkers and Therapeutic Targets. Cells 2023; 12:1443. [PMID: 37408276 DOI: 10.3390/cells12101443] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 07/07/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an incurable motor neuron disease caused by upper and lower motor neuron death. Despite advances in our understanding of ALS pathogenesis, effective treatment for this fatal disease remains elusive. As aging is a major risk factor for ALS, age-related molecular changes may provide clues for the development of new therapeutic strategies. Dysregulation of age-dependent RNA metabolism plays a pivotal role in the pathogenesis of ALS. In addition, failure of RNA editing at the glutamine/arginine (Q/R) site of GluA2 mRNA causes excitotoxicity due to excessive Ca2+ influx through Ca2+-permeable α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors, which is recognized as an underlying mechanism of motor neuron death in ALS. Circular RNAs (circRNAs), a circular form of cognate RNA generated by back-splicing, are abundant in the brain and accumulate with age. Hence, they are assumed to play a role in neurodegeneration. Emerging evidence has demonstrated that age-related dysregulation of RNA editing and changes in circRNA expression are involved in ALS pathogenesis. Herein, we review the potential associations between age-dependent changes in circRNAs and RNA editing, and discuss the possibility of developing new therapies and biomarkers for ALS based on age-related changes in circRNAs and dysregulation of RNA editing.
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Affiliation(s)
- Takashi Hosaka
- Department of Neurology, Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
- University of Tsukuba Hospital/Jichi Medical University Joint Ibaraki Western Regional Clinical Education Center, Chikusei 308-0813, Japan
- Department of Internal Medicine, Ibaraki Western Medical Center, Chikusei 308-0813, Japan
| | - Hiroshi Tsuji
- Department of Neurology, Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Shin Kwak
- Department of Neurology, Tokyo Medical University, Tokyo 160-0023, Japan
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7
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Arutjunyan AV, Milyutina YP, Shcherbitskaia AD, Kerkeshko GO, Zalozniaia IV. Epigenetic Mechanisms Involved in the Effects of Maternal Hyperhomocysteinemia on the Functional State of Placenta and Nervous System Plasticity in the Offspring. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:435-456. [PMID: 37080931 DOI: 10.1134/s0006297923040016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
According to modern view, susceptibility to diseases, specifically to cognitive and neuropsychiatric disorders, can form during embryonic development. Adverse factors affecting mother during the pregnancy increase the risk of developing pathologies. Despite the association between elevated maternal blood homocysteine (Hcy) and fetal brain impairments, as well as cognitive deficits in the offspring, the role of brain plasticity in the development of these pathologies remains poorly studied. Here, we review the data on the negative impact of hyperhomocysteinemia (HHcy) on the neural plasticity, in particular, its possible influence on the offspring brain plasticity through epigenetic mechanisms, such as changes in intracellular methylation potential, activity of DNA methyltransferases, DNA methylation, histone modifications, and microRNA expression in brain cells. Since placenta plays a key role in the transport of nutrients and transmission of signals from mother to fetus, its dysfunction due to aberrant epigenetic regulation can affect the development of fetal CNS. The review also presents the data on the impact of maternal HHcy on the epigenetic regulation in the placenta. The data presented in the review are not only interesting from purely scientific point of view, but can help in understanding the role of HHcy and epigenetic mechanisms in the pathogenesis of diseases, such as pregnancy pathologies resulting in the delayed development of fetal brain, cognitive impairments in the offspring during childhood, and neuropsychiatric and neurodegenerative disorders later in life, as well as in the search for approaches for their prevention using neuroprotectors.
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Affiliation(s)
- Alexander V Arutjunyan
- Ott Research Institute of Obstetrics, Gynecology and Reproductive Medicine, St. Petersburg, 199034, Russia.
- St. Petersburg Institute of Bioregulation and Gerontology, St. Petersburg, 197110, Russia
| | - Yulia P Milyutina
- Ott Research Institute of Obstetrics, Gynecology and Reproductive Medicine, St. Petersburg, 199034, Russia
- St. Petersburg State Pediatric Medical University, St. Petersburg, 194100, Russia
| | - Anastasia D Shcherbitskaia
- Ott Research Institute of Obstetrics, Gynecology and Reproductive Medicine, St. Petersburg, 199034, Russia
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Saint Petersburg, 194223, Russia
| | - Gleb O Kerkeshko
- Ott Research Institute of Obstetrics, Gynecology and Reproductive Medicine, St. Petersburg, 199034, Russia
- St. Petersburg Institute of Bioregulation and Gerontology, St. Petersburg, 197110, Russia
| | - Irina V Zalozniaia
- Ott Research Institute of Obstetrics, Gynecology and Reproductive Medicine, St. Petersburg, 199034, Russia
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8
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Zhou Y, Wang X, Liu Y, Gu Y, Gu R, Zhang G, Lin Q. Mechanisms of abnormal adult hippocampal neurogenesis in Alzheimer's disease. Front Neurosci 2023; 17:1125376. [PMID: 36875663 PMCID: PMC9975352 DOI: 10.3389/fnins.2023.1125376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/31/2023] [Indexed: 02/17/2023] Open
Abstract
Alzheimer's disease (AD) is a degenerative disease of the central nervous system, the most common type of dementia in old age, which causes progressive loss of cognitive functions such as thoughts, memory, reasoning, behavioral abilities and social skills, affecting the daily life of patients. The dentate gyrus of the hippocampus is a key area for learning and memory functions, and an important site of adult hippocampal neurogenesis (AHN) in normal mammals. AHN mainly consists of the proliferation, differentiation, survival and maturation of newborn neurons and occurs throughout adulthood, but the level of AHN decreases with age. In AD, the AHN will be affected to different degrees at different times, and its exact molecular mechanisms are increasingly elucidated. In this review, we summarize the changes of AHN in AD and its alteration mechanism, which will help lay the foundation for further research on the pathogenesis and diagnostic and therapeutic approaches of AD.
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Affiliation(s)
- Yujuan Zhou
- Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Medical University, Fuzhou, China
| | - Xu Wang
- Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Medical University, Fuzhou, China
| | - Yingying Liu
- Department of Physiology and Pathophysiology, Health Science Center, Peking University, Beijing, China
| | - Yulu Gu
- Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Medical University, Fuzhou, China
| | - Renjun Gu
- School of Chinese Medicine and School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Geng Zhang
- Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Medical University, Fuzhou, China.,Laboratory of Clinical Applied Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Qing Lin
- Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Medical University, Fuzhou, China.,Laboratory of Clinical Applied Anatomy, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
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9
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Van Berkel AA, Koopmans F, Gonzalez-Lozano MA, Lammertse HCA, Feringa F, Bryois J, Sullivan PF, Smit AB, Toonen RF, Verhage M. Dysregulation of synaptic and developmental transcriptomic/proteomic profiles upon depletion of MUNC18-1. eNeuro 2022; 9:ENEURO.0186-22.2022. [PMID: 36257704 PMCID: PMC9668351 DOI: 10.1523/eneuro.0186-22.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/27/2022] [Accepted: 07/14/2022] [Indexed: 11/23/2022] Open
Abstract
Absence of presynaptic protein MUNC18-1 (gene: Stxbp1) leads to neuronal cell death at an immature stage before synapse formation. Here, we performed transcriptomic and proteomic profiling of immature Stxbp1 knockout (KO) cells to discover which cellular processes depend on MUNC18-1. Hippocampi of Stxbp1 KO mice showed cell-type specific dysregulation of 2123 transcripts primarily related to synaptic transmission and immune response. To further investigate direct, neuron-specific effects of MUNC18-1 depletion, a proteomic screen was performed on murine neuronal cultures at two developmental timepoints prior to onset of neuron degeneration. 399 proteins were differentially expressed, which were primarily involved in synaptic function (especially synaptic vesicle exocytosis) and neuron development. We further show that many of the downregulated proteins upon loss of MUNC18-1 are normally upregulated during this developmental stage. Thus, absence of MUNC18-1 extensively dysregulates the transcriptome and proteome, primarily affecting synaptic and developmental profiles. Lack of synaptic activity is unlikely to underlie these effects, as the changes were observed in immature neurons without functional synapses, and minimal overlap was found to activity-dependent proteins. We hypothesize that presence of MUNC18-1 is essential to advance neuron development, serving as a 'checkpoint' for neurons to initiate cell death in its absence.Significance StatementPresynaptic protein MUNC18-1 is essential for neuronal functioning. Pathogenic variants in its gene, STXBP1, are among the most common found in patients with developmental delay and epilepsy. To discern the pathogenesis in these patients, a thorough understanding of MUNC18-1's function in neurons is required. Here, we show that loss of MUNC18-1 results in extensive dysregulation of synaptic and developmental proteins in immature neurons before synapse formation. Many of the downregulated proteins are normally upregulated during this developmental stage. This indicates that MUNC18-1 is a critical regulator of neuronal development, which could play an important role in the pathogenesis of STXBP1 variant carriers.
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Affiliation(s)
- A A Van Berkel
- Dept. Functional Genomics, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
- Functional Genomics, Department of Human Genetics, CNCR, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands
| | - F Koopmans
- Dept. Functional Genomics, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
- Dept. Molecular & Cellular Neurobiology, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - M A Gonzalez-Lozano
- Dept. Molecular & Cellular Neurobiology, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - H C A Lammertse
- Dept. Functional Genomics, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
- Functional Genomics, Department of Human Genetics, CNCR, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands
| | - F Feringa
- Functional Genomics, Department of Human Genetics, CNCR, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands
| | - J Bryois
- Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Nobels vag 12A, 171 77 Stockholm, Sweden
| | - P F Sullivan
- UNC Center for Psychiatric Genomics, University of North Carolina at Chapel Hill, 101 Manning Drive, Chapel Hill, NC 27599-7160, USA
- Karolinska Institutet, Department of Medical Epidemiology and Biostatistics, Nobels vag 12A, 171 77 Stockholm, Sweden
| | - A B Smit
- Dept. Molecular & Cellular Neurobiology, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - R F Toonen
- Dept. Functional Genomics, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - M Verhage
- Dept. Functional Genomics, CNCR, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
- Functional Genomics, Department of Human Genetics, CNCR, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands
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10
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Dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm. Nat Commun 2022; 13:5447. [PMID: 36123357 PMCID: PMC9485127 DOI: 10.1038/s41467-022-32978-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/25/2022] [Indexed: 12/03/2022] Open
Abstract
Silencing of endogenous retroviruses (ERVs) is largely mediated by repressive chromatin modifications H3K9me3 and DNA methylation. On ERVs, these modifications are mainly deposited by the histone methyltransferase Setdb1 and by the maintenance DNA methyltransferase Dnmt1. Knock-out of either Setdb1 or Dnmt1 leads to ERV de-repression in various cell types. However, it is currently not known if H3K9me3 and DNA methylation depend on each other for ERV silencing. Here we show that conditional knock-out of Setdb1 in mouse embryonic endoderm results in ERV de-repression in visceral endoderm (VE) descendants and does not occur in definitive endoderm (DE). Deletion of Setdb1 in VE progenitors results in loss of H3K9me3 and reduced DNA methylation of Intracisternal A-particle (IAP) elements, consistent with up-regulation of this ERV family. In DE, loss of Setdb1 does not affect H3K9me3 nor DNA methylation, suggesting Setdb1-independent pathways for maintaining these modifications. Importantly, Dnmt1 knock-out results in IAP de-repression in both visceral and definitive endoderm cells, while H3K9me3 is unaltered. Thus, our data suggest a dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm cells. Our findings suggest that Setdb1-meditated H3K9me3 is not sufficient for IAP silencing, but rather critical for maintaining high DNA methylation. Silencing of endogenous retroviruses is crucial for maintaining transcriptional and genomic integrity of cells and is maintained by histone H3K9 methylation and/or DNA methylation in various cell types. Here the authors show that loss of DNA methyltransferase DNMT1 in endoderm results in ERV derepression while H3K9me3 is unaltered.
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11
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Zhang L, Li Q, Wang H, Wu Y, Ye X, Gong Z, Li Q, Xuan A. Gadd45g, a novel antidepressant target, mediates metformin-induced neuronal differentiation of neural stem cells via DNA demethylation. Stem Cells 2022; 40:59-73. [DOI: 10.1093/stmcls/sxab001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 07/28/2021] [Indexed: 11/14/2022]
Abstract
Abstract
Increased neurogenesis elicits antidepressive-like effects. The antidiabetic drug metformin (Met) reportedly promotes hippocampal neurogenesis, which ameliorates spatial memory deficits and depression-like behaviors. However, the precise molecular mechanisms underpinning Met-induced neuronal differentiation of neural stem cells (NSCs) remain unclear. We showed that Met enhanced neuronal differentiation of NSCs via Gadd45g but not Gadd45a and Gadd45b. We further found that Gadd45g increased demethylation of neurogenic differentiation 1 (NeuroD1) promoter by regulating the activity of passive and active DNA demethylation enzymes through an AMPK-independent mechanism in Met-treated NSCs. Importantly, genetic deficiency of Gadd45g decreased hippocampal neurogenesis, which could contribute to spatial memory decline, and depression-like behaviors in the adult mice, whereas forced expression of Gadd45g alleviated the depressive-like behaviors. Our findings provide a model that Gadd45g-mediated DNA demethylation contributes to Met-induced neuronal genesis and its antidepressant-like effects, and propose the concept that targeting Gadd45g regulation of neurogenesis might serve as a novel antidepressant strategy.
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Affiliation(s)
- Le Zhang
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
- Key Laboratory of Neurological Function and Health, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Qingfeng Li
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
- Key Laboratory of Neurological Function and Health, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Huan Wang
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
- Key Laboratory of Neurological Function and Health, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Yuanfei Wu
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
- Key Laboratory of Neurological Function and Health, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Xiujuan Ye
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
- Key Laboratory of Neurological Function and Health, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Zhuo Gong
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
- Key Laboratory of Neurological Function and Health, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Qingqing Li
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
- Key Laboratory of Neurological Function and Health, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Aiguo Xuan
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou, China
- Key Laboratory of Neurological Function and Health, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
- Guangdong Province Key Laboratory of Psychiatric Disorders, Guangzhou, China
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12
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Yildiz CB, Zimmer-Bensch G. Role of DNMTs in the Brain. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:363-394. [DOI: 10.1007/978-3-031-11454-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation. Nat Genet 2022; 54:1895-1906. [PMID: 36471082 PMCID: PMC9729108 DOI: 10.1038/s41588-022-01241-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 10/24/2022] [Indexed: 12/12/2022]
Abstract
Cytosine methylation efficiently silences CpG-rich regulatory regions of genes and repeats in mammalian genomes. To what extent this entails direct inhibition of transcription factor (TF) binding versus indirect inhibition via recruitment of methyl-CpG-binding domain (MBD) proteins is unclear. Here we show that combinatorial genetic deletions of all four proteins with functional MBDs in mouse embryonic stem cells, derived neurons or a human cell line do not reactivate genes or repeats with methylated promoters. These do, however, become activated by methylation-restricted TFs if DNA methylation is removed. We identify several causal TFs in neurons, including ONECUT1, which is methylation sensitive only at a motif variant. Rampantly upregulated retrotransposons in methylation-free neurons feature a CRE motif, which activates them in the absence of DNA methylation via methylation-sensitive binding of CREB1. Our study reveals methylation-sensitive TFs in vivo and argues that direct inhibition, rather than indirect repression by the tested MBD proteins, is the prevailing mechanism of methylation-mediated repression at regulatory regions and repeats.
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Genetic Studies on Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:111-136. [PMID: 36350508 PMCID: PMC9815518 DOI: 10.1007/978-3-031-11454-0_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cytosine methylation at the C5-position-generating 5-methylcytosine (5mC)-is a DNA modification found in many eukaryotic organisms, including fungi, plants, invertebrates, and vertebrates, albeit its levels vary greatly in different organisms. In mammals, cytosine methylation occurs predominantly in the context of CpG dinucleotides, with the majority (60-80%) of CpG sites in their genomes being methylated. DNA methylation plays crucial roles in the regulation of chromatin structure and gene expression and is essential for mammalian development. Aberrant changes in DNA methylation and genetic alterations in enzymes and regulators involved in DNA methylation are associated with various human diseases, including cancer and developmental disorders. In mammals, DNA methylation is mediated by two families of DNA methyltransferases (Dnmts), namely Dnmt1 and Dnmt3 proteins. Over the last three decades, genetic manipulations of these enzymes, as well as their regulators, in mice have greatly contributed to our understanding of the biological functions of DNA methylation in mammals. In this chapter, we discuss genetic studies on mammalian Dnmts, focusing on their roles in embryogenesis, cellular differentiation, genomic imprinting, and human diseases.
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Epigenetic Mechanisms in Memory and Cognitive Decline Associated with Aging and Alzheimer's Disease. Int J Mol Sci 2021; 22:ijms222212280. [PMID: 34830163 PMCID: PMC8618067 DOI: 10.3390/ijms222212280] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/21/2022] Open
Abstract
Epigenetic mechanisms, which include DNA methylation, a variety of post-translational modifications of histone proteins (acetylation, phosphorylation, methylation, ubiquitination, sumoylation, serotonylation, dopaminylation), chromatin remodeling enzymes, and long non-coding RNAs, are robust regulators of activity-dependent changes in gene transcription. In the brain, many of these epigenetic modifications have been widely implicated in synaptic plasticity and memory formation. Dysregulation of epigenetic mechanisms has been reported in the aged brain and is associated with or contributes to memory decline across the lifespan. Furthermore, alterations in the epigenome have been reported in neurodegenerative disorders, including Alzheimer’s disease. Here, we review the diverse types of epigenetic modifications and their role in activity- and learning-dependent synaptic plasticity. We then discuss how these mechanisms become dysregulated across the lifespan and contribute to memory loss with age and in Alzheimer’s disease. Collectively, the evidence reviewed here strongly supports a role for diverse epigenetic mechanisms in memory formation, aging, and neurodegeneration in the brain.
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Reichard J, Zimmer-Bensch G. The Epigenome in Neurodevelopmental Disorders. Front Neurosci 2021; 15:776809. [PMID: 34803599 PMCID: PMC8595945 DOI: 10.3389/fnins.2021.776809] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/04/2021] [Indexed: 12/26/2022] Open
Abstract
Neurodevelopmental diseases (NDDs), such as autism spectrum disorders, epilepsy, and schizophrenia, are characterized by diverse facets of neurological and psychiatric symptoms, differing in etiology, onset and severity. Such symptoms include mental delay, cognitive and language impairments, or restrictions to adaptive and social behavior. Nevertheless, all have in common that critical milestones of brain development are disrupted, leading to functional deficits of the central nervous system and clinical manifestation in child- or adulthood. To approach how the different development-associated neuropathologies can occur and which risk factors or critical processes are involved in provoking higher susceptibility for such diseases, a detailed understanding of the mechanisms underlying proper brain formation is required. NDDs rely on deficits in neuronal identity, proportion or function, whereby a defective development of the cerebral cortex, the seat of higher cognitive functions, is implicated in numerous disorders. Such deficits can be provoked by genetic and environmental factors during corticogenesis. Thereby, epigenetic mechanisms can act as an interface between external stimuli and the genome, since they are known to be responsive to external stimuli also in cortical neurons. In line with that, DNA methylation, histone modifications/variants, ATP-dependent chromatin remodeling, as well as regulatory non-coding RNAs regulate diverse aspects of neuronal development, and alterations in epigenomic marks have been associated with NDDs of varying phenotypes. Here, we provide an overview of essential steps of mammalian corticogenesis, and discuss the role of epigenetic mechanisms assumed to contribute to pathophysiological aspects of NDDs, when being disrupted.
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Affiliation(s)
- Julia Reichard
- Functional Epigenetics in the Animal Model, Institute for Biology II, RWTH Aachen University, Aachen, Germany
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany
| | - Geraldine Zimmer-Bensch
- Functional Epigenetics in the Animal Model, Institute for Biology II, RWTH Aachen University, Aachen, Germany
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany
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17
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Chaudhury S. Epigenetic regulation in Autism spectrum disorder. AIMS GENETICS 2021. [DOI: 10.3934/genet.2016.4.292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
AbstractAutism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by an impaired social communication skill and often results in repetitive, stereotyped behavior which is observed in children during the first few years of life. Other characteristic of this disorder includes language disabilities, difficulties in sensory integration, lack of reciprocal interactions and in some cases, cognitive delays. One percentage of the general population is affected by ASD and is four times more common in boys than girls. There are hundreds of genes, which has been identified to be associated with ASD etiology. However it remains difficult to comprehend our understanding in defining the genetic architecture necessary for complete exposition of its pathophysiology. Seeing the complexity of the disease, it is important to adopt a multidisciplinary approach which should not only focus on the “genetics” of autism but also on epigenetics, transcriptomics, immune system disruption and environmental factors that could all impact the pathogenesis of the disease. As environmental factors also play a key role in regulating the trigger of ASD, the role of chromatin remodeling and DNA methylation has started to emerge. Such epigenetic modifications directly link molecular regulatory pathways and environmental factors, which might be able to explain some aspects of complex disorders like ASD. The present review will focus on the role of epigenetic regulation in defining the underlying cause for ASD.
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Affiliation(s)
- Sraboni Chaudhury
- Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI-48109, USA
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18
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Eyolfson E, Bhatt D, Wang M, Lohman AW, Mychasiuk R. Paternal exposure to exercise and/or caffeine and alcohol modify offspring behavioral and pathophysiological recovery from repetitive mild traumatic brain injury in adolescence. GENES, BRAIN, AND BEHAVIOR 2021; 20:egbb12736. [PMID: 33876557 DOI: 10.1111/gbb.12736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 11/30/2022]
Abstract
Only recently has the scope of parental research expanded to include the paternal sphere with epidemiological studies implicating stress, nutrition and alcohol consumption in the neurobiological and behavioral characteristics of offspring. This study was designed to determine if paternal exposure to caffeine, alcohol and exercise prior to conception would improve or exacerbate offspring recovery from adolescent repetitive mild traumatic brain injury (RmTBI). Sires received 7 weeks of standard drinking water, or caffeine and ethanol and were housed in regular cages or cages with running wheels, prior to being mated to control females. At postnatal day 40, offspring were administered RmTBI or sham injuries and were assessed for post concussive symptomology. Post-mortem quantitative real-time polymerase chain reaction (qRT-PCR) was used to assess gene expression in the prefrontal cortex (PFC), nucleus accumbens (NAc) and changes in telomere length. Additionally, enzyme-linked immunosorbent assay (ELISA's) were run on serum to detect levels of cytokines, chemokines and sex hormones. Paternal experience did not improve or exacerbate RmTBI behavioral outcomes. However, female and male offspring displayed unique responses to RmTBI and paternal experience, resulting in changes in physical, behavioral and molecular outcomes. Injury and paternal exercise modified changes in female offspring, whereas male offspring were affected by paternal exercise, caffeine and alcohol treatment. Additionally, paternal experience and RmTBI modified expression of many genes in the PFC, NAc, telomere length and levels of sex hormones. Although further exploration is required to understand the heterogeneity that exists in disease risk and resiliency, this study provides corroborating evidence that paternal experiences prior to conception influences offspring development.
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Affiliation(s)
- Eric Eyolfson
- Department of Psychology, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute and Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
| | - Dhyey Bhatt
- Hotchkiss Brain Institute and Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Melinda Wang
- Hotchkiss Brain Institute and Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
| | - Alexander W Lohman
- Hotchkiss Brain Institute and Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Richelle Mychasiuk
- Department of Psychology, University of Calgary, Calgary, Alberta, Canada
- Hotchkiss Brain Institute and Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
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Haq SU, Bhat UA, Kumar A. Prenatal stress effects on offspring brain and behavior: Mediators, alterations and dysregulated epigenetic mechanisms. J Biosci 2021. [DOI: 10.1007/s12038-021-00153-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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High Methionine Diet-Induced Alzheimer's Disease like Symptoms Are Accompanied by 5-Methylcytosine Elevated Levels in the Brain. Behav Neurol 2021; 2021:6683318. [PMID: 33880134 PMCID: PMC8046555 DOI: 10.1155/2021/6683318] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/16/2021] [Accepted: 03/23/2021] [Indexed: 01/09/2023] Open
Abstract
Background Excessive or insufficient intake of methionine (Met) causes neuronal dysfunction, neurodegeneration, cerebrovascular dysfunction, vascular leakage, and short-term memory loss, which result in the occurrence of Alzheimer's disease- (AD-) like symptoms. Objective To determine the relationship between high methionine diets (HMD) induced AD-like symptoms and 5-methylcytosine (5-mC) level. Methods C57BL/6J mice were randomly divided into two groups: the control group (Maintain diets) and the model group (2% HMD). Mice were fed with 2% HMD for 9 weeks. Animals were weighed and food intake was recorded weekly. Open field test, nesting ability test, Y maze test, new object recognition test, and Morris water maze test were used to detect the motor, learning, and memory ability. Hematoxylin-eosin (HE) staining was used to observe the damage of cells in hippocampus and cortex. Immunofluorescence (IF) staining was used to detect the expression and distribution of amyloid-β 1-40 (Aβ1-40), amyloid-β 1-42 (Aβ1-42), and 5-methylcytosine (5-mC) in hippocampus and cortex. Western blotting (WB) was used to determine the expression of Aβ and DNA methyltransferases- (DNMTs-) related proteins in the cortex. Enzyme-linked immunosorbent assay (ELISA) was performed to detect homocysteine (Hcy) level (ELISA). Results Feeding of HMD decreased the body weight and food intake of mice. Behavioral testing revealed that HMD caused learning, memory, and motor ability impairment in the mice. HE staining results showed that HMD feeding caused damage of hippocampal and cortical neurons, along with disordered cell arrangement, and loss of neurons. Furthermore, HMD increased the contents of Aβ1-40, Aβ1-42, and 5-mC in the hippocampus and cortex. WB results showed that HMD increased the expression of Aβ production-related proteins, such as amyloid precursor protein (APP) and beta-secretase 1 (BACE1), and decreased the expression of Aβ metabolism-related protein in the cortex, including insulin-degrading enzyme (IDE) and neprilysin (NEP). Additionally, the decreased expression of DNA methyltransferase1 (DNMT1) was observed in HMD-treated mice, but there was no significant change of DNMT3a level. ELISA results showed that HMD increased the levels of Hcy in serum. Conclusion Our result suggested that the HMD can cause neurotoxicity, leading to AD-like symptoms in mice, which may be related to 5-mC elevated.
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Whole genome methylation and transcriptome analyses to identify risk for cerebral palsy (CP) in extremely low gestational age neonates (ELGAN). Sci Rep 2021; 11:5305. [PMID: 33674671 PMCID: PMC7935929 DOI: 10.1038/s41598-021-84214-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 01/05/2021] [Indexed: 01/05/2023] Open
Abstract
Preterm birth remains the leading identifiable risk factor for cerebral palsy (CP), a devastating form of motor impairment due to developmental brain injury occurring around the time of birth. We performed genome wide methylation and whole transcriptome analyses to elucidate the early pathogenesis of CP in extremely low gestational age neonates (ELGANs). We evaluated peripheral blood cell specimens collected during a randomized trial of erythropoietin for neuroprotection in the ELGAN (PENUT Trial, NCT# 01378273). DNA methylation data were generated from 94 PENUT subjects (n = 47 CP vs. n = 47 Control) on day 1 and 14 of life. Gene expression data were generated from a subset of 56 subjects. Only one differentially methylated region was identified for the day 1 to 14 change between CP versus no CP, without evidence for differential gene expression of the associated gene RNA Pseudouridine Synthase Domain Containing 2. iPathwayGuide meta-analyses identified a relevant upregulation of JAK1 expression in the setting of decreased methylation that was observed in control subjects but not CP subjects. Evaluation of whole transcriptome data identified several top pathways of potential clinical relevance including thermogenesis, ferroptossis, ribosomal activity and other neurodegenerative conditions that differentiated CP from controls.
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Analysis of transcript levels of a few schizophrenia candidate genes in neurons from a transgenic mouse embryonic stem cell model overexpressing DNMT1. Gene 2020; 757:144934. [PMID: 32640307 DOI: 10.1016/j.gene.2020.144934] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/23/2020] [Accepted: 07/01/2020] [Indexed: 02/08/2023]
Abstract
Overexpression of DNA Methyltransferase I (DNMT1) is considered as one of the etiological factors for schizophrenia (SZ). However, information on genes subjected to dysregulation because of DNMT1 overexpression is limited. To test whether a larger group of SZ-associated genes are affected, we selected 15 genes reported to be dysregulated in patients (Gad1, Reln, Ank3, Cacna1c, Dkk3, As3mt, Ppp1r11, Smad5, Syn1, Wnt1, Pdgfra, Gsk3b, Cxcl12, Tcf4 and Fez1). Transcript levels of these genes were compared between neurons derived from Dnmt1tet/tet (Tet/Tet) mouse embryonic stem cells (ESCs) that overexpress DNMT1 with R1 (wild-type) neurons. Transcript levels of thirteen genes were significantly altered in Tet/Tet neurons of which, the dysregulation patterns of 11 were similar to patients. Transcript levels of eight out of these eleven were also significantly altered in Tet/Tet ESCs, but the dysregulation patterns of only five were similar to neurons. Comparative analyses among ESCs, embryoid bodies and neurons divided the 15 genes into four distinct groups with a majority showing developmental stage-specific patterns of dysregulation. Reduced Representational Bisulfite Sequencing data from neurons did not show any altered promoter DNA methylation for the dysregulated genes. Doxycycline treatment of Tet/Tet ESCs that eliminated DNMT1, reversed the direction of dysregulation of only four genes (Gad1, Dkk3, As3mt and Syn1). These results suggest that 1. Increased DNMT1 affected the levels of a majority of the transcripts studied, 2. Dysregulation appears to be independent of promoter methylation, 3. Effects of increased DNMT1 levels were reversible for only a subset of the genes studied, and 4. Increased DNMT1 levels may affect transcript levels of multiple schizophrenia-associated genes.
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Linde J, Zimmer-Bensch G. DNA Methylation-Dependent Dysregulation of GABAergic Interneuron Functionality in Neuropsychiatric Diseases. Front Neurosci 2020; 14:586133. [PMID: 33041771 PMCID: PMC7525021 DOI: 10.3389/fnins.2020.586133] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 08/25/2020] [Indexed: 12/30/2022] Open
Abstract
Neuropsychiatric diseases, such as mood disorders, schizophrenia, and autism, represent multifactorial disorders, differing in causes, disease onset, severity, and symptoms. A common feature of numerous neuropsychiatric conditions are defects in the cortical inhibitory GABAergic system. The balance of excitation and inhibition is fundamental for proper and efficient information processing in the cerebral cortex. Thus, altered inhibition is suggested to account for pathological symptoms like cognitive impairments and dysfunctional multisensory integration. While it became apparent that most of these diseases have a clear genetic component, environmental influences emerged as an impact of disease manifestation, onset, and severity. Epigenetic mechanisms of transcriptional control, such as DNA methylation, are known to be responsive to external stimuli, and are suspected to be implicated in the functional impairments of GABAergic interneurons, and hence, the pathophysiology of neuropsychiatric diseases. Here, we provide an overview about the multifaceted functional implications of DNA methylation and DNA methyltransferases in cortical interneuron development and function in health and disease. Apart from the regulation of gamma-aminobutyric acid-related genes and genes relevant for interneuron development, we discuss the role of DNA methylation-dependent regulation of synaptic transmission by the modulation of endocytosis-related genes as potential pathophysiological mechanisms underlying neuropsychiatric conditions. Deciphering the hierarchy and mechanisms of changes in epigenetic signatures is crucial to develop effective strategies for treatment and prevention.
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Affiliation(s)
- Jenice Linde
- Division of Functional Epigenetics in the Animal Model, Institute for Biology II, RWTH Aachen University, Aachen, Germany.,Research Training Group 2416 MultiSenses - MultiScales, RWTH Aachen University, Aachen, Germany
| | - Geraldine Zimmer-Bensch
- Division of Functional Epigenetics in the Animal Model, Institute for Biology II, RWTH Aachen University, Aachen, Germany.,Research Training Group 2416 MultiSenses - MultiScales, RWTH Aachen University, Aachen, Germany
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Audesse AJ, Webb AE. Mechanisms of enhanced quiescence in neural stem cell aging. Mech Ageing Dev 2020; 191:111323. [PMID: 32781077 DOI: 10.1016/j.mad.2020.111323] [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: 03/26/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 12/24/2022]
Abstract
The maintenance of neural stem cell function is vital to ensure neurogenesis throughout adulthood. During aging, there is a significant reduction in adult neurogenesis that correlates with a decline in cognitive function. Although recent studies have revealed novel extrinsic and intrinsic mechanisms that regulate the adult neural stem cell (NSC) pool and lineage progression, the precise molecular mechanisms that drive dysregulation of adult neurogenesis in the context of aging are only beginning to emerge. Recent studies have shed light on mechanisms that regulate the earliest step of adult neurogenesis, the activation of quiescent NSCs. Interestingly, the ability of NSCs to enter the cell cycle in the aged brain significantly declines suggesting a deepend state of quiescence. Given the likely contribution of adult neurogenesis to supporting cognitive function in humans, enhancing neurogenesis may be a strategy to combat age-related cognitive decline. This review highlights the mechanisms that regulate the NSC pool throughout adulthood and discusses how dysregulation of these processes may contribute to the decline in neurogenesis and cognitive function throughout aging.
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Affiliation(s)
- Amanda J Audesse
- Graduate Program in Neuroscience, Brown University, USA; Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Ashley E Webb
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA; Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA; Center on the Biology of Aging, Brown University, Providence, RI 02912, USA.
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Arthur-Farraj P, Moyon S. DNA methylation in Schwann cells and in oligodendrocytes. Glia 2020; 68:1568-1583. [PMID: 31958184 DOI: 10.1002/glia.23784] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/17/2019] [Accepted: 01/10/2020] [Indexed: 12/12/2022]
Abstract
DNA methylation is one of many epigenetic marks, which directly modifies base residues, usually cytosines, in a multiple-step cycle. It has been linked to the regulation of gene expression and alternative splicing in several cell types, including during cell lineage specification and differentiation processes. DNA methylation changes have also been observed during aging, and aberrant methylation patterns have been reported in several neurological diseases. We here review the role of DNA methylation in Schwann cells and oligodendrocytes, the myelin-forming glia of the peripheral and central nervous systems, respectively. We first address how methylation and demethylation are regulating myelinating cells' differentiation during development and repair. We then mention how DNA methylation dysregulation in diseases and cancers could explain their pathogenesis by directly influencing myelinating cells' proliferation and differentiation capacities.
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Affiliation(s)
- Peter Arthur-Farraj
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Sarah Moyon
- Neuroscience Initiative Advanced Science Research Center, CUNY, New York, New York
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Epigenomic Remodeling in Huntington's Disease-Master or Servant? EPIGENOMES 2020; 4:epigenomes4030015. [PMID: 34968288 PMCID: PMC8594700 DOI: 10.3390/epigenomes4030015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 12/03/2022] Open
Abstract
In light of our aging population, neurodegenerative disorders are becoming a tremendous challenge, that modern societies have to face. They represent incurable, progressive conditions with diverse and complex pathological features, followed by catastrophic occurrences of massive neuronal loss at the later stages of the diseases. Some of these disorders, like Huntington’s disease (HD), rely on defined genetic factors. HD, as an incurable, fatal hereditary neurodegenerative disorder characterized by its mid-life onset, is caused by the expansion of CAG trinucleotide repeats coding for glutamine (Q) in exon 1 of the huntingtin gene. Apart from the genetic defect, environmental factors are thought to influence the risk, onset and progression of HD. As epigenetic mechanisms are known to readily respond to environmental stimuli, they are proposed to play a key role in HD pathogenesis. Indeed, dynamic epigenomic remodeling is observed in HD patients and in brains of HD animal models. Epigenetic signatures, such as DNA methylation, histone variants and modifications, are known to influence gene expression and to orchestrate various aspects of neuronal physiology. Hence, deciphering their implication in HD pathogenesis might open up new paths for novel therapeutic concepts, which are discussed in this review.
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Bayer C, Pitschelatow G, Hannemann N, Linde J, Reichard J, Pensold D, Zimmer-Bensch G. DNA Methyltransferase 1 (DNMT1) Acts on Neurodegeneration by Modulating Proteostasis-Relevant Intracellular Processes. Int J Mol Sci 2020; 21:E5420. [PMID: 32751461 PMCID: PMC7432412 DOI: 10.3390/ijms21155420] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023] Open
Abstract
The limited regenerative capacity of neurons requires a tightly orchestrated cell death and survival regulation in the context of longevity, as well as age-associated and neurodegenerative diseases. Subordinate to genetic networks, epigenetic mechanisms, such as DNA methylation and histone modifications, are involved in the regulation of neuronal functionality and emerge as key contributors to the pathophysiology of neurodegenerative diseases. DNA methylation, a dynamic and reversible process, is executed by DNA methyltransferases (DNMTs). DNMT1 was previously shown to act on neuronal survival in the aged brain, whereby a DNMT1-dependent modulation of processes relevant for protein degradation was proposed as an underlying mechanism. Properly operating proteostasis networks are a mandatory prerequisite for the functionality and long-term survival of neurons. Malfunctioning proteostasis is found, inter alia, in neurodegenerative contexts. Here, we investigated whether DNMT1 affects critical aspects of the proteostasis network by a combination of expression studies, live cell imaging, and protein biochemical analyses. We found that DNMT1 negatively impacts retrograde trafficking and autophagy, with both being involved in the clearance of aggregation-prone proteins by the aggresome-autophagy pathway. In line with this, we found that the transport of GFP-labeled mutant huntingtin (HTT) to perinuclear regions, proposed to be cytoprotective, also depends on DNMT1. Depletion of Dnmt1 accelerated perinuclear HTT aggregation and improved the survival of cells transfected with mutant HTT. This suggests that mutant HTT-induced cytotoxicity is at least in part mediated by DNMT1-dependent modulation of degradative pathways.
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Affiliation(s)
| | | | | | | | | | | | - Geraldine Zimmer-Bensch
- Division of Functional Epigenetics in the Animal Model, Institute for Biology II, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany; (C.B.); (G.P.); (N.H.); (J.L.); (J.R.); (D.P.)
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28
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Hahn A, Pensold D, Bayer C, Tittelmeier J, González-Bermúdez L, Marx-Blümel L, Linde J, Groß J, Salinas-Riester G, Lingner T, von Maltzahn J, Spehr M, Pieler T, Urbach A, Zimmer-Bensch G. DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons. Front Cell Dev Biol 2020; 8:639. [PMID: 32793592 PMCID: PMC7387673 DOI: 10.3389/fcell.2020.00639] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/25/2020] [Indexed: 01/19/2023] Open
Abstract
Increased life expectancy in modern society comes at the cost of age-associated disabilities and diseases. Aged brains not only show reduced excitability and plasticity, but also a decline in inhibition. Age-associated defects in inhibitory circuits likely contribute to cognitive decline and age-related disorders. Molecular mechanisms that exert epigenetic control of gene expression contribute to age-associated neuronal impairments. Both DNA methylation, mediated by DNA methyltransferases (DNMTs), and histone modifications maintain neuronal function throughout lifespan. Here we provide evidence that DNMT1 function is implicated in the age-related loss of cortical inhibitory interneurons. Dnmt1 deletion in parvalbumin-positive interneurons attenuates their age-related decline in the cerebral cortex. Moreover, conditional Dnmt1-deficient mice show improved somatomotor performance and reduced aging-associated transcriptional changes. A decline in the proteostasis network, responsible for the proper degradation and removal of defective proteins, is implicated in age- and disease-related neurodegeneration. Our data suggest that DNMT1 acts indirectly on interneuron survival in aged mice by modulating the proteostasis network during life-time.
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Affiliation(s)
- Anne Hahn
- Department of Functional Epigenetics, Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Daniel Pensold
- Department of Functional Epigenetics, Institute of Human Genetics, University Hospital Jena, Jena, Germany.,Department of Functional Epigenetics in the Animal Model, Institute of Biology II, RWTH Aachen University, Aachen, Germany
| | - Cathrin Bayer
- Department of Functional Epigenetics, Institute of Human Genetics, University Hospital Jena, Jena, Germany.,Department of Functional Epigenetics in the Animal Model, Institute of Biology II, RWTH Aachen University, Aachen, Germany
| | - Jessica Tittelmeier
- Department of Functional Epigenetics, Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Lourdes González-Bermúdez
- Department of Functional Epigenetics, Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Lisa Marx-Blümel
- Department of Functional Epigenetics, Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Jenice Linde
- Department of Functional Epigenetics in the Animal Model, Institute of Biology II, RWTH Aachen University, Aachen, Germany.,Research Training Group 2416 MultiSenses - MultiScales, RWTH Aachen University, Aachen, Germany
| | - Jonas Groß
- Department of Functional Epigenetics, Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Gabriela Salinas-Riester
- Transcriptome and Genome Analysis Laboratory (TAL), Department of Developmental Biochemistry, University of Göttingen, Göttingen, Germany
| | - Thomas Lingner
- Transcriptome and Genome Analysis Laboratory (TAL), Department of Developmental Biochemistry, University of Göttingen, Göttingen, Germany
| | - Julia von Maltzahn
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Marc Spehr
- Research Training Group 2416 MultiSenses - MultiScales, RWTH Aachen University, Aachen, Germany.,Department of Chemosensation, Institute of Biology II, RWTH Aachen University, Aachen, Germany
| | - Tomas Pieler
- Centre for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Department of Developmental Biochemistry, University of Göttingen, Göttingen, Germany
| | - Anja Urbach
- Institute of Neurology, University Hospital Jena, Jena, Germany
| | - Geraldine Zimmer-Bensch
- Department of Functional Epigenetics, Institute of Human Genetics, University Hospital Jena, Jena, Germany.,Department of Functional Epigenetics in the Animal Model, Institute of Biology II, RWTH Aachen University, Aachen, Germany.,Research Training Group 2416 MultiSenses - MultiScales, RWTH Aachen University, Aachen, Germany
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29
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Furlong MA, Paul KC, Yan Q, Chuang YH, Cockburn MG, Bronstein JM, Horvath S, Ritz B. An epigenome-wide association study of ambient pyrethroid pesticide exposures in California's central valley. Int J Hyg Environ Health 2020; 229:113569. [PMID: 32679516 DOI: 10.1016/j.ijheh.2020.113569] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 05/08/2020] [Accepted: 05/22/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Pyrethroid pesticide use is increasing worldwide, although the full extent of associated health effects is unknown. An epigenome-wide association study (EWAS) with exploratory pathway analysis may help identify potential pyrethroid-related health effects. METHODS We performed an exploratory EWAS of chronic ambient pyrethroid exposure using control participants' blood in the Parkinson's Environment and Genes Study in the Central Valley of California (N = 237). We estimated associations of living and working near agricultural pyrethroid pesticide applications in the past 5 years (binary) with site-specific differential methylation, and used a false discovery rate (FDR) cut off of 0.05 for significance. We controlled for age, sex, education, cell count, and an ancestral marker for Hispanic ethnicity. We normalized methylation values for Type I/II probe bias using Beta-Mixture Quantile (BMIQ) normalization, filtered out cross-reactive probes, and evaluated for remaining bias with Surrogate Variable Analysis (SVA). We also evaluated the effects of controlling for cell count and normalizing for Type I/II probe bias by comparing changes in effect estimates and p-values for the top hits across BMIQ and GenomeStudio normalization methods, and controlling for cell count. To facilitate broader interpretation, we annotated genes to the CpG sites and performed gene set overrepresentation analysis, using genes annotated to CpG sites that were associated with pyrethroids at a raw p < 0.05, and controlling for background representation of CpG sites on the chip. We did this for both a biological process context (Gene Ontology terms) using missMethyl, and a disease set context using WebGestalt. For these gene set overrepresentation analyses we also used an FDR cut off of 0.05 for significance of gene sets. RESULTS After controlling for cell count and applying BMIQ normalization, 4 CpG sites were differentially methylated in relation to pyrethroid exposures. When using GenomeStudio's Illumina normalization, 415 CpG sites were differentially methylated, including all four identified with the BMIQ method. In the gene set overrepresentation analyses, we identified 6 GO terms using BMIQ normalization, and 76 using Illumina normalization, including the 6 identified by BMIQ. For disease sets, we identified signals for Alzheimer's disease, leukemia and several other cancers, diabetes, birth defects, and other diseases, for both normalization methods. We identified minimal changes in effect estimates after controlling for cell count, and controlling for cell count generally weakened p-values. BMIQ normalization, however, resulted in different beta coefficients and weakened p-values. CONCLUSIONS Chronic ambient pyrethroid exposure is associated with differential methylation at CpG sites that annotate to a wide variety of disease states and biological mechanisms that align with prior research. However, this EWAS also implicates several novel diseases for future investigation, and highlights the relative importance of different background normalization methods in identifying associations.
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Affiliation(s)
- Melissa A Furlong
- Department of Community, Environment, and Policy, University of Arizona Mel and Enid Zuckerman College of Public Health, Tucson, AZ, USA.
| | - Kimberly C Paul
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Qi Yan
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Yu-Hsuan Chuang
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Myles G Cockburn
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, CA, USA
| | - Jeff M Bronstein
- Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, Los Angeles, CA, USA; Department of Biostatistics, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Beate Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA; Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
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30
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dnmt1 function is required to maintain retinal stem cells within the ciliary marginal zone of the zebrafish eye. Sci Rep 2020; 10:11293. [PMID: 32647199 PMCID: PMC7347529 DOI: 10.1038/s41598-020-68016-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/15/2020] [Indexed: 12/22/2022] Open
Abstract
The ciliary marginal zone (CMZ) of the zebrafish retina contains a population of actively proliferating resident stem cells, which generate retinal neurons throughout life. The maintenance methyltransferase, dnmt1, is expressed within the CMZ. Loss of dnmt1 function results in gene misregulation and cell death in a variety of developmental contexts, however, its role in retinal stem cell (RSC) maintenance is currently unknown. Here, we demonstrate that zebrafish dnmt1s872 mutants possess severe defects in RSC maintenance within the CMZ. Using a combination of immunohistochemistry, in situ hybridization, and a transgenic reporter assay, our results demonstrate a requirement for dnmt1 activity in the regulation of RSC proliferation, gene expression and in the repression of endogenous retroelements (REs). Ultimately, cell death is elevated in the dnmt1−/− CMZ, but in a p53-independent manner. Using a transgenic reporter for RE transposition activity, we demonstrate increased transposition in the dnmt1−/− CMZ. Taken together our data identify a critical role for dnmt1 function in RSC maintenance in the vertebrate eye.
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31
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Kyono Y, Raj S, Sifuentes CJ, Buisine N, Sachs L, Denver RJ. DNA methylation dynamics underlie metamorphic gene regulation programs in Xenopus tadpole brain. Dev Biol 2020; 462:180-196. [PMID: 32240642 PMCID: PMC7251973 DOI: 10.1016/j.ydbio.2020.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/28/2020] [Accepted: 03/23/2020] [Indexed: 01/07/2023]
Abstract
Methylation of cytosine residues in DNA influences chromatin structure and gene transcription, and its regulation is crucial for brain development. There is mounting evidence that DNA methylation can be modulated by hormone signaling. We analyzed genome-wide changes in DNA methylation and their relationship to gene regulation in the brain of Xenopus tadpoles during metamorphosis, a thyroid hormone-dependent developmental process. We studied the region of the tadpole brain containing neurosecretory neurons that control pituitary hormone secretion, a region that is highly responsive to thyroid hormone action. Using Methylated DNA Capture sequencing (MethylCap-seq) we discovered a diverse landscape of DNA methylation across the tadpole neural cell genome, and pairwise stage comparisons identified several thousand differentially methylated regions (DMRs). During the pre-to pro-metamorphic period, the number of DMRs was lowest (1,163), with demethylation predominating. From pre-metamorphosis to metamorphic climax DMRs nearly doubled (2,204), with methylation predominating. The largest changes in DNA methylation were seen from metamorphic climax to the completion of metamorphosis (2960 DMRs), with 80% of the DMRs representing demethylation. Using RNA sequencing, we found negative correlations between differentially expressed genes and DMRs localized to gene bodies and regions upstream of transcription start sites. DNA demethylation at metamorphosis revealed by MethylCap-seq was corroborated by increased immunoreactivity for the DNA demethylation intermediates 5-hydroxymethylcytosine and 5-carboxymethylcytosine, and the methylcytosine dioxygenase ten eleven translocation 3 that catalyzes DNA demethylation. Our findings show that the genome of tadpole neural cells undergoes significant changes in DNA methylation during metamorphosis, and these changes likely influence chromatin architecture, and gene regulation programs occurring during this developmental period.
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Affiliation(s)
- Yasuhiro Kyono
- Neuroscience Graduate Program, The University of Michigan, Ann Arbor, MI, 48109, USA
| | - Samhitha Raj
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, 48109, USA
| | - Christopher J Sifuentes
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, 48109, USA
| | - Nicolas Buisine
- UMR-7221, Centre National de la recherche scientifique (CNRS), Muséum National d'Histoire Naturelle, 75005, Paris, France
| | - Laurent Sachs
- UMR-7221, Centre National de la recherche scientifique (CNRS), Muséum National d'Histoire Naturelle, 75005, Paris, France
| | - Robert J Denver
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, 48109, USA.
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32
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The Synergism of PGN, LTA and LPS in Inducing Transcriptome Changes, Inflammatory Responses and a Decrease in Lactation as Well as the Associated Epigenetic Mechanisms in Bovine Mammary Epithelial Cells. Toxins (Basel) 2020; 12:toxins12060387. [PMID: 32545333 PMCID: PMC7354563 DOI: 10.3390/toxins12060387] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/07/2020] [Accepted: 06/09/2020] [Indexed: 12/15/2022] Open
Abstract
Mastitis is usually caused by a variety of pathogenic bacteria that include both Gram-positive and Gram-negative bacteria. Lipopolysaccharide (LPS) is the pathogen-associated molecular pattern (PAMP) of Gram-negative bacteria, and peptidoglycan (PGN) and lipoteichoic acid (LTA) are those of Gram-positive bacteria. The effects of LPS, PGN and/or LTA on inflammatory response and lactation in bovine mammary epithelial cells (BMECs) are well studied, but the epigenetic mechanisms of their effects received less attention. Furthermore, since the three PAMPs are often simultaneously present in the udder of cows with mastitis, it has implications in practice to study their additive effects. The results show that co-stimulation of bovine mammary epithelial cells with PGN, LTA, and LPS induced a higher number of differentially expressed genes (DEGs) and greater expressions of inflammatory factors including interleukin (IL)-1β, IL-6, IL-8, tumor necrosis factor-α (TNF-α), chemokine (C-X-C motif) ligand (CXCL)1, and CXCL6. In addition, co-stimulation further increased DNA hypomethylation compared with sole LPS stimulation. Co-stimulation greatly decreased casein expression but did not further decrease histone acetylation levels and affect the activity of histone acetyltransferase (HAT) and histone deacetylase (HDAC), compared with sole LPS stimulation. Collectively, this study demonstrated that PGN, LTA, and LPS had an additive effect on inducing transcriptome changes and inflammatory responses in BMECs, probably through inducing a greater decrease in DNA methylation. Co-stimulation with PGN, LTA, and LPS decreased casein expression to a greater degree, but it might not be linked to histone acetylation and HAT and HDAC activity.
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33
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Butler C, Sprowls S, Szalai G, Arsiwala T, Saralkar P, Straight B, Hatcher S, Tyree E, Yost M, Kohler WJ, Wolff B, Putnam E, Lockman P, Liu T. Hypomethylating Agent Azacitidine Is Effective in Treating Brain Metastasis Triple-Negative Breast Cancer Through Regulation of DNA Methylation of Keratin 18 Gene. Transl Oncol 2020; 13:100775. [PMID: 32408199 PMCID: PMC7225776 DOI: 10.1016/j.tranon.2020.100775] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 01/11/2023] Open
Abstract
Breast cancer patients presenting with symptomatic brain metastases have poor prognosis, and current chemotherapeutic agents are largely ineffective. In this study, we evaluated the hypomethylating agent azacitidine (AZA) for its potential as a novel therapeutic in preclinical models of brain metastasis of breast cancer. We used the parental triple-negative breast cancer MDA-MB-231 (231) cells and their brain colonizing counterpart (231Br) to ascertain phenotypic differences in response to AZA. We observed that 231Br cells have higher metastatic potential compared to 231 cells. With regard to therapeutic value, the AZA IC50 value in 231Br cells is significantly lower than that in parental cells (P < .01). AZA treatment increased apoptosis and inhibited the Wnt signaling transduction pathway, angiogenesis, and cell metastatic capacity to a significantly higher extent in the 231Br line. AZA treatment in mice with experimental brain metastases significantly reduced tumor burden (P = .0112) and increased survival (P = .0026) compared to vehicle. Lastly, we observed a decreased expression of keratin 18 (an epithelial maker) in 231Br cells due to hypermethylation, elucidating a potential mechanism of action of AZA in treating brain metastases from breast cancer.
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Affiliation(s)
- Christopher Butler
- Department of Biomedical Sciences, West Virginia School of Osteopathic Medicine, 400 Lee Street North, Lewisburg, WV
| | - Samuel Sprowls
- Department of Pharmaceutical Sciences, College of Pharmacy, West Virginia University, Morgantown, WV
| | - Gabor Szalai
- Department of Biomedical Sciences, West Virginia School of Osteopathic Medicine, 400 Lee Street North, Lewisburg, WV; Department of Biomedical Sciences, Burrell College of Osteopathic Medicine, Las Cruces, NM
| | - Tasneem Arsiwala
- Department of Pharmaceutical Sciences, College of Pharmacy, West Virginia University, Morgantown, WV
| | - Pushkar Saralkar
- Department of Pharmaceutical Sciences, College of Pharmacy, West Virginia University, Morgantown, WV
| | - Benjamin Straight
- Department of Biomedical Sciences, West Virginia School of Osteopathic Medicine, 400 Lee Street North, Lewisburg, WV
| | - Shea Hatcher
- Department of Biomedical Sciences, West Virginia School of Osteopathic Medicine, 400 Lee Street North, Lewisburg, WV
| | - Evan Tyree
- Department of Biomedical Sciences, West Virginia School of Osteopathic Medicine, 400 Lee Street North, Lewisburg, WV
| | - Michael Yost
- Department of Biomedical Sciences, West Virginia School of Osteopathic Medicine, 400 Lee Street North, Lewisburg, WV
| | - William J Kohler
- Department of Biomedical Sciences, West Virginia School of Osteopathic Medicine, 400 Lee Street North, Lewisburg, WV
| | - Benjamin Wolff
- Department of Biomedical Sciences, West Virginia School of Osteopathic Medicine, 400 Lee Street North, Lewisburg, WV
| | | | - Paul Lockman
- Department of Pharmaceutical Sciences, College of Pharmacy, West Virginia University, Morgantown, WV
| | - Tuoen Liu
- Department of Biomedical Sciences, West Virginia School of Osteopathic Medicine, 400 Lee Street North, Lewisburg, WV.
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34
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Pensold D, Reichard J, Van Loo KMJ, Ciganok N, Hahn A, Bayer C, Liebmann L, Groß J, Tittelmeier J, Lingner T, Salinas-Riester G, Symmank J, Halfmann C, González-Bermúdez L, Urbach A, Gehrmann J, Costa I, Pieler T, Hübner CA, Vatter H, Kampa B, Becker AJ, Zimmer-Bensch G. DNA Methylation-Mediated Modulation of Endocytosis as Potential Mechanism for Synaptic Function Regulation in Murine Inhibitory Cortical Interneurons. Cereb Cortex 2020; 30:3921-3937. [PMID: 32147726 PMCID: PMC7264686 DOI: 10.1093/cercor/bhaa009] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/14/2019] [Accepted: 01/10/2020] [Indexed: 12/25/2022] Open
Abstract
The balance of excitation and inhibition is essential for cortical information processing, relying on the tight orchestration of the underlying subcellular processes. Dynamic transcriptional control by DNA methylation, catalyzed by DNA methyltransferases (DNMTs), and DNA demethylation, achieved by ten–eleven translocation (TET)-dependent mechanisms, is proposed to regulate synaptic function in the adult brain with implications for learning and memory. However, focus so far is laid on excitatory neurons. Given the crucial role of inhibitory cortical interneurons in cortical information processing and in disease, deciphering the cellular and molecular mechanisms of GABAergic transmission is fundamental. The emerging relevance of DNMT and TET-mediated functions for synaptic regulation irrevocably raises the question for the targeted subcellular processes and mechanisms. In this study, we analyzed the role dynamic DNA methylation has in regulating cortical interneuron function. We found that DNMT1 and TET1/TET3 contrarily modulate clathrin-mediated endocytosis. Moreover, we provide evidence that DNMT1 influences synaptic vesicle replenishment and GABAergic transmission, presumably through the DNA methylation-dependent transcriptional control over endocytosis-related genes. The relevance of our findings is supported by human brain sample analysis, pointing to a potential implication of DNA methylation-dependent endocytosis regulation in the pathophysiology of temporal lobe epilepsy, a disease characterized by disturbed synaptic transmission.
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Affiliation(s)
- Daniel Pensold
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany.,Division of Functional Epigenetics, Institute of Zoology (Biology 2), RWTH Aachen University, 52074 Aachen, Germany
| | - Julia Reichard
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany.,Division of Functional Epigenetics, Institute of Zoology (Biology 2), RWTH Aachen University, 52074 Aachen, Germany.,Research Training Group 2416 Multi Senses-Multi Scales, RWTH Aachen University, 52074 Aachen, Germany
| | - Karen M J Van Loo
- Department of Neuropathology, Section for Translational Epilepsy Research, University of Bonn Medical Center, 53105 Bonn, Germany
| | - Natalja Ciganok
- Division of Systems Neurophysiology, Institute of Zoology (Biology 2), RWTH Aachen University, 52074 Aachen, Germany
| | - Anne Hahn
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany
| | - Cathrin Bayer
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany.,Division of Functional Epigenetics, Institute of Zoology (Biology 2), RWTH Aachen University, 52074 Aachen, Germany
| | - Lutz Liebmann
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany
| | - Jonas Groß
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany
| | | | - Thomas Lingner
- Department of Developmental Biochemistry, Transcriptome and Genome Analysis Laboratory (TAL), University of Goettingen, 37077 Goettingen, Germany
| | - Gabriela Salinas-Riester
- Department of Developmental Biochemistry, Transcriptome and Genome Analysis Laboratory (TAL), University of Goettingen, 37077 Goettingen, Germany
| | - Judit Symmank
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany
| | - Claas Halfmann
- Division of Systems Neurophysiology, Institute of Zoology (Biology 2), RWTH Aachen University, 52074 Aachen, Germany
| | | | - Anja Urbach
- Clinic for Neurology, University Hospital Jena, 07743 Jena, Germany
| | - Julia Gehrmann
- Institute for Computational Genomics, University Hospital Aachen, RWTH Aachen University, 52074 Aachen, Germany
| | - Ivan Costa
- Institute for Computational Genomics, University Hospital Aachen, RWTH Aachen University, 52074 Aachen, Germany
| | - Tomas Pieler
- Department of Developmental Biochemistry, Centre for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University of Goettingen, 37077 Goettingen, Germany
| | - Christian A Hübner
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany
| | - Hartmut Vatter
- Clinic for Neurosurgery, University of Bonn Medical Center, 53105 Bonn, Germany
| | - Björn Kampa
- Division of Systems Neurophysiology, Institute of Zoology (Biology 2), RWTH Aachen University, 52074 Aachen, Germany.,JARA BRAIN, Institute for Neuroscience and Medicine, Forschungszentrum Jülich, 52425, Germany
| | - Albert J Becker
- Department of Neuropathology, Section for Translational Epilepsy Research, University of Bonn Medical Center, 53105 Bonn, Germany
| | - Geraldine Zimmer-Bensch
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany.,Division of Functional Epigenetics, Institute of Zoology (Biology 2), RWTH Aachen University, 52074 Aachen, Germany.,Research Training Group 2416 Multi Senses-Multi Scales, RWTH Aachen University, 52074 Aachen, Germany
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35
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Abstract
Maintenance of genome stability requires control over the expression of transposable elements (TEs), whose activity can have substantial deleterious effects on the host. Chemical modification of DNA is a commonly used strategy to achieve this, and it has long been argued that the emergence of 5-methylcytosine (5mC) in many species was driven by the requirement to silence TEs. Potential roles in TE regulation have also been suggested for other DNA modifications, such as N6-methyladenine and oxidation derivatives of 5mC, although the underlying mechanistic relationships are poorly understood. Here, we discuss current evidence implicating DNA modifications and DNA-modifying enzymes in TE regulation across different species.
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Affiliation(s)
- Özgen Deniz
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London, UK
| | - Jennifer M Frost
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London, UK
| | - Miguel R Branco
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London, UK.
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36
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Kong X, Gong Z, Zhang L, Sun X, Ou Z, Xu B, Huang J, Long D, He X, Lin X, Li Q, Xu L, Xuan A. JAK2/STAT3 signaling mediates IL-6-inhibited neurogenesis of neural stem cells through DNA demethylation/methylation. Brain Behav Immun 2019; 79:159-173. [PMID: 30763768 DOI: 10.1016/j.bbi.2019.01.027] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 01/10/2019] [Accepted: 01/30/2019] [Indexed: 10/27/2022] Open
Abstract
Neuroinflammation, considered as a pathological hallmark of Alzheimer's disease (AD), has been demonstrated to affect hippocampal neurogenesis and cognitive function. Interleukin-6 (IL-6) is a proinflammatory cytokine known to modulate neurogenesis. However, the mechanisms are still largely unknown. Here, we reported that IL-6 suppressed neurogenesis via a JAK2/STAT3 signaling in neural stem cells (NSCs). Importantly, we found that NeuroD1 (Neurogenic differentiation 1) gene expression, which drives NSCs neurodifferentiation, was regulated by TET3 and DNMT1 in a JAK2/STAT3-dependent manner. We further found that JAK2/STAT3 inhibition enhanced demethylation of NeuroD1 regulatory elements in IL-6-treated cells, which is related to the significant upregulation of TET3 expression as well as the decreased expression of DNMT1. Furthermore, Inhibiting JAK2/STAT3 significantly rescued the memory deficits and hippocampal neurogenesis dysfunction in APP/PS1 mice. Our data suggest that JAK2/STAT3 signaling plays a vital role in suppressing neurogenesis of NSCs exposed to IL-6 at the epigenetic level, by regulating DNA methylation/demethylation.
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Affiliation(s)
- Xuejian Kong
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China; Department of Neurology of the Sixth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511518, China
| | - Zhuo Gong
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Le Zhang
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Xiangdong Sun
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Zhenri Ou
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Biao Xu
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Jingyi Huang
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Dahong Long
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Xiaosong He
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Xiaohong Lin
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Qingqing Li
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Liping Xu
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Aiguo Xuan
- Institute of Neuroscience of the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China.
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37
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Kular L, Needhamsen M, Adzemovic MZ, Kramarova T, Gomez-Cabrero D, Ewing E, Piket E, Tegnér J, Beck S, Piehl F, Brundin L, Jagodic M. Neuronal methylome reveals CREB-associated neuro-axonal impairment in multiple sclerosis. Clin Epigenetics 2019; 11:86. [PMID: 31146783 PMCID: PMC6543588 DOI: 10.1186/s13148-019-0678-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 04/30/2019] [Indexed: 11/21/2022] Open
Abstract
Background Due to limited access to brain tissue, the precise mechanisms underlying neuro-axonal dysfunction in neurological disorders such as multiple sclerosis (MS) are largely unknown. In that context, profiling DNA methylation, which is a stable and cell type-specific regulatory epigenetic mark of genome activity, offers a unique opportunity to characterize the molecular mechanisms underpinning brain pathology in situ. We examined DNA methylation patterns of neuronal nuclei isolated from post-mortem brain tissue to infer processes that occur in neurons of MS patients. Results We isolated subcortical neuronal nuclei from post-mortem white matter tissue of MS patients and non-neurological controls using flow cytometry. We examined bulk DNA methylation changes (total n = 29) and further disentangled true DNA methylation (5mC) from neuron-specific DNA hydroxymethylation (5hmC) (n = 17), using Illumina Infinium 450K arrays. We performed neuronal sub-type deconvolution using glutamate and GABA methylation profiles to further reduce neuronal sample heterogeneity. In total, we identified 2811 and 1534 significant (genome-wide adjusted P value < 0.05) differentially methylated and hydroxymethylated positions between MS patients and controls. We found striking hypo-5mC and hyper-5hmC changes occurring mainly within gene bodies, which correlated with reduced transcriptional activity, assessed using published RNAseq data from bulk brain tissue of MS patients and controls. Pathway analyses of the two cohorts implicated dysregulation of genes involved in axonal guidance and synaptic plasticity, with meta-analysis confirming CREB signalling as the most highly enriched pathway underlying these processes. We functionally investigated DNA methylation changes of CREB signalling-related genes by immunohistofluoresence of phosphorylated CREB in neurons from brain sections of a subcohort of MS patients and controls (n = 15). Notably, DNA methylation changes associated with a reduction of CREB activity in white matter neurons of MS patients compared to controls. Conclusions Our data demonstrate that investigating 5mC and 5hmC modifications separately allows the discovery of a substantial fraction of changes occurring in neurons, which can escape traditional bisulfite-based DNA methylation analysis. Collectively, our findings indicate that neurons of MS patients acquire sustained hypo-5mC and hyper-5hmC, which may impair CREB-mediated neuro-axonal integrity, in turn relating to clinical symptoms. Electronic supplementary material The online version of this article (10.1186/s13148-019-0678-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Milena Z Adzemovic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Tatiana Kramarova
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - David Gomez-Cabrero
- Department of Medicine, Unit of Computational Medicine, Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden.,Mucosal and Salivary Biology Division, King's College London Dental Institute, London, SE1 9RT, UK.,Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - Ewoud Ewing
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Eliane Piket
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Tegnér
- Department of Medicine, Unit of Computational Medicine, Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden.,Biological and Environmental Sciences and Engineering Division, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Stephan Beck
- Medical Genomics, UCL Cancer Institute, University College London, London, UK
| | - Fredrik Piehl
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
| | - Lou Brundin
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
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Amberg N, Laukoter S, Hippenmeyer S. Epigenetic cues modulating the generation of cell-type diversity in the cerebral cortex. J Neurochem 2019; 149:12-26. [PMID: 30276807 PMCID: PMC6587822 DOI: 10.1111/jnc.14601] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 09/13/2018] [Accepted: 09/26/2018] [Indexed: 12/29/2022]
Abstract
The cerebral cortex is composed of a large variety of distinct cell-types including projection neurons, interneurons, and glial cells which emerge from distinct neural stem cell lineages. The vast majority of cortical projection neurons and certain classes of glial cells are generated by radial glial progenitor cells in a highly orchestrated manner. Recent studies employing single cell analysis and clonal lineage tracing suggest that neural stem cell and radial glial progenitor lineage progression are regulated in a profound deterministic manner. In this review we focus on recent advances based mainly on correlative phenotypic data emerging from functional genetic studies in mice. We establish hypotheses to test in future research and outline a conceptual framework how epigenetic cues modulate the generation of cell-type diversity during cortical development.
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Affiliation(s)
- Nicole Amberg
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Susanne Laukoter
- Institute of Science and Technology AustriaKlosterneuburgAustria
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39
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Walton E, Relton CL, Caramaschi D. Using Openly Accessible Resources to Strengthen Causal Inference in Epigenetic Epidemiology of Neurodevelopment and Mental Health. Genes (Basel) 2019; 10:E193. [PMID: 30832291 PMCID: PMC6470715 DOI: 10.3390/genes10030193] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/25/2019] [Indexed: 12/18/2022] Open
Abstract
The recent focus on the role of epigenetic mechanisms in mental health has led to several studies examining the association of epigenetic processes with psychiatric conditions and neurodevelopmental traits. Some studies suggest that epigenetic changes might be causal in the development of the psychiatric condition under investigation. However, other scenarios are possible, e.g., statistical confounding or reverse causation, making it particularly challenging to derive conclusions on causality. In the present review, we examine the evidence from human population studies for a possible role of epigenetic mechanisms in neurodevelopment and mental health and discuss methodological approaches on how to strengthen causal inference, including the need for replication, (quasi-)experimental approaches and Mendelian randomization. We signpost openly accessible resources (e.g., "MR-Base" "EWAS catalog" as well as tissue-specific methylation and gene expression databases) to aid the application of these approaches.
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Affiliation(s)
- Esther Walton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN Bristol, UK.
- Department of Psychology, University of Bath, BA2 7AY Bath, UK.
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN Bristol, UK.
| | - Doretta Caramaschi
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN Bristol, UK.
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40
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Dai YJ, Wu DC, Feng B, Chen B, Tang YS, Jin MM, Zhao HW, Dai HB, Wang Y, Chen Z. Prolonged febrile seizures induce inheritable memory deficits in rats through DNA methylation. CNS Neurosci Ther 2019; 25:601-611. [PMID: 30666786 PMCID: PMC6488897 DOI: 10.1111/cns.13088] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/08/2018] [Accepted: 11/10/2018] [Indexed: 01/08/2023] Open
Abstract
Aims Febrile seizures (FSs) are the most common types of seizures in young children. However, little is known whether the memory deficits induced by early‐life FSs could transmit across generations or not. Methods The memory functions of different generations of FS rats were behaviorally evaluated by morris water maze, inhibitory avoidance task, and contextual fear conditioning task. Meanwhile, molecular biology and pharmacological methods were used to investigate the role of DNA methylation in transgenerational transmission of memory defects. Results Prolonged FSs in infant rats resulted in memory deficits in adult and transgenerationally transmitted to next generation, which was mainly through mothers. For these two generations, DNA methyltransferase (DNMT) 1 was upregulated, leading to transcriptional inhibition of the synaptic plasticity protein reelin but not the memory suppressor protein phosphatase 1. DNMT inhibitors prevented the high expression of DNMT1 and hypermethylation of reelin gene and reversed the transgenerationally memory deficits. In addition, enriched environment in juvenile rats rescued memory deficits induced by prolonged FSs. Conclusions Our study demonstrated early experience of prolonged FSs led to memory deficits in adult rats and their unaffected offspring, which involved epigenetic mechanisms, suggesting early environmental experiences had a significant impact on the transgenerational transmission of neurological diseases.
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Affiliation(s)
- Yun-Jian Dai
- Institute of Pharmacology & Toxicology, NHC and CAMS Key Laboratory of Medical Neurobiology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,Department of Pharmacy, Second Affiliated hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Deng-Chang Wu
- Institute of Pharmacology & Toxicology, NHC and CAMS Key Laboratory of Medical Neurobiology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Bo Feng
- Institute of Pharmacology & Toxicology, NHC and CAMS Key Laboratory of Medical Neurobiology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Bin Chen
- Institute of Pharmacology & Toxicology, NHC and CAMS Key Laboratory of Medical Neurobiology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yang-Shun Tang
- Institute of Pharmacology & Toxicology, NHC and CAMS Key Laboratory of Medical Neurobiology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Miao-Miao Jin
- Institute of Pharmacology & Toxicology, NHC and CAMS Key Laboratory of Medical Neurobiology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Hua-Wei Zhao
- Institute of Pharmacology & Toxicology, NHC and CAMS Key Laboratory of Medical Neurobiology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,Department of Pharmacy, School of Medicine, Children's hospital, Zhejiang University, Hangzhou, China
| | - Hai-Bin Dai
- Department of Pharmacy, Second Affiliated hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Epilepsy Center, Department of Neurology, School of Medicine, Second Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Yi Wang
- Institute of Pharmacology & Toxicology, NHC and CAMS Key Laboratory of Medical Neurobiology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Zhong Chen
- Institute of Pharmacology & Toxicology, NHC and CAMS Key Laboratory of Medical Neurobiology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,Epilepsy Center, Department of Neurology, School of Medicine, Second Affiliated Hospital, Zhejiang University, Hangzhou, China
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41
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Román GC, Mancera-Páez O, Bernal C. Epigenetic Factors in Late-Onset Alzheimer's Disease: MTHFR and CTH Gene Polymorphisms, Metabolic Transsulfuration and Methylation Pathways, and B Vitamins. Int J Mol Sci 2019; 20:E319. [PMID: 30646578 PMCID: PMC6359124 DOI: 10.3390/ijms20020319] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/10/2019] [Accepted: 01/11/2019] [Indexed: 12/17/2022] Open
Abstract
DNA methylation and other epigenetic factors are important in the pathogenesis of late-onset Alzheimer's disease (LOAD). Methylenetetrahydrofolate reductase (MTHFR) gene mutations occur in most elderly patients with memory loss. MTHFR is critical for production of S-adenosyl-l-methionine (SAM), the principal methyl donor. A common mutation (1364T/T) of the cystathionine-γ-lyase (CTH) gene affects the enzyme that converts cystathionine to cysteine in the transsulfuration pathway causing plasma elevation of total homocysteine (tHcy) or hyperhomocysteinemia-a strong and independent risk factor for cognitive loss and AD. Other causes of hyperhomocysteinemia include aging, nutritional factors, and deficiencies of B vitamins. We emphasize the importance of supplementing vitamin B12 (methylcobalamin), vitamin B₉ (folic acid), vitamin B₆ (pyridoxine), and SAM to patients in early stages of LOAD.
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Affiliation(s)
- Gustavo C Román
- Department of Neurology, Methodist Neurological Institute, Institute for Academic Medicine Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX 77030, USA.
- Weill Cornell Medical College, Department of Neurology, Cornell University, New York, NY 10065, USA.
| | - Oscar Mancera-Páez
- Universidad Nacional de Colombia, Hospital Universitario Nacional, Faculty of Medicine, Department of Neurology, Bogotá ZC 57, Colombia.
- David Cabello International Alzheimer Disease Scholarship Fund, Houston Methodist Hospital, Houston, TX77030, USA.
| | - Camilo Bernal
- Universidad Nacional de Colombia, Hospital Universitario Nacional, Faculty of Medicine, Department of Neurology, Bogotá ZC 57, Colombia.
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42
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Joseph DB, Strand DW, Vezina CM. DNA methylation in development and disease: an overview for prostate researchers. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2018; 6:197-218. [PMID: 30697577 PMCID: PMC6334199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 12/14/2018] [Indexed: 06/09/2023]
Abstract
Epigenetic mechanisms including DNA methylation are critical regulators of organismal development and tissue homeostasis. DNA methylation is the transfer of methyl groups to cytosines, which adds an additional layer of complexity to the genome. DNA methylation marks are recognized by the cellular machinery to regulate transcription. Disruption of DNA methylation with aging or exposure to environmental toxins can change susceptibility to disease or trigger processes that lead to disease. In this review, we provide an overview of the DNA methylation machinery. More specifically, we describe DNA methylation in the context of prostate development, prostate cancer, and benign prostatic hyperplasia (BPH) as well as the impact of dietary and environmental factors on DNA methylation in the prostate.
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Affiliation(s)
- Diya B Joseph
- Department of Comparative Biosciences, University of Wisconsin-MadisonMadison, WI 53706, USA
| | - Douglas W Strand
- Department of Urology, UT Southwestern Medical CenterDallas, TX 75390, USA
| | - Chad M Vezina
- Department of Comparative Biosciences, University of Wisconsin-MadisonMadison, WI 53706, USA
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43
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Taylor RM, Smith R, Collins CE, Evans TJ, Hure AJ. Dietary intake and food sources of one-carbon metabolism nutrients in preschool aged children. Eur J Clin Nutr 2018; 73:1179-1193. [PMID: 30538300 PMCID: PMC6760623 DOI: 10.1038/s41430-018-0376-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/14/2018] [Accepted: 11/19/2018] [Indexed: 11/09/2022]
Abstract
BACKGROUND It is hypothesised that epigenetic mechanisms including DNA methylation may underlie the relationship between early-life nutrition and child cognitive outcomes. This study aimed to identify dietary patterns associated with the intake of one-carbon metabolism nutrients in children aged 2-3 years. METHODS A validated 120-item semi-quantitative food frequency questionnaires at 2-3 years of age were used to estimate the intake of one-carbon metabolism nutrients (methionine, folate, choline and vitamins B2, B6, B12) and to quantify mean number of serves consumed of the food groups specified by the Australian Guide to Healthy Eating (AGHE). Descriptive statistics were used to analyse the contribution of each food group and food items to the total intake of one-carbon metabolism nutrients. Linear regression was used to test for linear trends in food group servings by nutrient intake quintiles. RESULTS No child (n = 60) from the Women And Their Children's Health (WATCH) study consumed the recommended number of serves for all AGHE food groups. Dairy and alternatives (18-44%), discretionary foods (6-33%) and meat and alternatives (6-31%) were the main sources of most one-carbon metabolism nutrients. Most child intakes of one-carbon metabolism nutrients exceeded the nutrient reference values (NRVs), except for the intake of choline, for which the mean intake was 9% below the adequate intake (AI). CONCLUSION Dairy and alternatives, discretionary foods and meat and alternatives food groups contributed significantly to the children's intake of one-carbon metabolism nutrients. The children generally had low intakes of meat and alternative foods, which may explain their inadequate intake of choline.
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Affiliation(s)
- Rachael M Taylor
- Priority Research Centre for Reproductive Science, University of Newcastle, Callaghan, NSW, 2308, Australia. .,Faculty of Health and Medicine, School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, 2308, Australia. .,Hunter Medical Research Institute, 1 Kookaburra Circuit, New Lambton Heights, NSW, 2305, Australia.
| | - Roger Smith
- Priority Research Centre for Reproductive Science, University of Newcastle, Callaghan, NSW, 2308, Australia.,Faculty of Health and Medicine, School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, 2308, Australia.,Hunter Medical Research Institute, 1 Kookaburra Circuit, New Lambton Heights, NSW, 2305, Australia
| | - Clare E Collins
- Faculty of Health and Medicine, School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, 2308, Australia.,Hunter Medical Research Institute, 1 Kookaburra Circuit, New Lambton Heights, NSW, 2305, Australia.,Faculty of Health and Medicine, School of Health Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia.,Priority Research Centre in Physical Activity and Nutrition, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Tiffany-Jane Evans
- Hunter Medical Research Institute, 1 Kookaburra Circuit, New Lambton Heights, NSW, 2305, Australia.,Clinical Research Design IT and Statistical Support (CReDITSS) Unit, Hunter Medical Research Institute, 1 Kookaburra Circuit, New Lambton Heights, NSW, 2305, Australia
| | - Alexis J Hure
- Faculty of Health and Medicine, School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, 2308, Australia.,Hunter Medical Research Institute, 1 Kookaburra Circuit, New Lambton Heights, NSW, 2305, Australia.,Priority Research Centre for Generational, Health and Ageing, University of Newcastle, Callaghan, NSW, 2308, Australia
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44
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Diverse facets of cortical interneuron migration regulation – Implications of neuronal activity and epigenetics. Brain Res 2018; 1700:160-169. [DOI: 10.1016/j.brainres.2018.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 09/02/2018] [Accepted: 09/03/2018] [Indexed: 01/21/2023]
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45
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Griñán-Ferré C, Izquierdo V, Otero E, Puigoriol-Illamola D, Corpas R, Sanfeliu C, Ortuño-Sahagún D, Pallàs M. Environmental Enrichment Improves Cognitive Deficits, AD Hallmarks and Epigenetic Alterations Presented in 5xFAD Mouse Model. Front Cell Neurosci 2018; 12:224. [PMID: 30158856 PMCID: PMC6104164 DOI: 10.3389/fncel.2018.00224] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 07/10/2018] [Indexed: 01/05/2023] Open
Abstract
Cumulative evidence shows that modifications in lifestyle factors constitute an effective strategy to modulate molecular events related to neurodegenerative diseases, confirming the relevant role of epigenetics. Accordingly, Environmental Enrichment (EE) represents an approach to ameliorate cognitive decline and neuroprotection in Alzheimer’s disease (AD). AD is characterized by specific neuropathological hallmarks, such as β-amyloid plaques and Neurofibrillary Tangles, which severely affect the areas of the brain responsible for learning and memory. We evaluated EE neuroprotective influence on 5xFAD mice. We found a better cognitive performance on EE vs. Control (Ct) 5xFAD mice, until being similar to Wild-Type (Wt) mice group. Neurodegenerative markers as β-CTF and tau hyperphosphorylation, reduced protein levels whiles APPα, postsynaptic density 95 (PSD95) and synaptophysin (SYN) protein levels increased protein levels in the hippocampus of 5xFAD-EE mice group. Furthermore, a reduction in gene expression of Il-6, Gfap, Hmox1 and Aox1 was determined. However, no changes were found in the gene expression of neurotrophins, such as Brain-derived neurotrophic factor (Bdnf), Nerve growth factor (Ngf), Tumor growth factor (Tgf) and Nerve growth factor inducible (Vgf) in mice with EE. Specifically, we found a reduced DNA-methylation level (5-mC) and an increased hydroxymethylation level (5-hmC), as well as an increased histone H3 and H4 acetylation level. Likewise, we found changes in the hippocampal gene expression of some chromatin-modifying enzyme, such as Dnmt3a/b, Hdac1, and Tet2. Extensive molecular analysis revealed a correlation between neuronal function and changes in epigenetic marks after EE that explain the cognitive improvement in 5xFAD.
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Affiliation(s)
- Christian Griñán-Ferré
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències, University of Barcelona, Barcelona, Spain
| | - Vanesa Izquierdo
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències, University of Barcelona, Barcelona, Spain
| | - Eduard Otero
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències, University of Barcelona, Barcelona, Spain
| | - Dolors Puigoriol-Illamola
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències, University of Barcelona, Barcelona, Spain
| | - Rubén Corpas
- Institut d'Investigacions Biomèdiques de Barcelona (IIBB), CSIC, IDIBAPS and CIBERESP, Barcelona, Spain
| | - Coral Sanfeliu
- Institut d'Investigacions Biomèdiques de Barcelona (IIBB), CSIC, IDIBAPS and CIBERESP, Barcelona, Spain
| | - Daniel Ortuño-Sahagún
- Laboratorio de Neuroinmunomodulación Molecular, Instituto de Investigación en Ciencias Biomédicas (IICB), Centro Universitario de Ciencias de las Salud (CUCS), Universidad de Guadalajara, Guadalajara, Mexico
| | - Mercè Pallàs
- Department of Pharmacology and Therapeutic Chemistry, Institut de Neurociències, University of Barcelona, Barcelona, Spain
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46
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Symmank J, Bayer C, Schmidt C, Hahn A, Pensold D, Zimmer-Bensch G. DNMT1 modulates interneuron morphology by regulating Pak6 expression through crosstalk with histone modifications. Epigenetics 2018; 13:536-556. [PMID: 29912614 DOI: 10.1080/15592294.2018.1475980] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Epigenetic mechanisms of gene regulation, including DNA methylation and histone modifications, call increasing attention in the context of development and human health. Thereby, interactions between DNA methylating enzymes and histone modifications tremendously multiply the spectrum of potential regulatory functions. Epigenetic networks are critically involved in the establishment and functionality of neuronal circuits that are composed of gamma-aminobutyric acid (GABA)-positive inhibitory interneurons and excitatory principal neurons in the cerebral cortex. We recently reported a crucial role of the DNA methyltransferase 1 (DNMT1) during the migration of immature POA-derived cortical interneurons by promoting the migratory morphology through repression of Pak6. However, the DNMT1-dependent regulation of Pak6 expression appeared to occur independently of direct DNA methylation. Here, we show that in addition to its DNA methylating activity, DNMT1 can act on gene transcription by modulating permissive H3K4 and repressive H3K27 trimethylation in developing inhibitory interneurons, similar to what was found in other cell types. In particular, the transcriptional control of Pak6, interactions of DNMT1 with the Polycomb-repressor complex 2 (PCR2) core enzyme EZH2, mediating repressive H3K27 trimethylations at regulatory regions of the Pak6 gene locus. Similar to what was observed upon Dnmt1 depletion, inhibition of EZH2 caused elevated Pak6 expression levels accompanied by increased morphological complexity, which was rescued by siRNA-mediated downregulation of Pak6 expression. Together, our data emphasise the relevance of DNMT1-dependent crosstalk with histone tail methylation for transcriptional control of genes like Pak6 required for proper cortical interneuron migration.
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Affiliation(s)
- Judit Symmank
- a Institute of Human Genetics , University Hospital Jena , Jena , Germany
| | - Cathrin Bayer
- a Institute of Human Genetics , University Hospital Jena , Jena , Germany
| | - Christiane Schmidt
- a Institute of Human Genetics , University Hospital Jena , Jena , Germany
| | - Anne Hahn
- a Institute of Human Genetics , University Hospital Jena , Jena , Germany
| | - Daniel Pensold
- a Institute of Human Genetics , University Hospital Jena , Jena , Germany
| | - Geraldine Zimmer-Bensch
- a Institute of Human Genetics , University Hospital Jena , Jena , Germany.,b Institute for Biology II , Division of Functional Epigenetics in the Animal Model, RWTH Aachen University , Aachen , Germany
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Pensold D, Symmank J, Hahn A, Lingner T, Salinas-Riester G, Downie BR, Ludewig F, Rotzsch A, Haag N, Andreas N, Schubert K, Hübner CA, Pieler T, Zimmer G. The DNA Methyltransferase 1 (DNMT1) Controls the Shape and Dynamics of Migrating POA-Derived Interneurons Fated for the Murine Cerebral Cortex. Cereb Cortex 2018; 27:5696-5714. [PMID: 29117290 DOI: 10.1093/cercor/bhw341] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Indexed: 01/24/2023] Open
Abstract
The proliferative niches in the subpallium generate a rich cellular variety fated for diverse telencephalic regions. The embryonic preoptic area (POA) represents one of these domains giving rise to the pool of cortical GABAergic interneurons and glial cells, in addition to striatal and residual POA cells. The migration from sites of origin within the subpallium to the distant targets like the cerebral cortex, accomplished by the adoption and maintenance of a particular migratory morphology, is a critical step during interneuron development. To identify factors orchestrating this process, we performed single-cell transcriptome analysis and detected Dnmt1 expression in murine migratory GABAergic POA-derived cells. Deletion of Dnmt1 in postmitotic immature cells of the POA caused defective migration and severely diminished adult cortical interneuron numbers. We found that DNA methyltransferase 1 (DNMT1) preserves the migratory shape in part through negative regulation of Pak6, which stimulates neuritogenesis at postmigratory stages. Our data underline the importance of DNMT1 for the migration of POA-derived cells including cortical interneurons.
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Affiliation(s)
- Daniel Pensold
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany
| | - Judit Symmank
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany
| | - Anne Hahn
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany
| | - Thomas Lingner
- Transcriptome and Genome Analysis Laboratory (TAL), Department of Developmental Biochemistry, University of Goettingen, 37077 Goettingen, Germany
| | - Gabriela Salinas-Riester
- Transcriptome and Genome Analysis Laboratory (TAL), Department of Developmental Biochemistry, University of Goettingen, 37077 Goettingen, Germany
| | - Bryan R Downie
- Transcriptome and Genome Analysis Laboratory (TAL), Department of Developmental Biochemistry, University of Goettingen, 37077 Goettingen, Germany
| | - Fabian Ludewig
- Transcriptome and Genome Analysis Laboratory (TAL), Department of Developmental Biochemistry, University of Goettingen, 37077 Goettingen, Germany
| | - Anne Rotzsch
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany
| | - Natja Haag
- Institute of Biochemistry I, University Hospital Jena, 07743 Jena, Germany.,Institute of Human Genetics, University Hospital RWTH Aachen, Aachen, Germany
| | - Nico Andreas
- FACS Core Facility, Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Katrin Schubert
- FACS Core Facility, Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Christian A Hübner
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany
| | - Tomas Pieler
- Centre for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Department of Developmental Biochemistry, University of Goettingen, 37077 Goettingen, Germany
| | - Geraldine Zimmer
- Institute of Human Genetics, University Hospital Jena, 07743 Jena, Germany
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48
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Lardenoije R, Pishva E, Lunnon K, van den Hove DL. Neuroepigenetics of Aging and Age-Related Neurodegenerative Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 158:49-82. [PMID: 30072060 DOI: 10.1016/bs.pmbts.2018.04.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Neurodegenerative diseases are complex, progressive disorders and affect millions of people worldwide, contributing significantly to the global burden of disease. In recent years, research has begun to investigate epigenetic mechanisms for a potential role in disease etiology. In this chapter, we describe the current state of play for epigenetic research into neurodegenerative disorders including Alzheimer's disease, Parkinson's disease and Huntington's disease. We focus on the recent evidence for a potential role of DNA modifications, histone modifications and non-coding RNA in the etiology of these disorders. Finally, we discuss how new technological and bioinformatics advances in the field of epigenetics could further progress our understanding about the underlying mechanisms of neurodegenerative diseases.
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Affiliation(s)
- Roy Lardenoije
- Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Ehsan Pishva
- Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands; University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Katie Lunnon
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Daniel L van den Hove
- Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands.
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Np95/Uhrf1 regulates tumor suppressor gene expression of neural stem/precursor cells, contributing to neurogenesis in the adult mouse brain. Neurosci Res 2018; 143:31-43. [PMID: 29859850 DOI: 10.1016/j.neures.2018.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 01/30/2023]
Abstract
Adult neurogenesis is a process of generating new neurons from neural stem/precursor cells (NS/PCs) in restricted adult brain regions throughout life. It is now generally known that adult neurogenesis in the hippocampal dentate gyrus (DG) and subventricular zone participates in various higher brain functions, such as learning and memory formation, olfactory discrimination and repair after brain injury. However, the mechanisms underlying adult neurogenesis remain to be fully understood. Here, we show that Nuclear protein 95 KDa (Np95, also known as UHRF1 or ICBP90), which is an essential protein for maintaining DNA methylation during cell division, is involved in multiple processes of adult neurogenesis. Specific ablation of Np95 in adult NS/PCs (aNS/PCs) led to a decrease in their proliferation and an impairment of neuronal differentiation and to suppression of neuronal maturation associated with the impairment of dendritic formation in the hippocampal DG. We also found that deficiency of Np95 in NS/PCs increased the expression of tumor suppressor genes p16 and p53, and confirmed that expression of these genes in NS/PCs recapitulates the phenotype of Np95-deficient NS/PCs. Taken together, our findings suggest that Np95 plays an essential role in proliferation and differentiation of aNS/PCs through the regulation of tumor suppressor gene expression in adult neurogenesis.
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50
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Targeting G-quadruplex DNA as cognitive function therapy for ATR-X syndrome. Nat Med 2018; 24:802-813. [DOI: 10.1038/s41591-018-0018-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 02/12/2018] [Indexed: 01/08/2023]
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