1
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Luo S, Wu F, Fang Q, Hu Y, Zhang H, Yuan S, Yang C, Shi Y, Luo Y. Antidepressant effect of teriflunomide via oligodendrocyte protection in a mouse model. Heliyon 2024; 10:e29481. [PMID: 38655332 PMCID: PMC11036017 DOI: 10.1016/j.heliyon.2024.e29481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
Addressing the treatment of depression is crucial; nevertheless, the etiology and pathogenesis remain unelucidated. Therefore, this study investigated the effects of teriflunomide (TF) on corticosterone (CORT)-induced depression-like behaviors in mice. Notably, TF administration resulted in a substantial amelioration of anxiety and depression-like behaviors observed in CORT-treated mice. This was evidenced by behavioral assessments conducted via the sucrose preference test (SPT), open-field test (OFT), novelty-suppressed feeding test (NSFT), forced swimming test (FST), and tail suspension test (TST). The administration of CORT inflicts damage upon oligodendrocytes and neurons within the hippocampus. Our findings indicate that TF offers significant protective effects on oligodendrocytes, mitigating apoptosis both invivo and invitro. Additionally, TF was found to counteract the CORT-induced neuronal loss and synaptic damage, as demonstrated by an increase in Nissl-positive cells across hippocampal regions CA1, CA3, and the dentate gyrus (DG) alongside elevated levels of synapse-related proteins including PSD-95 and synaptophysin. Additionally, TF treatment facilitated a reduction in the levels of apoptosis-related proteins while simultaneously augmenting the levels of Bcl2. Our findings indicate that TF administration effectively mitigates CORT-induced depression-like behaviors and reverses damage to oligodendrocytes and neurons in the hippocampus, suggesting TF as a promising candidate for depression.
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Affiliation(s)
- Shuting Luo
- School of Medicine, Hunan Normal University, Changsha, 410081, China
| | - Feilong Wu
- School of Medicine, Hunan Normal University, Changsha, 410081, China
| | - Qian Fang
- School of Medicine, Hunan Normal University, Changsha, 410081, China
| | - Yue Hu
- School of Medicine, Hunan Normal University, Changsha, 410081, China
| | - Huihui Zhang
- School of Medicine, Hunan Normal University, Changsha, 410081, China
| | - Shishan Yuan
- School of Medicine, Hunan Normal University, Changsha, 410081, China
| | - Chang Yang
- School of Medicine, Hunan Normal University, Changsha, 410081, China
| | - Yan Shi
- School of Medicine, Hunan Normal University, Changsha, 410081, China
| | - Yixiao Luo
- School of Medicine, Hunan Normal University, Changsha, 410081, China
- Hunan Province People's Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha, China
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2
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Yang K, Wei R, Liu Q, Tao Y, Wu Z, Yang L, Wang QH, Wang H, Pan Z. Specific inhibition of TET1 in the spinal dorsal horn alleviates inflammatory pain in mice by regulating synaptic plasticity. Neuropharmacology 2024; 244:109799. [PMID: 38008374 DOI: 10.1016/j.neuropharm.2023.109799] [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: 09/04/2023] [Revised: 10/19/2023] [Accepted: 11/20/2023] [Indexed: 11/28/2023]
Abstract
DNA demethylation mediated by ten-eleven translocation 1 (TET1) is a critical epigenetic mechanism in which gene expression is regulated via catalysis of 5-methylcytosine to 5-hydroxymethylcytosine. Previously, we demonstrated that TET1 is associated with the genesis of chronic inflammatory pain. However, how TET1 participates in enhanced nociceptive responses in chronic pain remains poorly understood. Here, we report that conditional knockout of Tet1 in dorsal horn neurons via intrathecal injection of rAAV-hSyn-Cre in Tet1fl/fl mice not only reversed the inflammation-induced upregulation of synapse-associated proteins (post-synaptic density protein 95 (PSD95) and synaptophysin (SYP)) in the dorsal horn but also ameliorated abnormalities in dendritic spine morphology and alleviated pain hypersensitivities. Pharmacological blockade of TET1 by intrathecal injection of a TET1-specific inhibitor-Bobcat 339-produced similar results, as did knockdown of Tet1 by intrathecal injection of siRNA. Thus, our data strongly suggest that increased TET1 expression during inflammatory pain upregulates the expression of multiple synapse-associated proteins and dysregulates synaptic morphology in dorsal horn neurons, suggesting that Tet1 may be a potential target for analgesic strategies.
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Affiliation(s)
- Kehui Yang
- Jiangsu Province Key Laboratory of Anesthesiology, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, China; NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, 221004, China
| | - Runa Wei
- Jiangsu Province Key Laboratory of Anesthesiology, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, China; NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, 221004, China
| | - Qiaoqiao Liu
- Jiangsu Province Key Laboratory of Anesthesiology, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, China; NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, 221004, China
| | - Yang Tao
- Jiangsu Province Key Laboratory of Anesthesiology, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, China; NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, 221004, China
| | - Zixuan Wu
- Jiangsu Province Key Laboratory of Anesthesiology, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, China; NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, 221004, China
| | - Li Yang
- Jiangsu Province Key Laboratory of Anesthesiology, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, China; NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, 221004, China
| | - Qi-Hui Wang
- Jiangsu Province Key Laboratory of Anesthesiology, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, China; NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, 221004, China
| | - Hongjun Wang
- Jiangsu Province Key Laboratory of Anesthesiology, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, China; NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, 221004, China.
| | - Zhiqiang Pan
- Jiangsu Province Key Laboratory of Anesthesiology, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, China; NMPA Key Laboratory for Research and Evaluation of Narcotic and Psychotropic Drugs, Xuzhou Medical University, Xuzhou, 221004, China.
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3
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Zhong S, Wang M, Huang L, Chen Y, Ge Y, Zhang J, Shi Y, Dong H, Zhou X, Wang B, Lu T, Jing X, Lu Y, Zhang J, Wang X, Wu Q. Single-cell epigenomics and spatiotemporal transcriptomics reveal human cerebellar development. Nat Commun 2023; 14:7613. [PMID: 37993461 PMCID: PMC10665552 DOI: 10.1038/s41467-023-43568-6] [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: 06/07/2023] [Accepted: 11/10/2023] [Indexed: 11/24/2023] Open
Abstract
Human cerebellar development is orchestrated by molecular regulatory networks to achieve cytoarchitecture and coordinate motor and cognitive functions. Here, we combined single-cell transcriptomics, spatial transcriptomics and single cell chromatin accessibility states to systematically depict an integrative spatiotemporal landscape of human fetal cerebellar development. We revealed that combinations of transcription factors and cis-regulatory elements (CREs) play roles in governing progenitor differentiation and cell fate determination along trajectories in a hierarchical manner, providing a gene expression regulatory map of cell fate and spatial information for these cells. We also illustrated that granule cells located in different regions of the cerebellar cortex showed distinct molecular signatures regulated by different signals during development. Finally, we mapped single-nucleotide polymorphisms (SNPs) of disorders related to cerebellar dysfunction and discovered that several disorder-associated genes showed spatiotemporal and cell type-specific expression patterns only in humans, indicating the cellular basis and possible mechanisms of the pathogenesis of neuropsychiatric disorders.
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Affiliation(s)
- Suijuan Zhong
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China.
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China.
- Changping Laboratory, Beijing, 102206, China.
| | - Mengdi Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Luwei Huang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Youqiao Chen
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Yuxin Ge
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Jiyao Zhang
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Yingchao Shi
- Guangdong Institute of Intelligence Science and Technology, Guangdong, 519031, China
| | - Hao Dong
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Zhou
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
- Changping Laboratory, Beijing, 102206, China
| | - Bosong Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Tian Lu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxi Jing
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Yufeng Lu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Junjing Zhang
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
| | - Xiaoqun Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
- Changping Laboratory, Beijing, 102206, China
| | - Qian Wu
- State Key Laboratory of Cognitive Neuroscience and Learning, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, 100875, China.
- IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China.
- Changping Laboratory, Beijing, 102206, China.
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4
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Zhang X, Zhang Y, Wang C, Wang X. TET (Ten-eleven translocation) family proteins: structure, biological functions and applications. Signal Transduct Target Ther 2023; 8:297. [PMID: 37563110 PMCID: PMC10415333 DOI: 10.1038/s41392-023-01537-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 08/12/2023] Open
Abstract
Ten-eleven translocation (TET) family proteins (TETs), specifically, TET1, TET2 and TET3, can modify DNA by oxidizing 5-methylcytosine (5mC) iteratively to yield 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxycytosine (5caC), and then two of these intermediates (5fC and 5caC) can be excised and return to unmethylated cytosines by thymine-DNA glycosylase (TDG)-mediated base excision repair. Because DNA methylation and demethylation play an important role in numerous biological processes, including zygote formation, embryogenesis, spatial learning and immune homeostasis, the regulation of TETs functions is complicated, and dysregulation of their functions is implicated in many diseases such as myeloid malignancies. In addition, recent studies have demonstrated that TET2 is able to catalyze the hydroxymethylation of RNA to perform post-transcriptional regulation. Notably, catalytic-independent functions of TETs in certain biological contexts have been identified, further highlighting their multifunctional roles. Interestingly, by reactivating the expression of selected target genes, accumulated evidences support the potential therapeutic use of TETs-based DNA methylation editing tools in disorders associated with epigenetic silencing. In this review, we summarize recent key findings in TETs functions, activity regulators at various levels, technological advances in the detection of 5hmC, the main TETs oxidative product, and TETs emerging applications in epigenetic editing. Furthermore, we discuss existing challenges and future directions in this field.
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Affiliation(s)
- Xinchao Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yue Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chaofu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Xu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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5
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Mätlik K, Govek EE, Paul MR, Allis CD, Hatten ME. Histone bivalency regulates the timing of cerebellar granule cell development. Genes Dev 2023; 37:570-589. [PMID: 37491148 PMCID: PMC10499015 DOI: 10.1101/gad.350594.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/10/2023] [Indexed: 07/27/2023]
Abstract
Developing neurons undergo a progression of morphological and gene expression changes as they transition from neuronal progenitors to mature neurons. Here we used RNA-seq and H3K4me3 and H3K27me3 ChIP-seq to analyze how chromatin modifications control gene expression in a specific type of CNS neuron: the mouse cerebellar granule cell (GC). We found that in proliferating GC progenitors (GCPs), H3K4me3/H3K27me3 bivalency is common at neuronal genes and undergoes dynamic changes that correlate with gene expression during migration and circuit formation. Expressing a fluorescent sensor for bivalent domains revealed subnuclear bivalent foci in proliferating GCPs. Inhibiting H3K27 methyltransferases EZH1 and EZH2 in vitro and in organotypic cerebellar slices dramatically altered the expression of bivalent genes, induced the down-regulation of migration-related genes and up-regulation of synaptic genes, inhibited glial-guided migration, and accelerated terminal differentiation. Thus, histone bivalency is required to regulate the timing of the progression from progenitor cells to mature neurons.
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Affiliation(s)
- Kärt Mätlik
- Laboratory of Developmental Neurobiology, Rockefeller University, New York, New York 10065, USA
| | - Eve-Ellen Govek
- Laboratory of Developmental Neurobiology, Rockefeller University, New York, New York 10065, USA
| | - Matthew R Paul
- Bioinformatics Resource Center, Rockefeller University, New York, New York 10065, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, Rockefeller University, New York, New York 10065, USA
| | - Mary E Hatten
- Laboratory of Developmental Neurobiology, Rockefeller University, New York, New York 10065, USA;
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6
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Mätlik K, Govek EE, Paul MR, Allis CD, Hatten ME. Histone bivalency regulates the timing of cerebellar granule cell development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.02.526881. [PMID: 36778390 PMCID: PMC9915618 DOI: 10.1101/2023.02.02.526881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Developing neurons undergo a progression of morphological and gene expression changes as they transition from neuronal progenitors to mature, multipolar neurons. Here we use RNA-seq and H3K4me3 and H3K27me3 ChIP-seq to analyze how chromatin modifications control gene expression in a specific type of CNS neuron, the mouse cerebellar granule cell (GC). We find that in proliferating GC progenitors (GCPs), H3K4me3/H3K27me3 bivalency is common at neuronal genes and undergoes dynamic changes that correlate with gene expression during migration and circuit formation. Expressing a fluorescent sensor for bivalent H3K4me3 and H3K27me3 domains revealed subnuclear bivalent foci in proliferating GCPs. Inhibiting H3K27 methyltransferases EZH1 and EZH2 in vitro and in organotypic cerebellar slices dramatically altered the expression of bivalent genes and induced the downregulation of migration-related genes and upregulation of synaptic genes, inhibited glial-guided migration, and accelerated terminal differentiation. Thus, histone bivalency is required to regulate the timing of the progression from progenitor cells to mature neurons.
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Affiliation(s)
- Kärt Mätlik
- Laboratory of Developmental Neurobiology, Rockefeller University, 10065, New York, NY, USA
| | - Eve-Ellen Govek
- Laboratory of Developmental Neurobiology, Rockefeller University, 10065, New York, NY, USA
| | - Matthew R. Paul
- Bioinformatics Resource Center, Rockefeller University, 10065, New York, NY, USA
| | - C. David Allis
- Laboratory of Chromatin Biology and Epigenetics, Rockefeller University, 10065, New York, NY, USA
| | - Mary E. Hatten
- Laboratory of Developmental Neurobiology, Rockefeller University, 10065, New York, NY, USA
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7
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Wu PR, Chiang SY, Midence R, Kao WC, Lai CL, Cheng IC, Chou SJ, Chen CC, Huang CY, Chen RH. Wdr4 promotes cerebellar development and locomotion through Arhgap17-mediated Rac1 activation. Cell Death Dis 2023; 14:52. [PMID: 36681682 PMCID: PMC9867761 DOI: 10.1038/s41419-022-05442-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 01/22/2023]
Abstract
Patients with mutations of WDR4, a substrate adaptor of the CUL4 E3 ligase complex, develop cerebellar atrophy and gait phenotypes. However, the underlying mechanisms remain unexplored. Here, we identify a crucial role of Wdr4 in cerebellar development. Wdr4 deficiency in granule neuron progenitors (GNPs) not only reduces foliation and the sizes of external and internal granular layers but also compromises Purkinje neuron organization and the size of the molecular layer, leading to locomotion defects. Mechanistically, Wdr4 supports the proliferation of GNPs by preventing their cell cycle exit. This effect is mediated by Wdr4-induced ubiquitination and degradation of Arhgap17, thereby activating Rac1 to facilitate cell cycle progression. Disease-associated Wdr4 variants, however, cannot provide GNP cell cycle maintenance. Our study identifies Wdr4 as a previously unappreciated participant in cerebellar development and locomotion, providing potential insights into treatment strategies for diseases with WDR4 mutations, such as primordial dwarfism and Galloway-Mowat syndrome.
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Affiliation(s)
- Pei-Rung Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.
- Cardiovascular and Mitochondrial Related Disease Research Center, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, 970, Taiwan.
| | - Shang-Yin Chiang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Robert Midence
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Wen-Chao Kao
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Chun-Lun Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - I-Cheng Cheng
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Shen-Ju Chou
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Chih-Cheng Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
| | - Chih-Yang Huang
- Cardiovascular and Mitochondrial Related Disease Research Center, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, 970, Taiwan
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, 404, Taiwan
| | - Ruey-Hwa Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.
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Dynamic Regulation of DNA Methylation and Brain Functions. BIOLOGY 2023; 12:biology12020152. [PMID: 36829430 PMCID: PMC9952911 DOI: 10.3390/biology12020152] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
DNA cytosine methylation is a principal epigenetic mechanism underlying transcription during development and aging. Growing evidence suggests that DNA methylation plays a critical role in brain function, including neurogenesis, neuronal differentiation, synaptogenesis, learning, and memory. However, the mechanisms underlying aberrant DNA methylation in neurodegenerative diseases remain unclear. In this review, we provide an overview of the contribution of 5-methycytosine (5mC) and 5-hydroxylcytosine (5hmC) to brain development and aging, with a focus on the roles of dynamic 5mC and 5hmC changes in the pathogenesis of neurodegenerative diseases, particularly Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD). Identification of aberrant DNA methylation sites could provide potential candidates for epigenetic-based diagnostic and therapeutic strategies for neurodegenerative diseases.
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Jiang D, Li T, Guo C, Tang TS, Liu H. Small molecule modulators of chromatin remodeling: from neurodevelopment to neurodegeneration. Cell Biosci 2023; 13:10. [PMID: 36647159 PMCID: PMC9841685 DOI: 10.1186/s13578-023-00953-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
The dynamic changes in chromatin conformation alter the organization and structure of the genome and further regulate gene transcription. Basically, the chromatin structure is controlled by reversible, enzyme-catalyzed covalent modifications to chromatin components and by noncovalent ATP-dependent modifications via chromatin remodeling complexes, including switch/sucrose nonfermentable (SWI/SNF), inositol-requiring 80 (INO80), imitation switch (ISWI) and chromodomain-helicase DNA-binding protein (CHD) complexes. Recent studies have shown that chromatin remodeling is essential in different stages of postnatal and adult neurogenesis. Chromatin deregulation, which leads to defects in epigenetic gene regulation and further pathological gene expression programs, often causes a wide range of pathologies. This review first gives an overview of the regulatory mechanisms of chromatin remodeling. We then focus mainly on discussing the physiological functions of chromatin remodeling, particularly histone and DNA modifications and the four classes of ATP-dependent chromatin-remodeling enzymes, in the central and peripheral nervous systems under healthy and pathological conditions, that is, in neurodegenerative disorders. Finally, we provide an update on the development of potent and selective small molecule modulators targeting various chromatin-modifying proteins commonly associated with neurodegenerative diseases and their potential clinical applications.
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Affiliation(s)
- Dongfang Jiang
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Tingting Li
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Caixia Guo
- grid.9227.e0000000119573309Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Tie-Shan Tang
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Hongmei Liu
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China
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Got milk? Maternal immune activation during the mid-lactational period affects nutritional milk quality and adolescent offspring sensory processing in male and female rats. Mol Psychiatry 2022; 27:4829-4842. [PMID: 36056174 PMCID: PMC9771965 DOI: 10.1038/s41380-022-01744-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/08/2022] [Accepted: 08/11/2022] [Indexed: 01/14/2023]
Abstract
Previous studies have underscored the importance of breastfeeding and parental care on offspring development and behavior. However, their contribution as dynamic variables in animal models of early life stress are often overlooked. In the present study, we investigated how lipopolysaccharide (LPS)-induced maternal immune activation (MIA) on postnatal day (P)10 affects maternal care, milk, and offspring development. MIA was associated with elevated milk corticosterone concentrations on P10, which recovered by P11. In contrast, both milk triglyceride and percent creamatocrit values demonstrated a prolonged decrease following inflammatory challenge. Adolescent MIA offspring were heavier, which is often suggestive of poor early life nutrition. While MIA did not decrease maternal care quality, there was a significant compensatory increase in maternal licking and grooming the day following inflammatory challenge. However, this did not protect against disrupted neonatal huddling or later-life alterations in sensorimotor gating, conditioned fear, mechanical allodynia, or reductions in hippocampal parvalbumin expression in MIA offspring. MIA-associated changes in brain and behavior were likely driven by differences in milk nutritional values and not by direct exposure to LPS or inflammatory molecules as neither LPS binding protein nor interleukin-6 milk levels differed between groups. These findings reflected comparable microbiome and transcriptomic patterns at the genome-wide level. Animal models of early life stress can impact both parents and their offspring. One mechanism that can mediate the effects of such stressors is changes to maternal lactation quality which our data show can confer multifaceted and compounding effects on offspring physiology and behavior.
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11
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Lodato MA, Ziegenfuss JS. The two faces of DNA oxidation in genomic and functional mosaicism during aging in human neurons. FRONTIERS IN AGING 2022; 3:991460. [PMID: 36313183 PMCID: PMC9596766 DOI: 10.3389/fragi.2022.991460] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/26/2022] [Indexed: 11/29/2022]
Abstract
Maintaining genomic integrity in post-mitotic neurons in the human brain is paramount because these cells must survive for an individual's entire lifespan. Due to life-long synaptic plasticity and electrochemical transmission between cells, the brain engages in an exceptionally high level of mitochondrial metabolic activity. This activity results in the generation of reactive oxygen species with 8-oxo-7,8-dihydroguanine (8-oxoG) being one of the most prevalent oxidation products in the cell. 8-oxoG is important for the maintenance and transfer of genetic information into proper gene expression: a low basal level of 8-oxoG plays an important role in epigenetic modulation of neurodevelopment and synaptic plasticity, while a dysregulated increase in 8-oxoG damages the genome leading to somatic mutations and transcription errors. The slow yet persistent accumulation of DNA damage in the background of increasing cellular 8-oxoG is associated with normal aging as well as neurological disorders such as Alzheimer's disease and Parkinson's disease. This review explores the current understanding of how 8-oxoG plays a role in brain function and genomic instability, highlighting new methods being used to advance pathological hallmarks that differentiate normal healthy aging and neurodegenerative disease.
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Li Y, Qu C, Song H, Li T, Zheng J, Wu L, Yan N, Xu L, Qu C, Zhang J. Enriched environment priors to TET1 hippocampal administration for regulating psychiatric behaviors via glial reactivity in chronic cerebral hypoperfusion models. J Affect Disord 2022; 310:198-212. [PMID: 35461822 DOI: 10.1016/j.jad.2022.04.087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/08/2022] [Accepted: 04/13/2022] [Indexed: 01/29/2023]
Abstract
BACKGROUND Chronic cerebral hypoperfusion (CCH) has been gradually regarded as a common etiologic mechanism for cognitive and psychiatric disturbances. Ten-eleven translocation methylcytosine dioxygenase 1 (TET1) played an important role in adult hippocampal neurogenesis (AHN), neuronal circuits formation, cognition and psychiatric disorders. Enriched environment (EE) showed a beneficial effect on cognition and depression via effectively regulating AHN and glial reactivity. This study aimed to assess which strategy was feasible to improve cognition and psychiatric disturbances by comparing the TET1 hippocampal microinjection and EE in CCH models and to investigate the possible mechanisms. METHOD CCH rats were established via permanent bilateral common carotid artery occlusion (2-VO). Rats were stereotaxically injected with the human catalytic domain of TET1 (hTET1) to overexpress the hTET1 in the hippocampus 10 days before 2-VO. 3 days after 2-VO, rats were subjected to standard environment or EE with free access to food and water. Behavioral tests were used to appraise depression and cognition before sacrifice. Epigenetic molecules, adult neurogenesis, synaptic proteins expression, and glial activation were analyzed using immunofluorescent staining, qRT-PCR and western blot. RESULTS In the present study, we found both EE and genetical treatment with overexpressing hTET1 were sufficient for stimulating AHN. However, promoting ANH could not deal with the cognitive dysfunction and depressive-like behaviors in CCH rats. Notably, a healthy local brain environment with elevated BDNF and astrocytes was conducive to improving cognitive dysfunction. Meanwhile, astrocytes were involved in the cognitive regulating process of neurons, presynaptic function and microglia. In general, we held that depressive disturbances were determined by BDNF levels, neuronal and presynaptic function, as well as glial activation containing astrocytes and microglia. To further support this point, we investigated severe depressive symptoms that were strongly correlated with the activation of astroglia and microglia. Importantly, causal mediation analysis showed significant mediation by the presence of reactive glial cells in the relation between neural plasticity and depressive symptoms. Finally, we showed EE performed better than hTET1 treatment for cognitive deficits and depression. EE with less glial reactivity was much more resistant to depression, while hTET1 with more glial activation was more vulnerable to depressive disorders. CONCLUSIONS EE was likely to be superior to TET1 hippocampal administration for cognition and psychiatric behaviors in CCH rats. Furthermore, a healthy local brain environment with elevated BDNF and astrocytes was conducive to improving cognitive dysfunction. More glial activation, and more vulnerable to depressive disorders. These results were important for our understanding of disease mechanisms and provided valuable tools for the overall management of CCH patients.
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Affiliation(s)
- Yaqing Li
- Department of Neurology, Zhongnan Hospital, Wuhan University, No.169, Donghu Road, Wuhan 430071, Hubei, China
| | - Chujie Qu
- Department of Neurology, Zhongnan Hospital, Wuhan University, No.169, Donghu Road, Wuhan 430071, Hubei, China
| | - Hao Song
- Department of Neurology, Zhongnan Hospital, Wuhan University, No.169, Donghu Road, Wuhan 430071, Hubei, China
| | - Tian Li
- Department of Neurology, Zhongnan Hospital, Wuhan University, No.169, Donghu Road, Wuhan 430071, Hubei, China
| | - Jiaxin Zheng
- Department of Neurology, Zhongnan Hospital, Wuhan University, No.169, Donghu Road, Wuhan 430071, Hubei, China
| | - Liyang Wu
- Department of Neurology, Zhongnan Hospital, Wuhan University, No.169, Donghu Road, Wuhan 430071, Hubei, China
| | - Nao Yan
- Department of Neurology, Zhongnan Hospital, Wuhan University, No.169, Donghu Road, Wuhan 430071, Hubei, China
| | - Linling Xu
- Department of Neurology, Zhongnan Hospital, Wuhan University, No.169, Donghu Road, Wuhan 430071, Hubei, China
| | - Changhua Qu
- Department of Neurology, Zhongnan Hospital, Wuhan University, No.169, Donghu Road, Wuhan 430071, Hubei, China
| | - Junjian Zhang
- Department of Neurology, Zhongnan Hospital, Wuhan University, No.169, Donghu Road, Wuhan 430071, Hubei, China.
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13
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Milking It for All It's Worth: The Effects of Environmental Enrichment on Maternal Nurturance, Lactation Quality, and Offspring Social Behavior. eNeuro 2022; 9:ENEURO.0148-22.2022. [PMID: 35995560 PMCID: PMC9417599 DOI: 10.1523/eneuro.0148-22.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/10/2022] [Accepted: 07/15/2022] [Indexed: 12/17/2022] Open
Abstract
Breastfeeding confers robust benefits to offspring development in terms of growth, immunity, and neurophysiology. Similarly, improving environmental complexity, i.e., environmental enrichment (EE), contributes developmental advantages to both humans and laboratory animal models. However, the impact of environmental context on maternal care and milk quality has not been thoroughly evaluated, nor are the biological underpinnings of EE on offspring development understood. Here, Sprague Dawley rats were housed and bred in either EE or standard-housed (SD) conditions. EE dams gave birth to a larger number of pups, and litters were standardized and cross-fostered across groups on postnatal day (P)1. Maternal milk samples were then collected on P1 (transitional milk phase) and P10 (mature milk phase) for analysis. While EE dams spent less time nursing, postnatal enrichment exposure was associated with heavier offspring bodyweights. Milk from EE mothers had increased triglyceride levels, a greater microbiome diversity, and a significantly higher abundance of bacterial families related to bodyweight and energy metabolism. These differences reflected comparable transcriptomic changes at the genome-wide level. In addition to changes in lactational quality, we observed elevated levels of cannabinoid receptor 1 in the hypothalamus of EE dams, and sex-dependent and time-dependent effects of EE on offspring social behavior. Together, these results underscore the multidimensional impact of the combined neonatal and maternal environments on offspring development and maternal health. Moreover, they highlight potential deficiencies in the use of "gold standard" laboratory housing in the attempt to design translationally relevant animal models in biomedical research.
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14
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Fan BF, Hao B, Dai YD, Xue L, Shi YW, Liu L, Xuan SM, Yang N, Wang XG, Zhao H. Deficiency of Tet3 in nucleus accumbens enhances fear generalization and anxiety-like behaviors in mice. Brain Pathol 2022; 32:e13080. [PMID: 35612904 PMCID: PMC9616092 DOI: 10.1111/bpa.13080] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/02/2022] [Indexed: 11/30/2022] Open
Abstract
Stress‐induced neuroepigenetic programming gains growing more and more interest in the studies of the etiology of posttraumatic stress disorder (PTSD). However, seldom attention is focused on DNA demethylation in fear memory generalization, which is the core characteristic of PTSD. Here, we show that ten‐eleven translocation protein 3 (TET3), the most abundant DNA demethylation enzyme of the TET family in neurons, senses environmental stress and bridges neuroplasticity with behavioral adaptation during fear generalization. Foot shock strength dependently induces fear generalization and TET3 expression in nucleus accumbens (NAc) in mice. Inhibition of DNA demethylation by infusing demethyltransferase inhibitors or AAV‐Tet3‐shRNA virus in NAc enhances the fear generalization and anxiety‐like behavior. Furthermore, TET3 knockdown impairs the dendritic spine density, PSD length, and thickness of neurons, decreases DNA hydroxymethylation (5hmC), reduces the expression of synaptic plasticity‐related genes including Homer1, Cdkn1a, Cdh8, Vamp8, Reln, Bdnf, while surprisingly increases immune‐related genes Stat1, B2m, H2‐Q7, H2‐M2, C3, Cd68 shown by RNA‐seq. Notably, knockdown of TET3 in NAc activates microglia and CD39‐P2Y12R signaling pathway, and inhibition of CD39 reverses the effects of TET3 knockdown on the fear memory generalization and anxiety. Overexpression of TET3 by Crispr‐dSaCas9 virus delivery to activate endogenous Tet3 in NAc increases dendritic spine density of neurons in NAc and reverses fear memory generalization and anxiety‐like behavior in mice. These results suggest that TET3 modulates fear generalization and anxiety via regulating synaptic plasticity and CD39 signaling pathway.
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Affiliation(s)
- Bu-Fang Fan
- Faculty of Forensic Medicine, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Bo Hao
- Faculty of Forensic Medicine, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yun-Da Dai
- Faculty of Forensic Medicine, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Li Xue
- Department of Psychology, School of Public Medicine, Southern Medical University, Guangzhou, China
| | - Yan-Wei Shi
- Faculty of Forensic Medicine, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lu Liu
- Faculty of Forensic Medicine, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shou-Min Xuan
- Faculty of Forensic Medicine, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ning Yang
- Faculty of Forensic Medicine, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiao-Guang Wang
- Faculty of Forensic Medicine, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hu Zhao
- Faculty of Forensic Medicine, Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.,Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
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15
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Smit MJ, Martini TEI, Armandari I, Bočkaj I, Zomerman WW, de Camargo Magalhães ES, Siragna Z, Meeuwsen TGJ, Scherpen FJG, Schoots MH, Ritsema M, den Dunnen WFA, Hoving EW, Paridaen JTML, de Haan G, Guryev V, Bruggeman SWM. The developmental stage of the medulloblastoma cell-of-origin restricts Hedgehog pathway usage and drug sensitivity. J Cell Sci 2022; 135:275628. [PMID: 35535520 PMCID: PMC9234672 DOI: 10.1242/jcs.258608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/03/2022] [Indexed: 11/20/2022] Open
Abstract
Sonic hedgehog (SHH) medulloblastoma originates from the cerebellar granule neuron progenitor (CGNP) lineage, which depends on Hedgehog signaling for its perinatal expansion. Whereas SHH tumors exhibit overall deregulation of this pathway, they also show patient age-specific aberrations. To investigate whether the developmental stage of the CGNP can account for these age-specific lesions, we analyzed developing murine CGNP transcriptomes and observed highly dynamic gene expression as a function of age. Cross-species comparison with human SHH medulloblastoma showed partial maintenance of these expression patterns, and highlighted low primary cilium expression as hallmark of infant medulloblastoma and early embryonic CGNPs. This coincided with reduced responsiveness to upstream SHH pathway component Smoothened, whereas sensitivity to downstream components SUFU and GLI family proteins was retained. Together, these findings can explain the preference for SUFU mutations in infant medulloblastoma and suggest that drugs targeting the downstream SHH pathway will be most appropriate for infant patients. Summary: There is a relationship between the age of the medulloblastoma patient and the developmental age of the tumor cell-of-origin, and this influences the SHH pathway signaling route used by the tumor.
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Affiliation(s)
- Marlinde J Smit
- European Research Institute for the Biology of Ageing/ERIBA, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB, Groningen, the Netherlands
| | - Tosca E I Martini
- European Research Institute for the Biology of Ageing/ERIBA, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB, Groningen, the Netherlands
| | - Inna Armandari
- European Research Institute for the Biology of Ageing/ERIBA, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB, Groningen, the Netherlands
| | - Irena Bočkaj
- European Research Institute for the Biology of Ageing/ERIBA, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB, Groningen, the Netherlands
| | - Walderik W Zomerman
- Department of Pediatrics/Pediatric Oncology and Hematology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB, Groningen, the Netherlands
| | - Eduardo S de Camargo Magalhães
- European Research Institute for the Biology of Ageing/ERIBA, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB, Groningen, the Netherlands.,Glial Cell Biology Laboratory, Biomedical Sciences Institute, Federal University of Rio de Janeiro, Rio de Janeiro, 21949-590, Brazil
| | - Zillah Siragna
- European Research Institute for the Biology of Ageing/ERIBA, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB, Groningen, the Netherlands
| | - Tiny G J Meeuwsen
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB, Groningen, the Netherlands
| | - Frank J G Scherpen
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB, Groningen, the Netherlands
| | - Mirthe H Schoots
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB, Groningen, the Netherlands
| | - Martha Ritsema
- European Research Institute for the Biology of Ageing/ERIBA, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB, Groningen, the Netherlands
| | - Wilfred F A den Dunnen
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB, Groningen, the Netherlands
| | - Eelco W Hoving
- Princess Máxima Center for Pediatric Oncology, Lundlaan 6, 3584 EA Utrecht, the Netherlands
| | - Judith T M L Paridaen
- European Research Institute for the Biology of Ageing/ERIBA, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB, Groningen, the Netherlands
| | - Gerald de Haan
- European Research Institute for the Biology of Ageing/ERIBA, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB, Groningen, the Netherlands.,Present address: Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, 1066CX Amsterdam, the Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing/ERIBA, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB, Groningen, the Netherlands
| | - Sophia W M Bruggeman
- European Research Institute for the Biology of Ageing/ERIBA, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB, Groningen, the Netherlands
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16
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Corticosterone induces discrete epigenetic signatures in the dorsal and ventral hippocampus that depend upon sex and genotype: focus on methylated Nr3c1 gene. Transl Psychiatry 2022; 12:109. [PMID: 35296634 PMCID: PMC8927334 DOI: 10.1038/s41398-022-01864-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/17/2022] [Accepted: 02/24/2022] [Indexed: 02/07/2023] Open
Abstract
The genomic effects of circulating glucocorticoids are particularly relevant in cortico-limbic structures, which express a high concentration of steroid hormone receptors. To date, no studies have investigated genomic differences in hippocampal subregions, namely the dorsal (dHPC) and ventral (vHPC) hippocampus, in preclinical models treated with exogenous glucocorticoids. Chronic oral corticosterone (CORT) in mouse is a pharmacological approach that disrupts the activity of the hypothalamic-pituitary-adrenal axis, increases affective behavior, and induces genomic changes after stress in the HPC of wildtype (WT) mice and mice heterozygous for the gene coding for brain-derived neurotrophic factor Val66Met (hMet), a variant associated with genetic susceptibility to stress. Using RNA-sequencing, we investigated the genomic signatures of oral CORT in the dHPC and vHPC of WT and hMet male and female mice, and examined sex and genotype differences in response to oral CORT. Males under CORT showed lower glycemia and increased anxiety- and depression-like behavior compared to females that showed instead opposite affective behavior in response to CORT. Rank-rank-hypergeometric overlap (RRHO) was used to identify genes from a continuous gradient of significancy that were concordant across groups. RRHO showed that CORT-induced differentially expressed genes (DEGs) in WT mice and hMet mice converged in the dHPC of males and females, while in the vHPC, DEGs converged in males and diverged in females. The vHPC showed a higher number of DEGs compared to the dHPC and exhibited sex differences related to glucocorticoid receptor (GR)-binding genes and epigenetic modifiers. Methyl-DNA-immunoprecipitation in the vHPC revealed differential methylation of the exons 1C and 1F of the GR gene (Nr3c1) in hMet females. Together, we report behavioral and endocrinological sex differences in response to CORT, as well as epigenetic signatures that i) differ in the dHPC and vHPC,ii) are distinct in males and females, and iii) implicate differential methylation of Nr3c1 selectively in hMet females.
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17
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Stoyanova E, Riad M, Rao A, Heintz N. 5-Hydroxymethylcytosine-mediated active demethylation is required for mammalian neuronal differentiation and function. eLife 2021; 10:66973. [PMID: 34919053 PMCID: PMC8683082 DOI: 10.7554/elife.66973] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 11/02/2021] [Indexed: 01/02/2023] Open
Abstract
Although high levels of 5-hydroxymethylcytosine (5hmC) accumulate in mammalian neurons, our knowledge of its roles in terminal differentiation or as an intermediate in active DNA demethylation is incomplete. We report high-resolution mapping of DNA methylation and hydroxymethylation, chromatin accessibility, and histone marks in developing postmitotic Purkinje cells (PCs) in Mus musculus. Our data reveal new relationships between PC transcriptional and epigenetic programs, and identify a class of genes that lose both 5-methylcytosine (5mC) and 5hmC during terminal differentiation. Deletion of the 5hmC writers Tet1, Tet2, and Tet3 from postmitotic PCs prevents loss of 5mC and 5hmC in regulatory domains and gene bodies, and hinders transcriptional and epigenetic developmental transitions. Our data demonstrate that Tet-mediated active DNA demethylation occurs in vivo, and that acquisition of the precise molecular properties of adult PCs require continued oxidation of 5mC to 5hmC during the final phases of differentiation. At birth, the mammalian brain contains tens of billions of neurons. Although the number does not increase much as the animal grows, there are many dramatic changes to their size and structure. These changes allow the neurons to communicate with one another, develop into networks, and learn the tasks of the adult brain. One way that these changes occur is by the accumulation of chemical marks on each neuron’s DNA that help dictate which genes switch on, and which turn off. One of the most common ways that DNA can be marked is through the addition of a chemical group called a methyl group to one of the four DNA bases, cytosine. This process is called methylation. When methylation occurs, cytosine becomes 5-methylcytosine, or 5mC for short. In 2009, researchers found another modification present in the DNA in the brain: 5-hydroxymethylcytosine, or 5hmC. This modification appears when a group of proteins called the Tet hydroxylases turn 5mC into 5hmC. Converting 5mC to 5hmC normally helps cells remove marks on their DNA before they divide and expand. This is important because the newly generated cells need to be able to accumulate their own methylation marks to perform their roles properly. However, neurons in the brain accumulate 5hmC after birth, when the cells are no longer dividing, indicating that 5hmC may be required for the neurons to mature. Stoyanova et al. set out to determine whether mouse neurons need 5hmC to get their adult characteristics by tracking the chemical changes that occur in DNA from birth to adulthood. Some of the mice they tested produced 5hmC normally, while others lacked the genes necessary to make the Tet proteins in a specific class of neurons, preventing them from converting 5mC to 5hmC as they differentiate. The results reveal that neurons do not mature properly if 5hmC is not produced continuously following the first week of life. This is because neurons need to have the right genes switched on and off to differentiate correctly, and this only happens when 5hmC accumulates in some genes, while 5hmC and 5mC are removed from others. The data highlight the role of the Tet proteins, which convert 5mC into 5hmC, in preparing the marks for removal and demonstrate that active removal of these marks is essential for neuronal differentiation. Given the role of 5hmC in the development of neurons, it is possible that problems in this system could contribute to brain disorders. Further studies aimed at understanding how cells control 5hmC levels could lead to new ways to improve brain health. Research has also shown that if dividing cells lose the ability to make 5hmC, they can become cancerous. Future work could explain more about how and why this happens.
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Affiliation(s)
- Elitsa Stoyanova
- Laboratory of Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Michael Riad
- Laboratory of Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Anjana Rao
- Sanford Consortium for Regenerative Medicine, La Jolla, United States.,La Jolla Institute for Allergy and Immunology, La Jolla, United States.,Department of Pharmacology, University of California San Diego, La Jolla, United States
| | - Nathaniel Heintz
- Laboratory of Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
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18
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Xu W, Zhang X, Liang F, Cao Y, Li Z, Qu W, Zhang J, Bi Y, Sun C, Zhang J, Sun B, Shu Q, Li X. Tet1 Regulates Astrocyte Development and Cognition of Mice Through Modulating GluA1. Front Cell Dev Biol 2021; 9:644375. [PMID: 34778243 PMCID: PMC8581465 DOI: 10.3389/fcell.2021.644375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
Tet (Ten eleven translocation) family proteins-mediated 5-hydroxymethylcytosine (5hmC) is highly enriched in the neuronal system, and is involved in diverse biological processes and diseases. However, the function of 5hmC in astrocyte remains completely unknown. In the present study, we show that Tet1 deficiency alters astrocyte morphology and impairs neuronal function. Specific deletion of Tet1 in astrocyte impairs learning and memory ability of mice. Using 5hmC high-throughput DNA sequencing and RNA sequencing, we present the distribution of 5hmC among genomic features in astrocyte and show that Tet1 deficiency induces differentially hydroxymethylated regions (DhMRs) and alters gene expression. Mechanistically, we found that Tet1 deficiency leads to the abnormal Ca2+ signaling by regulating the expression of GluA1, which can be rescued by ectopic GluA1. Collectively, our findings suggest that Tet1 plays important function in astrocyte physiology by regulating Ca2+ signaling.
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Affiliation(s)
- Weize Xu
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Clinical Research Center for Child Health, Hangzhou, China
| | - Xicheng Zhang
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Clinical Research Center for Child Health, Hangzhou, China
| | - Feng Liang
- The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yuhang Cao
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Clinical Research Center for Child Health, Hangzhou, China.,The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Wenzheng Qu
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Clinical Research Center for Child Health, Hangzhou, China
| | - Jinyu Zhang
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Clinical Research Center for Child Health, Hangzhou, China.,The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yanhua Bi
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Chongran Sun
- The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jianmin Zhang
- The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Binggui Sun
- Department of Neurobiology and Department of Neurology of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiang Shu
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Clinical Research Center for Child Health, Hangzhou, China
| | - Xuekun Li
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,National Clinical Research Center for Child Health, Hangzhou, China.,The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
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19
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Zhou Y, Zhang F, Jiang H, Xu D, Deng D. Fumaric acid and succinic acid treat gestational hypertension by downregulating the expression of KCNMB1 and TET1. Exp Ther Med 2021; 22:1072. [PMID: 34447465 PMCID: PMC8355717 DOI: 10.3892/etm.2021.10506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 11/11/2019] [Indexed: 11/19/2022] Open
Abstract
The present study hypothesized that fumaric acid and succinic acid may exhibit therapeutic effects on gestational hypertension. During pregnancy, estrogen upregulates ten-eleven translocation 1 (TET1) expression, which subsequently increases calcium-activated potassium channel subunit β1 (KCNMB1) expression. KCNMB1 is associated with hypertension. Fumaric acid and succinic acid are understood to inhibit TET. Therefore, the present study investigated whether fumaric acid and succinic acid exhibit therapeutic effects on gestational hypertension and whether these effects are mediated by TET1 and KCNMB1. Nω-Nitro-L-arginine methyl ester hydrochloride was injected into rats to establish a gestational hypertension model. Dimethyl fumarate (DMF) and succinic acid were administrated into rats to treat gestational hypertension. Rats were divided into five groups: i) Control; ii) model; iii) DMF; iv) succinic acid; and v) DMF + succinic acid. Blood pressure was monitored by a noninvasive meter and urinary protein was determined using a urinary protein kit. Placenta pathology was examined by hematoxylin-eosin staining. Compared with the control group, urinary protein and blood pressure in the model group increased significantly. The placental cells in the control group were arranged orderly. However, in the model group, decidual cellular edema of placenta and vacuolar degeneration were observed, and the intervascular membrane was markedly thicker with plenty of fibrin deposition. These results indicate successful establishment of a gestational hypertension model. However, compared with the model group, urinary protein, blood pressure, edema, vacuoles and fibrin deposition were markedly reduced in the DMF, succinic acid and DMF + succinic acid groups. mRNA and protein levels of TET1 and KCNMB1 in placenta were evaluated by immunohistochemical analysis, reverse transcription-quantitative polymerase chain reaction and western blotting. The TET1 and KCNMB1 levels in the model group were markedly increased compared with those in the control group. However, compared with the model group, the expression levels were markedly downregulated in the DMF, succinic acid and DMF + succinic acid groups. In conclusion, fumaric acid and succinic acid may treat gestational hypertension by downregulating the expression of KCNMB1 and TET1.
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Affiliation(s)
- Yiyuan Zhou
- Department of Obstetrics, The First Affliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550001, P.R. China
| | - Fang Zhang
- Department of Obstetrics, The First Affliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550001, P.R. China
| | - Huijiao Jiang
- Department of Obstetrics, The First Affliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550001, P.R. China
| | - Di Xu
- Department of Obstetrics, The First Affliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550001, P.R. China
| | - Dongyang Deng
- Department of Obstetrics, The First Affliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550001, P.R. China
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20
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Moyon S, Frawley R, Marechal D, Huang D, Marshall-Phelps KLH, Kegel L, Bøstrand SMK, Sadowski B, Jiang YH, Lyons DA, Möbius W, Casaccia P. TET1-mediated DNA hydroxymethylation regulates adult remyelination in mice. Nat Commun 2021; 12:3359. [PMID: 34099715 PMCID: PMC8185117 DOI: 10.1038/s41467-021-23735-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/10/2021] [Indexed: 12/17/2022] Open
Abstract
The mechanisms regulating myelin repair in the adult central nervous system (CNS) are unclear. Here, we identify DNA hydroxymethylation, catalyzed by the Ten-Eleven-Translocation (TET) enzyme TET1, as necessary for myelin repair in young adults and defective in old mice. Constitutive and inducible oligodendrocyte lineage-specific ablation of Tet1 (but not of Tet2), recapitulate this age-related decline in repair of demyelinated lesions. DNA hydroxymethylation and transcriptomic analyses identify TET1-target in adult oligodendrocytes, as genes regulating neuro-glial communication, including the solute carrier (Slc) gene family. Among them, we show that the expression levels of the Na+/K+/Cl- transporter, SLC12A2, are higher in Tet1 overexpressing cells and lower in old or Tet1 knockout. Both aged mice and Tet1 mutants also present inefficient myelin repair and axo-myelinic swellings. Zebrafish mutants for slc12a2b also display swellings of CNS myelinated axons. Our findings suggest that TET1 is required for adult myelin repair and regulation of the axon-myelin interface.
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Affiliation(s)
- Sarah Moyon
- Neuroscience Initiative Advanced Science Research Center, New York, NY, USA.
| | - Rebecca Frawley
- Neuroscience Initiative Advanced Science Research Center, New York, NY, USA
| | - Damien Marechal
- Neuroscience Initiative Advanced Science Research Center, New York, NY, USA
| | - Dennis Huang
- Neuroscience Initiative Advanced Science Research Center, New York, NY, USA
| | | | - Linde Kegel
- Centre for Discovery Brain Sciences, Edinburgh, UK
| | | | - Boguslawa Sadowski
- Department of Neurogenetics, Göttingen, Germany
- Electron Microscopy Core Unit, Max-Planck-Institute of Experimental Medicine, Göttingen, Germany
- Center Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
| | - Yong-Hui Jiang
- Department of Neurobiology and Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | | | - Wiebke Möbius
- Department of Neurogenetics, Göttingen, Germany
- Electron Microscopy Core Unit, Max-Planck-Institute of Experimental Medicine, Göttingen, Germany
- Center Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
| | - Patrizia Casaccia
- Neuroscience Initiative Advanced Science Research Center, New York, NY, USA.
- Program of Biology and Biochemistry, The Graduate Center of The City University of New York, New York, NY, USA.
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21
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Kim H, Kang Y, Li Y, Chen L, Lin L, Johnson ND, Zhu D, Robinson MH, McSwain L, Barwick BG, Yuan X, Liao X, Zhao J, Zhang Z, Shu Q, Chen J, Allen EG, Kenney AM, Castellino RC, Van Meir EG, Conneely KN, Vertino PM, Jin P, Li J. Ten-eleven translocation protein 1 modulates medulloblastoma progression. Genome Biol 2021; 22:125. [PMID: 33926529 PMCID: PMC8082834 DOI: 10.1186/s13059-021-02352-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 04/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Medulloblastoma (MB) is the most common malignant pediatric brain tumor that originates in the cerebellum and brainstem. Frequent somatic mutations and deregulated expression of epigenetic regulators in MB highlight the substantial role of epigenetic alterations. 5-hydroxymethylcytosine (5hmC) is a highly abundant cytosine modification in the developing cerebellum and is regulated by ten-eleven translocation (TET) enzymes. RESULTS We investigate the alterations of 5hmC and TET enzymes in MB and their significance to cerebellar cancer formation. We show total abundance of 5hmC is reduced in MB, but identify significant enrichment of MB-specific 5hmC marks at regulatory regions of genes implicated in stem-like properties and Nanog-binding motifs. While TET1 and TET2 levels are high in MBs, only knockout of Tet1 in the smoothened (SmoA1) mouse model attenuates uncontrolled proliferation, leading to a favorable prognosis. The pharmacological Tet1 inhibition reduces cell viability and platelet-derived growth factor signaling pathway-associated genes. CONCLUSIONS These results together suggest a potential key role of 5hmC and indicate an oncogenic nature for TET1 in MB tumorigenesis, suggesting it as a potential therapeutic target for MBs.
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Affiliation(s)
- Hyerim Kim
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Yunhee Kang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Yujing Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Li Chen
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Li Lin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Nicholas D Johnson
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Dan Zhu
- Laboratory of Molecular Neuro-Oncology, Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - M Hope Robinson
- Department of Pediatric Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Leon McSwain
- Department of Pediatric Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Benjamin G Barwick
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA
| | - Xianrui Yuan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xinbin Liao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hydrocephalus Center, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Jie Zhao
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hydrocephalus Center, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Zhiping Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Hydrocephalus Center, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Qiang Shu
- The Children's Hospital and Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jianjun Chen
- Department of Systems Biology and Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA, 91010, USA
| | - Emily G Allen
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Anna M Kenney
- Department of Pediatric Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA
| | - Robert C Castellino
- Department of Pediatric Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Erwin G Van Meir
- Laboratory of Molecular Neuro-Oncology, Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA
| | - Karen N Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Paula M Vertino
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Jian Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- Hydrocephalus Center, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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22
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MacArthur IC, Dawlaty MM. TET Enzymes and 5-Hydroxymethylcytosine in Neural Progenitor Cell Biology and Neurodevelopment. Front Cell Dev Biol 2021; 9:645335. [PMID: 33681230 PMCID: PMC7930563 DOI: 10.3389/fcell.2021.645335] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/01/2021] [Indexed: 12/19/2022] Open
Abstract
Studies of tissue-specific epigenomes have revealed 5-hydroxymethylcytosine (5hmC) to be a highly enriched and dynamic DNA modification in the metazoan nervous system, inspiring interest in the function of this epigenetic mark in neurodevelopment and brain function. 5hmC is generated by oxidation of 5-methylcytosine (5mC), a process catalyzed by the ten–eleven translocation (TET) enzymes. 5hmC serves not only as an intermediate in DNA demethylation but also as a stable epigenetic mark. Here, we review the known functions of 5hmC and TET enzymes in neural progenitor cell biology and embryonic and postnatal neurogenesis. We also discuss how TET enzymes and 5hmC regulate neuronal activity and brain function and highlight their implications in human neurodevelopmental and neurodegenerative disorders. Finally, we present outstanding questions in the field and envision new research directions into the roles of 5hmC and TET enzymes in neurodevelopment.
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Affiliation(s)
- Ian C MacArthur
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, United States.,Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Meelad M Dawlaty
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, United States.,Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, United States
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23
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Cheng XJ, Guan FL, Li Q, Dai G, Li HF, Li XK. AlCl 3 exposure regulates neuronal development by modulating DNA modification. World J Stem Cells 2020; 12:1354-1365. [PMID: 33312403 PMCID: PMC7705460 DOI: 10.4252/wjsc.v12.i11.1354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 07/07/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND As the third most abundant element, aluminum is widespread in the environment. Previous studies have shown that aluminum has a neurotoxic effect and its exposure can impair neuronal development and cognitive function.
AIM To study the effects of aluminum on epigenetic modification in neural stem cells and neurons.
METHODS Neural stem cells were isolated from the forebrain of adult mice. Neurons were isolated from the hippocampi tissues of embryonic day 16-18 mice. AlCl3 at 100 and 200 μmol/L was applied to stem cells and neurons.
RESULTS Aluminum altered the differentiation of adult neural stem cells and caused apoptosis of newborn neurons while having no significant effects on the proliferation of neural stem cells. Aluminum application also significantly inhibited the dendritic development of hippocampal neurons. Mechanistically, aluminum exposure significantly affected the levels of DNA 5-hydroxy-methylcytosine, 5-methylcytosine, and N6-methyladenine in stem cells and neurons.
CONCLUSION Our findings indicate that aluminum may regulate neuronal development by modulating DNA modifications.
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Affiliation(s)
- Xue-Jun Cheng
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, Zhejiang Province, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, Zhejiang Province, China
- National Clinical Research Center for Child Health, Hangzhou 310052, Zhejiang Province, China
| | - Fu-Lai Guan
- School of Basic Medicine, Weifang Medical University, Weifang 261053, Shandong Province, China
| | - Qian Li
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, Zhejiang Province, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, Zhejiang Province, China
- National Clinical Research Center for Child Health, Hangzhou 310052, Zhejiang Province, China
| | - Gong Dai
- School of Basic Medicine, Weifang Medical University, Weifang 261053, Shandong Province, China
| | - Hai-Feng Li
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, Zhejiang Province, China
- National Clinical Research Center for Child Health, Hangzhou 310052, Zhejiang Province, China
| | - Xue-Kun Li
- The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, Zhejiang Province, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, Zhejiang Province, China
- National Clinical Research Center for Child Health, Hangzhou 310052, Zhejiang Province, China
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24
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Suppression of DNA Double-Strand Break Formation by DNA Polymerase β in Active DNA Demethylation Is Required for Development of Hippocampal Pyramidal Neurons. J Neurosci 2020; 40:9012-9027. [PMID: 33087478 DOI: 10.1523/jneurosci.0319-20.2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 10/02/2020] [Accepted: 10/16/2020] [Indexed: 01/04/2023] Open
Abstract
Genome stability is essential for brain development and function, as de novo mutations during neuronal development cause psychiatric disorders. However, the contribution of DNA repair to genome stability in neurons remains elusive. Here, we demonstrate that the base excision repair protein DNA polymerase β (Polβ) is involved in hippocampal pyramidal neuron differentiation via a TET-mediated active DNA demethylation during early postnatal stages using Nex-Cre/Polβ fl/fl mice of either sex, in which forebrain postmitotic excitatory neurons lack Polβ expression. Polβ deficiency induced extensive DNA double-strand breaks (DSBs) in hippocampal pyramidal neurons, but not dentate gyrus granule cells, and to a lesser extent in neocortical neurons, during a period in which decreased levels of 5-methylcytosine and 5-hydroxymethylcytosine were observed in genomic DNA. Inhibition of the hydroxylation of 5-methylcytosine by expression of microRNAs miR-29a/b-1 diminished DSB formation. Conversely, its induction by TET1 catalytic domain overexpression increased DSBs in neocortical neurons. Furthermore, the damaged hippocampal neurons exhibited aberrant neuronal gene expression profiles and dendrite formation, but not apoptosis. Comprehensive behavioral analyses revealed impaired spatial reference memory and contextual fear memory in adulthood. Thus, Polβ maintains genome stability in the active DNA demethylation that occurs during early postnatal neuronal development, thereby contributing to differentiation and subsequent learning and memory.SIGNIFICANCE STATEMENT Increasing evidence suggests that de novo mutations during neuronal development cause psychiatric disorders. However, strikingly little is known about how DNA repair is involved in neuronal differentiation. We found that Polβ, a component of base excision repair, is required for differentiation of hippocampal pyramidal neurons in mice. Polβ deficiency transiently led to increased DNA double-strand breaks, but not apoptosis, in early postnatal hippocampal pyramidal neurons. This aberrant double-strand break formation was attributed to active DNA demethylation as an epigenetic regulation. Furthermore, the damaged neurons exhibited aberrant gene expression profiles and dendrite formation, resulting in impaired learning and memory in adulthood. Thus, these findings provide new insight into the contribution of DNA repair to the neuronal genome in early brain development.
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25
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Novel genetic features of human and mouse Purkinje cell differentiation defined by comparative transcriptomics. Proc Natl Acad Sci U S A 2020; 117:15085-15095. [PMID: 32546527 PMCID: PMC7334519 DOI: 10.1073/pnas.2000102117] [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] [Indexed: 12/20/2022] Open
Abstract
Comparative transcriptomics between differentiating human pluripotent stem cells (hPSCs) and developing mouse neurons offers a powerful approach to compare genetic and epigenetic pathways in human and mouse neurons. To analyze human Purkinje cell (PC) differentiation, we optimized a protocol to generate human pluripotent stem cell-derived Purkinje cells (hPSC-PCs) that formed synapses when cultured with mouse cerebellar glia and granule cells and fired large calcium currents, measured with the genetically encoded calcium indicator jRGECO1a. To directly compare global gene expression of hPSC-PCs with developing mouse PCs, we used translating ribosomal affinity purification (TRAP). As a first step, we used Tg(Pcp2-L10a-Egfp) TRAP mice to profile actively transcribed genes in developing postnatal mouse PCs and used metagene projection to identify the most salient patterns of PC gene expression over time. We then created a transgenic Pcp2-L10a-Egfp TRAP hPSC line to profile gene expression in differentiating hPSC-PCs, finding that the key gene expression pathways of differentiated hPSC-PCs most closely matched those of late juvenile mouse PCs (P21). Comparative bioinformatics identified classical PC gene signatures as well as novel mitochondrial and autophagy gene pathways during the differentiation of both mouse and human PCs. In addition, we identified genes expressed in hPSC-PCs but not mouse PCs and confirmed protein expression of a novel human PC gene, CD40LG, expressed in both hPSC-PCs and native human cerebellar tissue. This study therefore provides a direct comparison of hPSC-PC and mouse PC gene expression and a robust method for generating differentiated hPSC-PCs with human-specific gene expression for modeling developmental and degenerative cerebellar disorders.
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26
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Role of Chromatin Remodeling Genes and TETs in the Development of Human Midbrain Dopaminergic Neurons. Stem Cell Rev Rep 2020; 16:718-729. [DOI: 10.1007/s12015-020-09972-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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27
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Rao VK, Swarnaseetha A, Tham GH, Lin WQ, Han BB, Benoukraf T, Xu GL, Ong CT. Phosphorylation of Tet3 by cdk5 is critical for robust activation of BRN2 during neuronal differentiation. Nucleic Acids Res 2020; 48:1225-1238. [PMID: 31807777 PMCID: PMC7026633 DOI: 10.1093/nar/gkz1144] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 11/20/2019] [Accepted: 11/27/2019] [Indexed: 12/27/2022] Open
Abstract
Tet3 regulates the dynamic balance between 5-methylcyotsine (5mC) and 5-hydroxymethylcytosine (5hmC) in DNA during brain development and homeostasis. However, it remains unclear how its functions are modulated in a context-dependent manner during neuronal differentiation. Here, we show that cyclin-dependent kinase 5 (cdk5) phosphorylates Tet3 at the highly conserved serine 1310 and 1379 residues within its catalytic domain, changing its in vitro dioxygenase activity. Interestingly, when stably expressed in Tet1, 2, 3 triple-knockout mouse embryonic stem cells (ESCs), wild-type Tet3 induces higher level of 5hmC and concomitant expression of genes associated with neurogenesis whereas phosphor-mutant (S1310A/S1379A) Tet3 causes elevated 5hmC and expression of genes that are linked to metabolic processes. Consistent with this observation, Tet3-knockout mouse ESCs rescued with wild-type Tet3 have higher level of 5hmC at the promoter of neuron-specific gene BRN2 when compared to cells that expressed phosphor-mutant Tet3. Wild-type and phosphor-mutant Tet3 also exhibit differential binding affinity to histone variant H2A.Z. The differential 5hmC enrichment and H2A.Z occupancy at BRN2 promoter is correlated with higher gene expression and more efficient neuronal differentiation of ESCs that expressed wild-type Tet3. Taken together, our results suggest that cdk5-mediated phosphorylation of Tet3 is required for robust activation of neuronal differentiation program.
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Affiliation(s)
- Vinay Kumar Rao
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Adusumalli Swarnaseetha
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Guo-Hong Tham
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Wei-Qi Lin
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Bin-Bin Han
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Touati Benoukraf
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.,Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL A1B 3V6, Canada
| | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chin-Tong Ong
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
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28
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Beck DB, Petracovici A, He C, Moore HW, Louie RJ, Ansar M, Douzgou S, Sithambaram S, Cottrell T, Santos-Cortez RLP, Prijoles EJ, Bend R, Keren B, Mignot C, Nougues MC, Õunap K, Reimand T, Pajusalu S, Zahid M, Saqib MAN, Buratti J, Seaby EG, McWalter K, Telegrafi A, Baldridge D, Shinawi M, Leal SM, Schaefer GB, Stevenson RE, Banka S, Bonasio R, Fahrner JA. Delineation of a Human Mendelian Disorder of the DNA Demethylation Machinery: TET3 Deficiency. Am J Hum Genet 2020; 106:234-245. [PMID: 31928709 DOI: 10.1016/j.ajhg.2019.12.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/11/2019] [Indexed: 12/11/2022] Open
Abstract
Germline pathogenic variants in chromatin-modifying enzymes are a common cause of pediatric developmental disorders. These enzymes catalyze reactions that regulate epigenetic inheritance via histone post-translational modifications and DNA methylation. Cytosine methylation (5-methylcytosine [5mC]) of DNA is the quintessential epigenetic mark, yet no human Mendelian disorder of DNA demethylation has yet been delineated. Here, we describe in detail a Mendelian disorder caused by the disruption of DNA demethylation. TET3 is a methylcytosine dioxygenase that initiates DNA demethylation during early zygote formation, embryogenesis, and neuronal differentiation and is intolerant to haploinsufficiency in mice and humans. We identify and characterize 11 cases of human TET3 deficiency in eight families with the common phenotypic features of intellectual disability and/or global developmental delay; hypotonia; autistic traits; movement disorders; growth abnormalities; and facial dysmorphism. Mono-allelic frameshift and nonsense variants in TET3 occur throughout the coding region. Mono-allelic and bi-allelic missense variants localize to conserved residues; all but one such variant occur within the catalytic domain, and most display hypomorphic function in an assay of catalytic activity. TET3 deficiency and other Mendelian disorders of the epigenetic machinery show substantial phenotypic overlap, including features of intellectual disability and abnormal growth, underscoring shared disease mechanisms.
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Affiliation(s)
- David B Beck
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ana Petracovici
- Graduate Group in Genetics and Epigenetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Chongsheng He
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Current address: Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha 410082 Hunan, P.R. China
| | | | | | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, 45320 Islamabad, Pakistan
| | - Sofia Douzgou
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Sivagamy Sithambaram
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Trudie Cottrell
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | | | | | - Renee Bend
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Boris Keren
- Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Département de Génétique, Paris 75013, France
| | - Cyril Mignot
- Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Département de Génétique, Paris 75013, France; Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris 75013, France
| | - Marie-Christine Nougues
- Assistance Publique-Hôpitaux de Paris, Armand Trousseau Hospital, Department of Neuropediatrics, Paris 75012, France
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia
| | - Tiia Reimand
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia; Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50406, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu 50406, Estonia; Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia; Yale University School of Medicine, Department of Genetics, New Haven, CT 06510, USA
| | - Muhammad Zahid
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, 45320 Islamabad, Pakistan
| | | | - Julien Buratti
- Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Département de Génétique, Paris 75013, France
| | - Eleanor G Seaby
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | - Dustin Baldridge
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Taub Institute for Alzheimer's D disease and the Aging Brain, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY 10032, USA
| | | | | | - Siddharth Banka
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Roberto Bonasio
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jill A Fahrner
- Department of Pediatrics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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Hoffman DP, Shtengel G, Xu CS, Campbell KR, Freeman M, Wang L, Milkie DE, Pasolli HA, Iyer N, Bogovic JA, Stabley DR, Shirinifard A, Pang S, Peale D, Schaefer K, Pomp W, Chang CL, Lippincott-Schwartz J, Kirchhausen T, Solecki DJ, Betzig E, Hess HF. Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells. Science 2020; 367:eaaz5357. [PMID: 31949053 PMCID: PMC7339343 DOI: 10.1126/science.aaz5357] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/20/2019] [Indexed: 12/27/2022]
Abstract
Within cells, the spatial compartmentalization of thousands of distinct proteins serves a multitude of diverse biochemical needs. Correlative super-resolution (SR) fluorescence and electron microscopy (EM) can elucidate protein spatial relationships to global ultrastructure, but has suffered from tradeoffs of structure preservation, fluorescence retention, resolution, and field of view. We developed a platform for three-dimensional cryogenic SR and focused ion beam-milled block-face EM across entire vitreously frozen cells. The approach preserves ultrastructure while enabling independent SR and EM workflow optimization. We discovered unexpected protein-ultrastructure relationships in mammalian cells including intranuclear vesicles containing endoplasmic reticulum-associated proteins, web-like adhesions between cultured neurons, and chromatin domains subclassified on the basis of transcriptional activity. Our findings illustrate the value of a comprehensive multimodal view of ultrastructural variability across whole cells.
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Affiliation(s)
- David P Hoffman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Gleb Shtengel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - C Shan Xu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Kirby R Campbell
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Melanie Freeman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Lei Wang
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel E Milkie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - H Amalia Pasolli
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Nirmala Iyer
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - John A Bogovic
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Daniel R Stabley
- Neuroimaging Laboratory, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Abbas Shirinifard
- Bioimage Analysis Core, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Song Pang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - David Peale
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Kathy Schaefer
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Wim Pomp
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Chi-Lun Chang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | | | - Tom Kirchhausen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - David J Solecki
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Department of Physics, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, Berkeley, CA 94720, USA
- Helen Wills Neuroscience Institute, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Harald F Hess
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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Marrocco J, Einhorn NR, Petty GH, Li H, Dubey N, Hoffman J, Berman KF, Goldman D, Lee FS, Schmidt PJ, McEwen BS. Epigenetic intersection of BDNF Val66Met genotype with premenstrual dysphoric disorder transcriptome in a cross-species model of estradiol add-back. Mol Psychiatry 2020; 25:572-583. [PMID: 30356121 PMCID: PMC7042769 DOI: 10.1038/s41380-018-0274-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/11/2018] [Indexed: 02/08/2023]
Abstract
Premenstrual dysphoric disorder (PMDD) affects over 5% of women, with symptoms similar to anxiety and major depression, and is associated with differential sensitivity to circulating ovarian hormones. Little is known about the genetic and epigenetic factors that increase the risk to develop PMDD. We report that 17β-estradiol (E2) affects the behavior and the epigenome in a mouse model carrying a single-nucleotide polymorphism of the brain-derived neurotrophic factor gene (BDNF Val66Met), in a way that recapitulates the hallmarks of PMDD. Ovariectomized mice heterozygous for the BDNF Met allele (Het-Met) and their matched wild-type (WT) mice were administered estradiol or vehicle in drinking water for 6 weeks. Using the open field and the splash test, we show that E2 add-back induces anxiety-like and depression-like behavior in Het-Met mice, but not in WT mice. RNA-seq of the ventral hippocampus (vHpc) highlights that E2-dependent gene expression is markedly different between WT mice and Het-Met mice. Through a comparative whole-genome RNA-seq analysis between mouse vHpc and lymphoblastoid cell line cultures from control women and women with PMDD, we discovered common epigenetic biomarkers that transcend species and cell types. Those genes include epigenetic modifiers of the ESC/E(Z) complex, an effector of response to ovarian steroids. Although the BDNF Met genotype intersects the behavioral and transcriptional traits of women with PMDD, we suggest that these similarities speak to the epigenetic factors by which ovarian steroids produce negative behavioral effects.
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Affiliation(s)
- Jordan Marrocco
- 0000 0001 2166 1519grid.134907.8Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY USA
| | - Nathan R. Einhorn
- 0000 0001 2166 1519grid.134907.8Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY USA
| | - Gordon H. Petty
- 0000 0001 2166 1519grid.134907.8Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY USA
| | - Howard Li
- 0000 0004 0464 0574grid.416868.5Behavioral Endocrinology Branch, National Institute of Mental Health, Bethesda, MD USA
| | - Neelima Dubey
- grid.440681.fDr. D. Y. Patil Biotechnology & Bioinformatics Institute, Pune, India
| | - Jessica Hoffman
- 0000 0001 0421 5525grid.265436.0Uniformed Services University of the Health Sciences, Bethesda, MD USA
| | - Karen F. Berman
- 0000 0004 0464 0574grid.416868.5Section on Integrative Neuroimaging, National Institute of Mental Health, Bethesda, MD USA
| | - David Goldman
- 0000 0004 0481 4802grid.420085.bLaboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD USA
| | - Francis S. Lee
- 000000041936877Xgrid.5386.8Department of Psychiatry, Sackler Institute for Developmental Psychobiology, Weill Cornell Medical College, New York, NY USA
| | - Peter J. Schmidt
- 0000 0004 0464 0574grid.416868.5Behavioral Endocrinology Branch, National Institute of Mental Health, Bethesda, MD USA
| | - Bruce S. McEwen
- 0000 0001 2166 1519grid.134907.8Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY USA
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Liu CH, Tan YZ, Li DD, Tang SS, Wen XA, Long Y, Sun HB, Hong H, Hu M. Zileuton ameliorates depressive-like behaviors, hippocampal neuroinflammation, apoptosis and synapse dysfunction in mice exposed to chronic mild stress. Int Immunopharmacol 2019; 78:105947. [PMID: 31796384 DOI: 10.1016/j.intimp.2019.105947] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/04/2019] [Accepted: 09/27/2019] [Indexed: 10/25/2022]
Abstract
Our previous study has found that zileuton, a selective 5-lipoxygenase (5LO) inhibitor, abrogated lipopolysaccharide-induced depressive-like behaviors and hippocampal neuroinflammation. Herein, we further extended our curiosity to investigate effects of zileuton on stress-induced depressive-like behaviors. Our data indicated that zileuton significantly ameliorated depressive-like behaviors in mice subjected to chronic mild stress (CMS), as shown in the tail suspension test, forced swimming test and novelty-suppressed feeding test. The further studies indicated that zileuton suppressed hippocampal neuroinflammation, evidenced by lower levels of TNF-α, IL-1β and nuclear NF-κB p65 as well as decreased number of Iba1-positive cells. It also significantly ameliorated hippocampal apoptosis, indicated by deceased number of TUNEL-positive cells, deceased ratio of cleaved caspase-3/procaspase-3 and increased ratio of Bcl-2/Bax. More importantly, zileuton increased the level of synaptic proteins PSD-95 and SYN and the number of NeuN+/BrdU+ cells in the hippocampus. Over all, zileuton alleviated CMS-induced depressive-like behaviors, neuroinflammatory and apoptotic responses, abnormalities of synapse and neurogenesis in the hippocampus, suggesting that it might has beneficial effects on depression.
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Affiliation(s)
- Cai-Hong Liu
- Department of Pharmacology, China Pharmaceutical University, Nanjing 210009, China
| | - Yuan-Zhi Tan
- Department of Pharmacology, China Pharmaceutical University, Nanjing 210009, China
| | - Dan-Dan Li
- Department of Pharmacology, China Pharmaceutical University, Nanjing 210009, China
| | - Su-Su Tang
- Department of Pharmacology, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao-An Wen
- Department of Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, China Pharmaceutical University, Nanjing 210009, China
| | - Yan Long
- Department of Pharmacology, China Pharmaceutical University, Nanjing 210009, China
| | - Hong-Bin Sun
- Department of Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, China Pharmaceutical University, Nanjing 210009, China
| | - Hao Hong
- Department of Pharmacology, China Pharmaceutical University, Nanjing 210009, China.
| | - Mei Hu
- Department of Pharmacology, China Pharmaceutical University, Nanjing 210009, China.
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Chen S, Zhang J, Zhang D, Jiao J. Acquisition of functional neurons by direct conversion: Switching the developmental clock directly. J Genet Genomics 2019; 46:459-465. [PMID: 31771824 DOI: 10.1016/j.jgg.2019.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/20/2019] [Accepted: 10/08/2019] [Indexed: 01/04/2023]
Abstract
Identifying approaches for treating neurodegeneration is a thorny task but is important for a growing number of patients. Researchers have focused on discovering the underlying molecular mechanisms of reprogramming and optimizing the technologies for acquiring neurons. Direct conversion is one of the most important processes for treating neurological disorders. Induced neurons derived from direct conversion, which bypass the pluripotency stage, are more effective, more quickly obtained, and are safer than those produced via induced pluripotent stem cells (iPSCs). Based on iPSC strategies, scientists have derived methods to obtain functional neurons by direct conversion, such as neuron-related transcriptional factors, small molecules, microRNAs, and epigenetic modifiers. In this review, we discuss the present strategies for direct conversion of somatic cells into functional neurons and the potentials of direct conversion for producing functional neurons and treating neurodegeneration.
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Affiliation(s)
- Shuangquan Chen
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
| | - Juan Zhang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dongming Zhang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jianwei Jiao
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
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EGR1 recruits TET1 to shape the brain methylome during development and upon neuronal activity. Nat Commun 2019; 10:3892. [PMID: 31467272 PMCID: PMC6715719 DOI: 10.1038/s41467-019-11905-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 08/12/2019] [Indexed: 02/07/2023] Open
Abstract
Life experience can leave lasting marks, such as epigenetic changes, in the brain. How life experience is translated into storable epigenetic information remains largely unknown. With unbiased data-driven approaches, we predicted that Egr1, a transcription factor important for memory formation, plays an essential role in brain epigenetic programming. We performed EGR1 ChIP-seq and validated thousands of EGR1 binding sites with methylation patterns established during postnatal brain development. More specifically, these EGR1 binding sites become hypomethylated in mature neurons but remain heavily methylated in glia. We further demonstrated that EGR1 recruits a DNA demethylase TET1 to remove the methylation marks and activate downstream genes. The frontal cortices from the knockout mice lacking Egr1 or Tet1 share strikingly similar profiles in both gene expression and DNA methylation. In summary, our study reveals EGR1 programs the brain methylome together with TET1 providing new insight into how life experience may shape the brain methylome. It is unclear why neuronal activity induced methylation changes are limited to specific loci in the genome. Here, authors show that the DNA demethylation enzyme, TET1, gains its specificity via the interaction with EGR1, a sequence specific DNA binding protein.
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Marrocco J, Gray JD, Kogan JF, Einhorn NR, O’Cinneide EM, Rubin TG, Carroll TS, Schmidt EF, McEwen BS. Early Life Stress Restricts Translational Reactivity in CA3 Neurons Associated With Altered Stress Responses in Adulthood. Front Behav Neurosci 2019; 13:157. [PMID: 31354448 PMCID: PMC6637287 DOI: 10.3389/fnbeh.2019.00157] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 06/27/2019] [Indexed: 12/27/2022] Open
Abstract
Early life experiences program brain structure and function and contribute to behavioral endophenotypes in adulthood. Epigenetic control of gene expression by those experiences affect discrete brain regions involved in mood, cognitive function and regulation of hypothalamic-pituitary-adrenal (HPA) axis. In rodents, acute restraint stress increases the expression of the repressive histone H3 lysine 9 tri-methylation (H3K9me3) in hippocampal fields, including the CA3 pyramidal neurons. These CA3 neurons are crucially involved in cognitive function and mood regulation as well as activation of glucocorticoid (CORT) secretion. CA3 neurons also exhibit structural and functional changes after early-life stress (ELS) as well as after chronic stress in adulthood. Using a protocol of chronic ELS induced by limited bedding and nesting material followed by acute-swim stress (AS) in adulthood, we show that mice with a history of ELS display a blunted CORT response to AS, despite exhibiting activation of immediate early genes after stress similar to that found in control mice. We find that ELS induced persistently increased expression of the repressive H3K9me3 histone mark in the CA3 subfield at baseline that was subsequently decreased following AS. In contrast, AS induced a transient increase of this mark in control mice. Using translating ribosome affinity purification (TRAP) method to isolate CA3 translating mRNAs, we found that expression of genes of the epigenetic gene family, GABA/glutamate family, and glucocorticoid receptors binding genes were decreased transiently in control mice by AS and showed a persistent reduction in ELS mice. In most cases, AS in ELS mice did not induce gene expression changes. A stringent filtering of genes affected by AS in control and ELS mice revealed a noteworthy decrease in gene expression change in ELS mice compared to control. Only 18 genes were selectively regulated by AS in ELS mice and encompassed pathways such as circadian rhythm, inflammatory response, opioid receptors, and more genes included in the glucocorticoid receptor binding family. Thus, ELS programs a restricted translational response to stress in stress-sensitive CA3 neurons leading to persistent changes in gene expression, some of which mimic the transient effects of AS in control mice, while leaving in operation the immediate early gene response to AS.
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Affiliation(s)
- Jordan Marrocco
- Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY, United States
| | - Jason D. Gray
- Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY, United States
| | - Joshua F. Kogan
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, United States
| | - Nathan R. Einhorn
- Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY, United States
| | - Emma M. O’Cinneide
- Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY, United States
| | - Todd G. Rubin
- Albert Einstein College of Medicine, Bronx, NY, United States
| | - Thomas S. Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, United States
| | - Eric F. Schmidt
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, United States
| | - Bruce S. McEwen
- Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY, United States
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Time series modeling of cell cycle exit identifies Brd4 dependent regulation of cerebellar neurogenesis. Nat Commun 2019; 10:3028. [PMID: 31292434 PMCID: PMC6620341 DOI: 10.1038/s41467-019-10799-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 05/09/2019] [Indexed: 01/22/2023] Open
Abstract
Cerebellar neuronal progenitors undergo a series of divisions before irreversibly exiting the cell cycle and differentiating into neurons. Dysfunction of this process underlies many neurological diseases including ataxia and the most common pediatric brain tumor, medulloblastoma. To better define the pathways controlling the most abundant neuronal cells in the mammalian cerebellum, cerebellar granule cell progenitors (GCPs), we performed RNA-sequencing of GCPs exiting the cell cycle. Time-series modeling of GCP cell cycle exit identified downregulation of activity of the epigenetic reader protein Brd4. Brd4 binding to the Gli1 locus is controlled by Casein Kinase 1δ (CK1 δ)-dependent phosphorylation during GCP proliferation, and decreases during GCP cell cycle exit. Importantly, conditional deletion of Brd4 in vivo in the developing cerebellum induces cerebellar morphological deficits and ataxia. These studies define an essential role for Brd4 in cerebellar granule cell neurogenesis and are critical for designing clinical trials utilizing Brd4 inhibitors in neurological indications. The mechanisms controlling irreversible cell cycle exit in cerebellar granule progenitors (GCPs) have not been fully elucidated. Here, the authors performed RNA-sequencing of GCPs exiting the cell cycle to identify downregulation of Brd4 activity as an early event during cell cycle exit which subsequently regulates Shh activity and is needed for proper cerebellar development
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36
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Young KG, Yan K, Picketts DJ. C3aR signaling and gliosis in response to neurodevelopmental damage in the cerebellum. J Neuroinflammation 2019; 16:135. [PMID: 31272467 PMCID: PMC6610970 DOI: 10.1186/s12974-019-1530-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 06/24/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Conditional ablation of the Smarca5 gene in mice severely impairs the postnatal growth of the cerebellum and causes an ataxic phenotype. Comparative gene expression studies indicated that complement-related proteins were upregulated in the cerebellum of Smarca5 mutant mice. Complement proteins play critical roles within innate immune signaling pathways and, in the brain, are produced by glial cells under both normal and pathological conditions. The C3 complement protein-derived signaling peptide, C3a, has been implicated in contributing to both tissue damage and repair in conditions such as multiple sclerosis and stroke. Here, we investigated whether C3a receptor (C3aR) signaling promoted damage or repair in the developing cerebellum of Smarca5 mutant mice. METHODS Brain and cerebellum lysates from single Smarca5 conditional knockout (Smarca5 cKO) mice, C3aR1 KO mice, or double mutant mice were used for qRT-PCR and immunoblotting to assess the contribution of C3aR to the Smarca5 cKO brain pathology. Immunohistochemistry was used to characterize alterations to astroglia and phagocyte cells in the developing cerebellum of each of the genotypes. RESULTS C3aR signaling was observed to limit gliosis and promote granule neuron survival during postnatal cerebellar development. In Smarca5 cKO mice, disorganized astroglia with increased GFAP expression develops concurrently with cerebellar granule neuron loss and phagocyte invasion over the first 10 days following birth. Potential ligand precursors of C3aR-VGF and C3-were found to have upregulated expression and/or altered processing during this time. Phagocytes (microglia and macrophages) in both the control and Smarca5 mutant mice were the only cells observed to express C3aR. Loss of C3aR in the Smarca5 cKO cerebellum resulted in increased numbers of apoptotic cells and early phagocyte invasion into the external granule cell layer, as well as an exacerbated disorganization of the Bergmann glia. The loss of C3aR expression also attenuated an increase in the expression of the efferocytosis-related protein, MerTK, whose transcript was upregulated ~ 2.5-fold in the Smarca5 mutant cerebellum at P10. CONCLUSIONS This data indicates that C3aR can play an important role in limiting astrogliosis and regulating phagocyte phenotypes following developmental cell loss in the brain.
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Affiliation(s)
- Kevin G Young
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada.,Present address: Therapeutic Products Directorate, Health Canada, 1600 Scott St, Ottawa, ON, K1A 0K9, Canada
| | - Keqin Yan
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, K1H 8L6, Canada. .,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada. .,Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.
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Lien YC, Condon DE, Georgieff MK, Simmons RA, Tran PV. Dysregulation of Neuronal Genes by Fetal-Neonatal Iron Deficiency Anemia Is Associated with Altered DNA Methylation in the Rat Hippocampus. Nutrients 2019; 11:nu11051191. [PMID: 31137889 PMCID: PMC6566599 DOI: 10.3390/nu11051191] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 02/06/2023] Open
Abstract
Early-life iron deficiency results in long-term abnormalities in cognitive function and affective behavior in adulthood. In preclinical models, these effects have been associated with long-term dysregulation of key neuronal genes. While limited evidence suggests histone methylation as an epigenetic mechanism underlying gene dysregulation, the role of DNA methylation remains unknown. To determine whether DNA methylation is a potential mechanism by which early-life iron deficiency induces gene dysregulation, we performed whole genome bisulfite sequencing to identify loci with altered DNA methylation in the postnatal day (P) 15 iron-deficient (ID) rat hippocampus, a time point at which the highest level of hippocampal iron deficiency is concurrent with peak iron demand for axonal and dendritic growth. We identified 229 differentially methylated loci and they were mapped within 108 genes. Among them, 63 and 45 genes showed significantly increased and decreased DNA methylation in the P15 ID hippocampus, respectively. To establish a correlation between differentially methylated loci and gene dysregulation, the methylome data were compared to our published P15 hippocampal transcriptome. Both datasets showed alteration of similar functional networks regulating nervous system development and cell-to-cell signaling that are critical for learning and behavior. Collectively, the present findings support a role for DNA methylation in neural gene dysregulation following early-life iron deficiency.
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Affiliation(s)
- Yu-Chin Lien
- Center for Research on Reproduction and Women's Health, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - David E Condon
- Center for Research on Reproduction and Women's Health, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Michael K Georgieff
- Department of Pediatrics, University of Minnesota School of Medicine, Minneapolis, MN 55455, USA.
| | - Rebecca A Simmons
- Center for Research on Reproduction and Women's Health, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA 19104, USA.
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Phu V Tran
- Department of Pediatrics, University of Minnesota School of Medicine, Minneapolis, MN 55455, USA.
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Noack F, Pataskar A, Schneider M, Buchholz F, Tiwari VK, Calegari F. Assessment and site-specific manipulation of DNA (hydroxy-)methylation during mouse corticogenesis. Life Sci Alliance 2019; 2:2/2/e201900331. [PMID: 30814272 PMCID: PMC6394126 DOI: 10.26508/lsa.201900331] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 12/17/2022] Open
Abstract
This work describes the dynamics of DNA modifications in specific cell types of the developing mammalian cortex. By providing a new method to manipulate this process in vivo, it is shown how this process can influence brain formation. Dynamic changes in DNA (hydroxy-)methylation are fundamental for stem cell differentiation. However, the signature of these epigenetic marks in specific cell types during corticogenesis is unknown. Moreover, site-specific manipulation of cytosine modifications is needed to reveal the significance and function of these changes. Here, we report the first assessment of (hydroxy-)methylation in neural stem cells, neurogenic progenitors, and newborn neurons during mammalian corticogenesis. We found that gain in hydroxymethylation and loss in methylation occur sequentially at specific cellular transitions during neurogenic commitment. We also found that these changes predominantly occur within enhancers of neurogenic genes up-regulated during neurogenesis and target of pioneer transcription factors. We further optimized the use of dCas9-Tet1 manipulation of (hydroxy-)methylation, locus-specifically, in vivo, showing the biological relevance of our observations for Dchs1, a regulator of corticogenesis involved in developmental malformations and cognitive impairment. Together, our data reveal the dynamics of cytosine modifications in lineage-related cell types, whereby methylation is reduced and hydroxymethylation gained during the neurogenic lineage concurrently with up-regulation of pioneer transcription factors and activation of enhancers for neurogenic genes.
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Affiliation(s)
- Florian Noack
- CRTD-Center for Regenerative Therapies, School of Medicine, Technische Universität Dresden, Dresden, Germany
| | | | - Martin Schneider
- Medical Systems Biology, School of Medicine, Technische Universität Dresden and Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Frank Buchholz
- Medical Systems Biology, School of Medicine, Technische Universität Dresden and Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Federico Calegari
- CRTD-Center for Regenerative Therapies, School of Medicine, Technische Universität Dresden, Dresden, Germany
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39
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Towers AJ, Tremblay MW, Chung L, Li XL, Bey AL, Zhang W, Cao X, Wang X, Wang P, Duffney LJ, Siecinski SK, Xu S, Kim Y, Kong X, Gregory S, Xie W, Jiang YH. Epigenetic dysregulation of Oxtr in Tet1-deficient mice has implications for neuropsychiatric disorders. JCI Insight 2018; 3:120592. [PMID: 30518695 DOI: 10.1172/jci.insight.120592] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 10/31/2018] [Indexed: 01/24/2023] Open
Abstract
OXTR modulates a variety of behaviors in mammals, including social memory and recognition. Genetic and epigenetic dysregulation of OXTR has been suggested to be implicated in neuropsychiatric disorders, including autism spectrum disorder (ASD). While the involvement of DNA methylation is suggested, the mechanism underlying epigenetic regulation of OXTR is largely unknown. This has hampered the experimental design and interpretation of the results of epigenetic studies of OXTR in neuropsychiatric disorders. From the generation and characterization of a new line of Tet1 mutant mice - by deleting the largest coding exon 4 (Tet1Δe4) - we discovered for the first time to our knowledge that Oxtr has an array of mRNA isoforms and a complex transcriptional regulation. Select isoforms of Oxtr are significantly reduced in the brain of Tet1Δe4-/- mice. Accordingly, CpG islands of Oxtr are hypermethylated during early development and persist into adulthood. Consistent with the reduced express of OXTR, Tet1Δe4-/- mice display impaired maternal care, social behavior, and synaptic responses to oxytocin stimulation. Our findings elucidate a mechanism mediated by TET1 protein in regulating Oxtr expression by preventing DNA hypermethylation of Oxtr. The discovery of epigenetic dysregulation of Oxtr in TET1-deficient mouse brain supports the necessity of a reassessment of existing findings and a value of future studies of OXTR in neuropsychiatric disorders.
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Affiliation(s)
| | | | - Leeyup Chung
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Xin-Lei Li
- Department of Pediatrics, Duke University, Durham, North Carolina, USA.,Laboratory of Molecular Genetics, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Alexandra L Bey
- Department of Neurobiology, Duke University, Durham, North Carolina, USA
| | - Wenhao Zhang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xinyu Cao
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Xiaoming Wang
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Ping Wang
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Lara J Duffney
- Department of Pediatrics, Duke University, Durham, North Carolina, USA.,Department of Neurobiology, Duke University, Durham, North Carolina, USA
| | | | - Sonia Xu
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Yuna Kim
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Xiangyin Kong
- Laboratory of Molecular Genetics, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Simon Gregory
- University Program in Genetics and Genomics and.,Department of Neurology and Duke Molecular Physiology Institute
| | - Wei Xie
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yong-Hui Jiang
- University Program in Genetics and Genomics and.,Department of Pediatrics, Duke University, Durham, North Carolina, USA.,Department of Neurobiology, Duke University, Durham, North Carolina, USA.,Duke Institute for Brain Sciences, and.,Program in Cellular and Molecular Biology, Duke University, Durham, North Carolina, USA
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40
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Abstract
Proper neuronal wiring is central to all bodily functions, sensory perception, cognition, memory, and learning. Establishment of a functional neuronal circuit is a highly regulated and dynamic process involving axonal and dendritic branching and navigation toward appropriate targets and connection partners. This intricate circuitry includes axo-dendritic synapse formation, synaptic connections formed with effector cells, and extensive dendritic arborization that function to receive and transmit mechanical and chemical sensory inputs. Such complexity is primarily achieved by extensive axonal and dendritic branch formation and pruning. Fundamental to neuronal branching are cytoskeletal dynamics and plasma membrane expansion, both of which are regulated via numerous extracellular and intracellular signaling mechanisms and molecules. This review focuses on recent advances in understanding the biology of neuronal branching.
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Affiliation(s)
- Shalini Menon
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Stephanie Gupton
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, Chapel Hill, NC, 27599, USA.,Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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41
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Profile of Mary E. Hatten. Proc Natl Acad Sci U S A 2018; 115:10537-10539. [DOI: 10.1073/pnas.1815359115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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42
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Bovio PP, Franz H, Heidrich S, Rauleac T, Kilpert F, Manke T, Vogel T. Differential Methylation of H3K79 Reveals DOT1L Target Genes and Function in the Cerebellum In Vivo. Mol Neurobiol 2018; 56:4273-4287. [PMID: 30302725 PMCID: PMC6505521 DOI: 10.1007/s12035-018-1377-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 10/01/2018] [Indexed: 12/21/2022]
Abstract
The disruptor of telomeric silencing 1-like (DOT1L) mediates methylation of histone H3 at position lysine 79 (H3K79). Conditional knockout of Dot1l in mouse cerebellar granule cells (Dot1l-cKOAtoh1) led to a smaller external granular layer with fewer precursors of granule neurons. Dot1l-cKOAtoh1 mice had impaired proliferation and differentiation of granular progenitors, which resulted in a smaller cerebellum. Mutant mice showed mild ataxia in motor behavior tests. In contrast, Purkinje cell-specific conditional knockout mice showed no obvious phenotype. Genome-wide transcription analysis of Dot1l-cKOAtoh1 cerebella using microarrays revealed changes in genes that function in cell cycle, cell migration, axon guidance, and metabolism. To identify direct DOT1L target genes, we used genome-wide profiling of H3K79me2 and transcriptional analysis. Analysis of differentially methylated regions (DR) and differentially expressed genes (DE) revealed in total 12 putative DOT1L target genes in Dot1l-cKOAtoh1 affecting signaling (Tnfaip8l3, B3galt5), transcription (Otx1), cell migration and axon guidance (Sema4a, Sema5a, Robo1), cholesterol and lipid metabolism (Lss, Cyp51), cell cycle (Cdkn1a), calcium-dependent cell-adhesion or exocytosis (Pcdh17, Cadps2), and unknown function (Fam174b). Dysregulated expression of these target genes might be implicated in the ataxia phenotype observed in Dot1l-cKOAtoh1.
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Affiliation(s)
- Patrick Piero Bovio
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, University of Freiburg, 79104, Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Henriette Franz
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, University of Freiburg, 79104, Freiburg, Germany
| | - Stefanie Heidrich
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, University of Freiburg, 79104, Freiburg, Germany
| | - Tudor Rauleac
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, University of Freiburg, 79104, Freiburg, Germany
| | - Fabian Kilpert
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Tanja Vogel
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, University of Freiburg, 79104, Freiburg, Germany.
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43
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Wu X, Li G, Xie R. Decoding the role of TET family dioxygenases in lineage specification. Epigenetics Chromatin 2018; 11:58. [PMID: 30290828 PMCID: PMC6172806 DOI: 10.1186/s13072-018-0228-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/28/2018] [Indexed: 02/07/2023] Open
Abstract
Since the discovery of methylcytosine oxidase ten-eleven translocation (TET) proteins, we have witnessed an exponential increase in studies examining their roles in epigenetic regulation. TET family proteins catalyze the sequential oxidation of 5-methylcytosine (5mC) to oxidized methylcytosines including 5-hydroxymethylcytosine (5hmC), 5-formylcytosine, and 5-carboxylcytosine. TETs contribute to the regulation of lineage-specific gene expression via modulating DNA 5mC/5hmC balances at the proximal and distal regulatory elements of cell identity genes, and therefore enhance chromatin accessibility and gene transcription. Emerging evidence suggests that TET dioxygenases participate in the establishment and/or maintenance of hypomethylated bivalent domains at multiple differentiation-associated genes, and thus ensure developmental plasticity. Here, we review the current state of knowledge concerning TET family proteins, DNA hydroxymethylation, their distribution, and function in endoderm, mesoderm, and neuroectoderm specification. We will summarize the evidence pertaining to their crucial regulatory roles in lineage commitment and development.
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Affiliation(s)
- Xinwei Wu
- Centre of Reproduction, Development & Aging, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China
| | - Gang Li
- Centre of Reproduction, Development & Aging, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China
| | - Ruiyu Xie
- Centre of Reproduction, Development & Aging, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China.
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Purzner T, Purzner J, Buckstaff T, Cozza G, Gholamin S, Rusert JM, Hartl TA, Sanders J, Conley N, Ge X, Langan M, Ramaswamy V, Ellis L, Litzenburger U, Bolin S, Theruvath J, Nitta R, Qi L, Li XN, Li G, Taylor MD, Wechsler-Reya RJ, Pinna LA, Cho YJ, Fuller MT, Elias JE, Scott MP. Developmental phosphoproteomics identifies the kinase CK2 as a driver of Hedgehog signaling and a therapeutic target in medulloblastoma. Sci Signal 2018; 11:11/547/eaau5147. [PMID: 30206138 DOI: 10.1126/scisignal.aau5147] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A major limitation of targeted cancer therapy is the rapid emergence of drug resistance, which often arises through mutations at or downstream of the drug target or through intrinsic resistance of subpopulations of tumor cells. Medulloblastoma (MB), the most common pediatric brain tumor, is no exception, and MBs that are driven by sonic hedgehog (SHH) signaling are particularly aggressive and drug-resistant. To find new drug targets and therapeutics for MB that may be less susceptible to common resistance mechanisms, we used a developmental phosphoproteomics approach in murine granule neuron precursors (GNPs), the developmental cell of origin of MB. The protein kinase CK2 emerged as a driver of hundreds of phosphorylation events during the proliferative, MB-like stage of GNP growth, including the phosphorylation of three of the eight proteins commonly amplified in MB. CK2 was critical to the stabilization and activity of the transcription factor GLI2, a late downstream effector in SHH signaling. CK2 inhibitors decreased the viability of primary SHH-type MB patient cells in culture and blocked the growth of murine MB tumors that were resistant to currently available Hh inhibitors, thereby extending the survival of tumor-bearing mice. Because of structural interactions, one CK2 inhibitor (CX-4945) inhibited both wild-type and mutant CK2, indicating that this drug may avoid at least one common mode of acquired resistance. These findings suggest that CK2 inhibitors may be effective for treating patients with MB and show how phosphoproteomics may be used to gain insight into developmental biology and pathology.
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Affiliation(s)
- Teresa Purzner
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. .,Division of Neurosurgery, University of Toronto, Toronto, Ontario M5S1A1, Canada
| | - James Purzner
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Division of Neurosurgery, University of Toronto, Toronto, Ontario M5S1A1, Canada
| | - Taylor Buckstaff
- Department of Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Giorgio Cozza
- Department of Molecular Medicine, University of Padua, Padova, PD 35122, Italy
| | - Sharareh Gholamin
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jessica M Rusert
- Tumor Initiation and Maintenance Program, National Cancer Institute-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Tom A Hartl
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John Sanders
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nicholas Conley
- Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xuecai Ge
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Molecular and Cell Biology, University of California, Merced, Merced, CA 95340, USA
| | | | - Vijay Ramaswamy
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.,Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Lauren Ellis
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ulrike Litzenburger
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Sara Bolin
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Johanna Theruvath
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ryan Nitta
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lin Qi
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiao-Nan Li
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gordon Li
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael D Taylor
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.,Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Robert J Wechsler-Reya
- Tumor Initiation and Maintenance Program, National Cancer Institute-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.,Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA 92123, USA
| | - Lorenzo A Pinna
- Department of Biomedical Sciences, University of Padua, Padova, PD 35122, Italy.,National Research Council Neuroscience Institute, Padova, PD 35122, Italy
| | - Yoon-Jae Cho
- Papé Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA.,Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Margaret T Fuller
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joshua E Elias
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew P Scott
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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45
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Santos-Cortez RLP, Khan V, Khan FS, Mughal ZUN, Chakchouk I, Lee K, Rasheed M, Hamza R, Acharya A, Ullah E, Saqib MAN, Abbe I, Ali G, Hassan MJ, Khan S, Azeem Z, Ullah I, Bamshad MJ, Nickerson DA, Schrauwen I, Ahmad W, Ansar M, Leal SM. Novel candidate genes and variants underlying autosomal recessive neurodevelopmental disorders with intellectual disability. Hum Genet 2018; 137:735-752. [PMID: 30167849 PMCID: PMC6201268 DOI: 10.1007/s00439-018-1928-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/10/2018] [Indexed: 01/30/2023]
Abstract
Identification of Mendelian genes for neurodevelopmental disorders using exome sequencing to study autosomal recessive (AR) consanguineous pedigrees has been highly successful. To identify causal variants for syndromic and non-syndromic intellectual disability (ID), exome sequencing was performed using DNA samples from 22 consanguineous Pakistani families with ARID, of which 21 have additional phenotypes including microcephaly. To aid in variant identification, homozygosity mapping and linkage analysis were performed. DNA samples from affected family member(s) from every pedigree underwent exome sequencing. Identified rare damaging exome variants were tested for co-segregation with ID using Sanger sequencing. For seven ARID families, variants were identified in genes not previously associated with ID, including: EI24, FXR1 and TET3 for which knockout mouse models have brain defects; and CACNG7 and TRAPPC10 where cell studies suggest roles in important neural pathways. For two families, the novel ARID genes CARNMT1 and GARNL3 lie within previously reported ID microdeletion regions. We also observed homozygous variants in two ID candidate genes, GRAMD1B and TBRG1, for which each has been previously reported in a single family. An additional 14 families have homozygous variants in established ID genes, of which 11 variants are novel. All ARID genes have increased expression in specific structures of the developing and adult human brain and 91% of the genes are differentially expressed in utero or during early childhood. The identification of novel ARID candidate genes and variants adds to the knowledge base that is required to further understand human brain function and development.
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Affiliation(s)
- Regie Lyn P Santos-Cortez
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, 1 Baylor Plaza 700D, Houston, TX, 77030, USA
- Department of Otolaryngology, University of Colorado School of Medicine, 12700 E. 19th Ave., Aurora, CO, 80045, USA
| | - Valeed Khan
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Falak Sher Khan
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Zaib-Un-Nisa Mughal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Imen Chakchouk
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, 1 Baylor Plaza 700D, Houston, TX, 77030, USA
| | - Kwanghyuk Lee
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, 1 Baylor Plaza 700D, Houston, TX, 77030, USA
| | - Memoona Rasheed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Rifat Hamza
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Anushree Acharya
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, 1 Baylor Plaza 700D, Houston, TX, 77030, USA
| | - Ehsan Ullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Arif Nadeem Saqib
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Pakistan Health Research Council, Shahrah-e-Jamhuriat, G-5/2, Islamabad, Pakistan
| | - Izoduwa Abbe
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, 1 Baylor Plaza 700D, Houston, TX, 77030, USA
| | - Ghazanfar Ali
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Muhammad Jawad Hassan
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Saadullah Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, KPK, Pakistan
| | - Zahid Azeem
- Department of Biochemistry, Azad Jammu and Kashmir Medical College, Muzaffarabad, Pakistan
| | - Irfan Ullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave. NE, Seattle, WA, 98195, USA
- Department of Pediatrics, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave. NE, Seattle, WA, 98195, USA
| | - Isabelle Schrauwen
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, 1 Baylor Plaza 700D, Houston, TX, 77030, USA
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Suzanne M Leal
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, 1 Baylor Plaza 700D, Houston, TX, 77030, USA.
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46
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Lackey EP, Heck DH, Sillitoe RV. Recent advances in understanding the mechanisms of cerebellar granule cell development and function and their contribution to behavior. F1000Res 2018; 7. [PMID: 30109024 PMCID: PMC6069759 DOI: 10.12688/f1000research.15021.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/20/2018] [Indexed: 12/20/2022] Open
Abstract
The cerebellum is the focus of an emergent series of debates because its circuitry is now thought to encode an unexpected level of functional diversity. The flexibility that is built into the cerebellar circuit allows it to participate not only in motor behaviors involving coordination, learning, and balance but also in non-motor behaviors such as cognition, emotion, and spatial navigation. In accordance with the cerebellum’s diverse functional roles, when these circuits are altered because of disease or injury, the behavioral outcomes range from neurological conditions such as ataxia, dystonia, and tremor to neuropsychiatric conditions, including autism spectrum disorders, schizophrenia, and attention-deficit/hyperactivity disorder. Two major questions arise: what types of cells mediate these normal and abnormal processes, and how might they accomplish these seemingly disparate functions? The tiny but numerous cerebellar granule cells may hold answers to these questions. Here, we discuss recent advances in understanding how the granule cell lineage arises in the embryo and how a stem cell niche that replenishes granule cells influences wiring when the postnatal cerebellum is injured. We discuss how precisely coordinated developmental programs, gene expression patterns, and epigenetic mechanisms determine the formation of synapses that integrate multi-modal inputs onto single granule cells. These data lead us to consider how granule cell synaptic heterogeneity promotes sensorimotor and non-sensorimotor signals in behaving animals. We discuss evidence that granule cells use ultrafast neurotransmission that can operate at kilohertz frequencies. Together, these data inspire an emerging view for how granule cells contribute to the shaping of complex animal behaviors.
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Affiliation(s)
- Elizabeth P Lackey
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA
| | - Detlef H Heck
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, 855 Monroe Avenue, Memphis, TN, 38163, USA
| | - Roy V Sillitoe
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA.,Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
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47
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Wang CX, Cui GS, Liu X, Xu K, Wang M, Zhang XX, Jiang LY, Li A, Yang Y, Lai WY, Sun BF, Jiang GB, Wang HL, Tong WM, Li W, Wang XJ, Yang YG, Zhou Q. METTL3-mediated m6A modification is required for cerebellar development. PLoS Biol 2018; 16:e2004880. [PMID: 29879109 PMCID: PMC6021109 DOI: 10.1371/journal.pbio.2004880] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 06/27/2018] [Accepted: 05/15/2018] [Indexed: 01/26/2023] Open
Abstract
N6-methyladenosine (m6A) RNA methylation is the most abundant modification on mRNAs and plays important roles in various biological processes. The formation of m6A is catalyzed by a methyltransferase complex including methyltransferase-like 3 (METTL3) as a key factor. However, the in vivo functions of METTL3 and m6A modification in mammalian development remain unclear. Here, we show that specific inactivation of Mettl3 in mouse nervous system causes severe developmental defects in the brain. Mettl3 conditional knockout (cKO) mice manifest cerebellar hypoplasia caused by drastically enhanced apoptosis of newborn cerebellar granule cells (CGCs) in the external granular layer (EGL). METTL3 depletion–induced loss of m6A modification causes extended RNA half-lives and aberrant splicing events, consequently leading to dysregulation of transcriptome-wide gene expression and premature CGC death. Our findings reveal a critical role of METTL3-mediated m6A in regulating the development of mammalian cerebellum. N6-methyladenosine (m6A) is an abundant modification in mRNA molecules and regulates mRNA metabolism and various biological processes, such as cell fate control, early embryonic development, sex determination, and diseases like diabetes and obesity. Adenosine methylation is regulated by a large methyltransferase complex and by demethylases, as well as by other binding proteins. METTL3 is one of the core subunits of the methyltransferase complex catalyzing m6A formation. However, the role of METTL3-mediated m6A in mammalian brain development remains unclear mainly because of the lack of specific spatiotemporal knockout animal models, as conventional METTL3 knockout in mice leads to early embryonic death. In this study, we specifically inactivated METTL3 in the developing mouse brain. We detected a drastic depletion of m6A accompanied by severe developmental defects in the cerebellum of these mice. Further analysis established that METTL3-mediated m6A participates in cerebellar development by controlling mRNA stability of genes related to cerebellar development and apoptosis and by regulating alternative splicing of pre-mRNAs of synapse-associated genes.
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Affiliation(s)
- Chen-Xin Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guan-Shen Cui
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
| | - Xiuying Liu
- Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Kai Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Meng Wang
- Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xin-Xin Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Li-Yuan Jiang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Ang Li
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Ying Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Wei-Yi Lai
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Bao-Fa Sun
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Gui-Bin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Hai-Lin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Wei-Min Tong
- Department of Pathology, Center for Experimental Animal Research, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Xiu-Jie Wang
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- * E-mail: (XJW); (YGY); (QZ)
| | - Yun-Gui Yang
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- * E-mail: (XJW); (YGY); (QZ)
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- * E-mail: (XJW); (YGY); (QZ)
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Berger ND, Stanley FKT, Moore S, Goodarzi AA. ATM-dependent pathways of chromatin remodelling and oxidative DNA damage responses. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0283. [PMID: 28847820 DOI: 10.1098/rstb.2016.0283] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2017] [Indexed: 12/14/2022] Open
Abstract
Ataxia-telangiectasia mutated (ATM) is a serine/threonine protein kinase with a master regulatory function in the DNA damage response. In this role, ATM commands a complex biochemical network that signals the presence of oxidative DNA damage, including the dangerous DNA double-strand break, and facilitates subsequent repair. Here, we review the current state of knowledge regarding ATM-dependent chromatin remodelling and epigenomic alterations that are required to maintain genomic integrity in the presence of DNA double-strand breaks and/or oxidative stress. We will focus particularly on the roles of ATM in adjusting nucleosome spacing at sites of unresolved DNA double-strand breaks within complex chromatin environments, and the impact of ATM on preserving the health of cells within the mammalian central nervous system.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- N Daniel Berger
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Fintan K T Stanley
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Shaun Moore
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Aaron A Goodarzi
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Departments of Biochemistry & Molecular Biology and Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4N1
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Jereb S, Hwang HW, Van Otterloo E, Govek EE, Fak JJ, Yuan Y, Hatten ME, Darnell RB. Differential 3' Processing of Specific Transcripts Expands Regulatory and Protein Diversity Across Neuronal Cell Types. eLife 2018; 7:34042. [PMID: 29578408 PMCID: PMC5898910 DOI: 10.7554/elife.34042] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/20/2018] [Indexed: 01/06/2023] Open
Abstract
Alternative polyadenylation (APA) regulates mRNA translation, stability, and protein localization. However, it is unclear to what extent APA regulates these processes uniquely in specific cell types. Using a new technique, cTag-PAPERCLIP, we discovered significant differences in APA between the principal types of mouse cerebellar neurons, the Purkinje and granule cells, as well as between proliferating and differentiated granule cells. Transcripts that differed in APA in these comparisons were enriched in key neuronal functions and many differed in coding sequence in addition to 3’UTR length. We characterize Memo1, a transcript that shifted from expressing a short 3’UTR isoform to a longer one during granule cell differentiation. We show that Memo1 regulates granule cell precursor proliferation and that its long 3’UTR isoform is targeted by miR-124, contributing to its downregulation during development. Our findings provide insight into roles for APA in specific cell types and establish a platform for further functional studies.
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Affiliation(s)
- Saša Jereb
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Hun-Way Hwang
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Eric Van Otterloo
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Eve-Ellen Govek
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, United States
| | - John J Fak
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Yuan Yuan
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Mary E Hatten
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, United States
| | - Robert B Darnell
- Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, United States
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50
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Zhou H, Wang B, Sun H, Xu X, Wang Y. Epigenetic Regulations in Neural Stem Cells and Neurological Diseases. Stem Cells Int 2018; 2018:6087143. [PMID: 29743892 PMCID: PMC5878882 DOI: 10.1155/2018/6087143] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 01/08/2018] [Indexed: 12/17/2022] Open
Abstract
Among the regulatory mechanisms of the renewal and differentiation of neural stem cells, recent evidences support that epigenetic modifications such as DNA methylation, histone modification, and noncoding RNAs play critical roles in the regulation on the proliferation and differentiation of neural stem cells. In this review, we discussed recent advances of DNA modifications on the regulative mechanisms of neural stem cells. Among these epigenetic modifications, DNA 5-hydroxymethylcytosine (5hmC) modification is emerging as an important modulator on the proliferation and differentiation of neural stem cells. At the same time, Ten-eleven translocation (Tet) methylcytosine dioxygenases, the rate-limiting enzyme for the 5-hydroxymethylation reaction from 5-methylcytosine to 5-hydroxymethylcytosine, play a critical role in the tumorigenesis and the proliferation and differentiation of stem cells. The functions of 5hmC and TET proteins on neural stem cells and their roles in neurological diseases are discussed.
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Affiliation(s)
- Hang Zhou
- Department of Neurology, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Bin Wang
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Hao Sun
- Department of Orthopedics, Clinical Medical School, Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou 225001, China
| | - Xingshun Xu
- Department of Neurology, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Neuroscience, Soochow University, Suzhou, China
| | - Yongxiang Wang
- Department of Orthopedics, Clinical Medical School, Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou 225001, China
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