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Singh M, Saxena S, Mohan KN. DNMT1 downregulation as well as its overexpression distinctly affect mostly overlapping genes implicated in schizophrenia, autism spectrum, epilepsy, and bipolar disorders. Front Mol Neurosci 2023; 16:1275697. [PMID: 38125006 PMCID: PMC10731955 DOI: 10.3389/fnmol.2023.1275697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023] Open
Abstract
Data on schizophrenia (SZ), epilepsy (EPD) and bipolar disorders (BPD) suggested an association of DNMT1 overexpression whereas certain variants of the gene were predicted to result in its increased expression in autism spectrum disorder (ASD). In addition, loss of DNMT1 in frontal cortex resulted in behavioral abnormalities in mice. Here we investigated the effects of increased as well as lack of DNMT1 expression using Dnmt1tet/tet neurons as a model for abnormal neurogenesis and 10,861 genes showing transcript level dysregulation in datasets from the four disorders. In case of overexpression, 3,211 (∼ 30%) genes were dysregulated, affecting pathways involved in neurogenesis, semaphorin signaling, ephrin receptor activity, etc. A disproportionately higher proportion of dysregulated genes were associated with epilepsy. When transcriptome data of Dnmt1tet/tet neurons treated with doxycycline that downregulated DNMT1 was used, 3,356 genes (∼31%) were dysregulated with a significant proportion involved in pathways similar to those in untreated cells. Both conditions resulted in ∼68% of dysregulated genes wherein a majority showed similar patterns of transcript level changes. Among the genes with transcripts returning to normal levels, ribosome assembly/biogenesis was most significant whereas in absence of DNMT1, a new set of 903 genes became dysregulated and are involved in similar pathways as mentioned above. These findings provide support for overexpression of DNMT1 as well as its downregulation as risk factor for the four disorders and that its levels within a tight range are essential for normal neurodevelopment/mental health.
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Affiliation(s)
- Minali Singh
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad, India
| | - Sonal Saxena
- Centre for Human Disease Research, Birla Institute of Technology and Science, Pilani, Hyderabad, India
| | - Kommu Naga Mohan
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad, India
- Centre for Human Disease Research, Birla Institute of Technology and Science, Pilani, Hyderabad, India
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2
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Mohan KN. DNMT1: catalytic and non-catalytic roles in different biological processes. Epigenomics 2022; 14:629-643. [PMID: 35410490 DOI: 10.2217/epi-2022-0035] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
DNMT1 is the main enzyme that uses the information on DNA methylation patterns in the parent strand and methylates the daughter strand in freshly replicated hemimethylated DNA. It is widely known that DNMT1 is a component of the epigenetic machinery mediating gene repression via increased promoter methylation. However, recent data suggest that DNMT1 can also modulate gene expression independent of its catalytic activity and participates in multiple processes including the cell cycle, DNA damage repair and stem cell function. This review summarizes the noncanonical functions of DNMT1, some of which are clearly independent of maintenance methylation. Finally, phenotypic data on altered DNMT1 levels suggesting that maintenance of optimal levels of DNMT1 is vital for normal development and health is presented.
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Affiliation(s)
- Kommu Naga Mohan
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500078, India
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3
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Chen S, Xu D, Fan L, Fang Z, Wang X, Li M. Roles of N-Methyl-D-Aspartate Receptors (NMDARs) in Epilepsy. Front Mol Neurosci 2022; 14:797253. [PMID: 35069111 PMCID: PMC8780133 DOI: 10.3389/fnmol.2021.797253] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022] Open
Abstract
Epilepsy is one of the most common neurological disorders characterized by recurrent seizures. The mechanism of epilepsy remains unclear and previous studies suggest that N-methyl-D-aspartate receptors (NMDARs) play an important role in abnormal discharges, nerve conduction, neuron injury and inflammation, thereby they may participate in epileptogenesis. NMDARs belong to a family of ionotropic glutamate receptors that play essential roles in excitatory neurotransmission and synaptic plasticity in the mammalian CNS. Despite numerous studies focusing on the role of NMDAR in epilepsy, the relationship appeared to be elusive. In this article, we reviewed the regulation of NMDAR and possible mechanisms of NMDAR in epilepsy and in respect of onset, development, and treatment, trying to provide more evidence for future studies.
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Li Y, Cao J, Hao Z, Liu A, Li X, Li H, Xia N, Wang Z, Zhang Z, Bai J, Zhang H. Aspirin ameliorates the cognition impairment in mice following benzo[a]pyrene treatment via down-regulating BDNF IV methylation. Neurotoxicology 2021; 89:20-30. [PMID: 34979192 DOI: 10.1016/j.neuro.2021.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/14/2021] [Accepted: 12/29/2021] [Indexed: 12/19/2022]
Abstract
Benzo[a]pyrene (B[a]P) is neurotoxic, however, the mechanisms remain unclear and there is no effective prevention. Available evidence suggests a role of DNA methylation in B[a]P-induced neurotoxicity. This study investigated the brain-derived neurotrophic factor (BDNF) IV methylation in the development of and aspirin intervention against B[a]P's neurotoxicity in mice and HT22 cells. Mice were intraperitoneally treated with solvent or B[a]P (0.5, 2, and 10 mg/kg b.w.) for 60 days. An intervention group was treated simultaneously with B[a]P (10 mg/kg, i.p.) and aspirin (10 mg/kg, daily water-drinking). The treated mice showed a dose-dependent cognitive and behavioral impairment, and cerebral cell apoptosis, which were alleviated by aspirin co-treatment. Following B[a]P treatment, DNA methyltransferase (DNMTs) and BDNF IV hypermethylation were increased in the cerebral cortex of mice compared to controls, while significant decreases were found in BDNF IV and BDNF mRNA, and BDNF protein levels. Aspirin co-treatment rescued DNMTs activation and BDNF IV hypermethylation, and mitigated the recession in BDNF mRNA and protein induced by B[a]P treatment. Similar results were shown in HT22 cells. These findings reveal a critical role of BDNF IV methylation in the neurotoxicity of B[a]P, and demonstrate a promising prevention of aspirin against B[a]P-induced cognitive impairment via inhibiting BDNF IV hypermethylation.
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Affiliation(s)
- Yangyang Li
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Jingjing Cao
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Zhongsuo Hao
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Aixiang Liu
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Xin Li
- Center of Disease Control and Prevention, Taiyuan Iron and Steel Company, Taiyuan, 030003, Shanxi, China
| | - Huan Li
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Na Xia
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Zemin Wang
- Laboratory of Investigative Toxicology and Pathology, Department of Environmental Health, Indiana University School of Public Health, 1025 E 7th St, Bloomington, IN, 47405, USA
| | - Zhihong Zhang
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Jianying Bai
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Hongmei Zhang
- Department of Environmental Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, Shanxi, China; Key Laboratory of Cellular Physiology (Shanxi Medical University), Ministry of Education, Taiyuan, 030001, Shanxi, China; Key Laboratory of Cellular Physiology, Shanxi Province, Taiyuan, 030001, Shanxi, China; Department of Physiology, Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
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5
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Saxena S, Choudhury S, Maroju PA, Anne A, Kumar L, Mohan KN. Dysregulation of schizophrenia-associated genes and genome-wide hypomethylation in neurons overexpressing DNMT1. Epigenomics 2021; 13:1539-1555. [PMID: 34647491 DOI: 10.2217/epi-2021-0133] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To study the effects of DNMT1 overexpression on transcript levels of genes dysregulated in schizophrenia and on genome-wide methylation patterns. Materials & methods: Transcriptome and DNA methylome comparisons were made between R1 (wild-type) and Dnmt1tet/tet mouse embryonic stem cells and neurons overexpressing DNMT1. Genes dysregulated in both Dnmt1tet/tet cells and schizophrenia patients were studied further. Results & conclusions: About 50% of dysregulated genes in patients also showed altered transcript levels in Tet/Tet neurons in a DNA methylation-independent manner. These neurons unexpectedly showed genome-wide hypomethylation, increased transcript levels of Tet1 and Apobec 1-3 genes and increased activity and copy number of LINE-1 elements. The observed similarities between Tet/Tet neurons and schizophrenia brain samples reinforce DNMT1 overexpression as a risk factor.
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Affiliation(s)
- Sonal Saxena
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Sumana Choudhury
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Pranay Amruth Maroju
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Anuhya Anne
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Lov Kumar
- Computer Science & Information Systems, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Kommu Naga Mohan
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
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Analysis of transcript levels of a few schizophrenia candidate genes in neurons from a transgenic mouse embryonic stem cell model overexpressing DNMT1. Gene 2020; 757:144934. [PMID: 32640307 DOI: 10.1016/j.gene.2020.144934] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/23/2020] [Accepted: 07/01/2020] [Indexed: 02/08/2023]
Abstract
Overexpression of DNA Methyltransferase I (DNMT1) is considered as one of the etiological factors for schizophrenia (SZ). However, information on genes subjected to dysregulation because of DNMT1 overexpression is limited. To test whether a larger group of SZ-associated genes are affected, we selected 15 genes reported to be dysregulated in patients (Gad1, Reln, Ank3, Cacna1c, Dkk3, As3mt, Ppp1r11, Smad5, Syn1, Wnt1, Pdgfra, Gsk3b, Cxcl12, Tcf4 and Fez1). Transcript levels of these genes were compared between neurons derived from Dnmt1tet/tet (Tet/Tet) mouse embryonic stem cells (ESCs) that overexpress DNMT1 with R1 (wild-type) neurons. Transcript levels of thirteen genes were significantly altered in Tet/Tet neurons of which, the dysregulation patterns of 11 were similar to patients. Transcript levels of eight out of these eleven were also significantly altered in Tet/Tet ESCs, but the dysregulation patterns of only five were similar to neurons. Comparative analyses among ESCs, embryoid bodies and neurons divided the 15 genes into four distinct groups with a majority showing developmental stage-specific patterns of dysregulation. Reduced Representational Bisulfite Sequencing data from neurons did not show any altered promoter DNA methylation for the dysregulated genes. Doxycycline treatment of Tet/Tet ESCs that eliminated DNMT1, reversed the direction of dysregulation of only four genes (Gad1, Dkk3, As3mt and Syn1). These results suggest that 1. Increased DNMT1 affected the levels of a majority of the transcripts studied, 2. Dysregulation appears to be independent of promoter methylation, 3. Effects of increased DNMT1 levels were reversible for only a subset of the genes studied, and 4. Increased DNMT1 levels may affect transcript levels of multiple schizophrenia-associated genes.
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7
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Saxena S, Choudhury S, Mohan KN. Genome-wide methylation data from R1 (wild-type) and the transgenic Dnmt1Tet/Tet mouse embryonic stem cells overexpressing DNA methyltransferase 1 (DNMT1). Data Brief 2020; 32:106242. [PMID: 32944600 PMCID: PMC7481814 DOI: 10.1016/j.dib.2020.106242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 08/25/2020] [Indexed: 12/23/2022] Open
Abstract
Defects in epigenetic mechanisms are well-recognized in multiple neurodevelopmental disorders including Schizophrenia (SZ). In addition to aberrant epigenetic marks, dysregulated epigenetic machinery was also identified among the contributory factors in SZ patients. Among these, overexpression of DNA methyltransferase 1 (DNMT1) was the first to be identified. In this context, Dnmt1tet/tet (Tet/Tet), a mouse embryonic stem cell (ESC) line that overexpresses DNMT1 in ESCs and neurons, was developed to study abnormal neurogenesis. In an attempt to understand whether DNMT1 overexpression is associated with aberrant DNA methylation, we compared the genome-wide methylation levels of R1 (wild-type) and Tet/Tet ESCs and their neuronal derivatives by RRBS. The RRBS data (GSE152817) showed an average mappability of ∼59% and an average coverage of 40X per locus. The data was processed to determine the methylation percentages of target genes and was visualized using the UCSC genome browser. The observed methylation differences were validated by Combined Bisulfite Restriction Analysis (COBRA). The methylome data described here can be used to study the relationship between DNMT1 overexpression, alterations in methylation levels and dysregulation of SZ-associated genes.
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Affiliation(s)
| | | | - K. Naga Mohan
- Department of Biological Sciences, BITS Pilani Hyderabad Campus, Jawahar Nagar, Hyderabad 500078, India
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8
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Dysregulation of Epigenetic Control Contributes to Schizophrenia-Like Behavior in Ebp1 +/- Mice. Int J Mol Sci 2020; 21:ijms21072609. [PMID: 32283721 PMCID: PMC7178112 DOI: 10.3390/ijms21072609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 11/17/2022] Open
Abstract
Dysregulation of epigenetic machinery can cause a variety of neurological disorders associated with cognitive abnormalities. In the hippocampus of postmortem Schizophrenia (SZ) patients, the most notable finding is the deregulation of GAD67 along with differential regulation of epigenetic factors associated with glutamate decarboxylase 67 (GAD67) expression. As we previously reported, ErbB3-binding protein 1 (EBP1) is a potent epigenetic regulator. EBP1 can induce repression of Dnmt1, a well-studied transcriptional repressor of GAD67. In this study, we investigated whether EBP1 contributes to the regulation of GAD67 expression in the hippocampus, controlling epigenetic machinery. In accordance with SZ-like behaviors in Ebp1(+/−) mice, heterozygous deletion of EBP1 led to a dramatic reduction of GAD67 expression, reflecting an abnormally high level of Dnmt1. Moreover, we found that EBP1 binds to the promoter region of HDAC1, which leads to histone deacetylation of GAD67, and suppresses histone deacetylase 1 (HDAC1) expression, inversely mirroring an unusually high level of HDAC1 in Ebp1(+/−) mice. However, EBP1 mutant (p.Glu 183 Ter) found in SZ patients did not elevate the expression of GAD67, failing to suppress Dnmt1 and/or HDAC1 expression. Therefore, this data supports the hypothesis that a reduced amount of EBP1 may contribute to an etiology of SZ due to a loss of transcriptional inhibition of epigenetic repressors, leading to a decreased expression of GAD67.
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Kawahori K, Hashimoto K, Yuan X, Tsujimoto K, Hanzawa N, Hamaguchi M, Kase S, Fujita K, Tagawa K, Okazawa H, Nakajima Y, Shibusawa N, Yamada M, Ogawa Y. Mild Maternal Hypothyroxinemia During Pregnancy Induces Persistent DNA Hypermethylation in the Hippocampal Brain-Derived Neurotrophic Factor Gene in Mouse Offspring. Thyroid 2018; 28:395-406. [PMID: 29415629 DOI: 10.1089/thy.2017.0331] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Thyroid hormones are essential for normal development of the central nervous system (CNS). Experimental rodents have shown that even a subtle thyroid hormone insufficiency in circulating maternal thyroid hormones during pregnancy may adversely affect neurodevelopment in offspring, resulting in irreversible cognitive deficits. This may be due to the persistent reduced expression of the hippocampal brain-derived neurotrophic factor gene Bdnf, which plays a crucial role in CNS development. However, the underlying molecular mechanisms remain unclear. METHODS Thiamazole (MMI; 0.025% [w/v]) was administered to dams from two weeks prior to conception until delivery, which succeeded in inducing mild maternal hypothyroxinemia during pregnancy. Serum thyroid hormone and thyrotropin levels of the offspring derived from dams with mild maternal hypothyroxinemia (M offspring) and the control offspring (C offspring) were measured. At 70 days after birth, several behavior tests were performed on the offspring. Gene expression and DNA methylation status were also evaluated in the promoter region of Bdnf exon IV, which is largely responsible for neural activity-dependent Bdnf gene expression, in the hippocampus of the offspring at day 28 and day 70. RESULTS No significant differences in serum thyroid hormone or thyrotropin levels were found between M and C offspring at day 28 and day 70. M offspring showed an impaired learning capacity in the behavior tests. Hippocampal steady-state Bdnf exon IV expression was significantly weaker in M offspring than it was in C offspring at day 28. At day 70, hippocampal Bdnf exon IV expression at the basal level was comparable between M and C offspring. However, it was significantly weaker in M offspring than in C offspring after the behavior tests. Persistent DNA hypermethylation was also found in the promoter region of Bdnf exon IV in the hippocampus of M offspring compared to that of C offspring, which may cause the attenuation of Bdnf exon IV expression in M offspring. CONCLUSIONS Mild maternal hypothyroxinemia induces persistent DNA hypermethylation in Bdnf exon IV in offspring as epigenetic memory, which may result in long-term cognitive disorders.
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Affiliation(s)
- Kenichi Kawahori
- 1 Department of Molecular Endocrinology and Metabolism, Tokyo Medical and Dental University , Tokyo, Japan
| | - Koshi Hashimoto
- 2 Department of Preemptive Medicine and Metabolism, Tokyo Medical and Dental University , Tokyo, Japan
| | - Xunmei Yuan
- 3 Department of Molecular and Cellular Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University , Tokyo, Japan
| | - Kazutaka Tsujimoto
- 1 Department of Molecular Endocrinology and Metabolism, Tokyo Medical and Dental University , Tokyo, Japan
| | - Nozomi Hanzawa
- 1 Department of Molecular Endocrinology and Metabolism, Tokyo Medical and Dental University , Tokyo, Japan
| | - Miho Hamaguchi
- 3 Department of Molecular and Cellular Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University , Tokyo, Japan
| | - Saori Kase
- 1 Department of Molecular Endocrinology and Metabolism, Tokyo Medical and Dental University , Tokyo, Japan
| | - Kyota Fujita
- 4 Department of Neuropathology, Medical Research Institute and Center for Brain Integration Research, Tokyo Medical and Dental University , Tokyo, Japan
| | - Kazuhiko Tagawa
- 4 Department of Neuropathology, Medical Research Institute and Center for Brain Integration Research, Tokyo Medical and Dental University , Tokyo, Japan
| | - Hitoshi Okazawa
- 4 Department of Neuropathology, Medical Research Institute and Center for Brain Integration Research, Tokyo Medical and Dental University , Tokyo, Japan
| | - Yasuyo Nakajima
- 5 Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine , Gunma, Japan
| | - Nobuyuki Shibusawa
- 5 Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine , Gunma, Japan
| | - Masanobu Yamada
- 5 Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine , Gunma, Japan
| | - Yoshihiro Ogawa
- 3 Department of Molecular and Cellular Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University , Tokyo, Japan
- 6 Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University , Fukuoka, Japan
- 7 Japan Agency for Medical Research and Development , CREST, Tokyo, Japan
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10
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Mata‐Balaguer T, Cuchillo‐Ibañez I, Calero M, Ferrer I, Sáez‐Valero J. Decreased generation of C‐terminal fragments of ApoER2 and increased reelin expression in Alzheimer's disease. FASEB J 2018; 32:3536-3546. [DOI: 10.1096/fj.201700736rr] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Trinidad Mata‐Balaguer
- Instituto de Neurociencias de AlicanteUniversidad Miguel Hernández‐Consejo Superior de Investigaciones Cientificas (CSIC)Sant Joan d'AlacantAlicanteSpain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)MadridSpain
| | - Inmaculada Cuchillo‐Ibañez
- Instituto de Neurociencias de AlicanteUniversidad Miguel Hernández‐Consejo Superior de Investigaciones Cientificas (CSIC)Sant Joan d'AlacantAlicanteSpain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)MadridSpain
| | - Miguel Calero
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)MadridSpain
- Alzheimer Disease Research UnitCentro Nacional de Investigación en Enfermedades Neurológicas (CIEN) FoundationQueen Sofia Foundation Alzheimer CenterMadridSpain
- Chronic Disease ProgrammeCarlos III Institute of HealthMadridSpain
| | - Isidro Ferrer
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)MadridSpain
- Instituto de NeuropatologíaHospital Universitario de BellvitgeUniversidad de BarcelonaHospitalet de LlobregatBarcelonaSpain
| | - Javier Sáez‐Valero
- Instituto de Neurociencias de AlicanteUniversidad Miguel Hernández‐Consejo Superior de Investigaciones Cientificas (CSIC)Sant Joan d'AlacantAlicanteSpain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)MadridSpain
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Stem Cell Models to Investigate the Role of DNA Methylation Machinery in Development of Neuropsychiatric Disorders. Stem Cells Int 2015; 2016:4379425. [PMID: 26798355 PMCID: PMC4699075 DOI: 10.1155/2016/4379425] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/10/2015] [Indexed: 12/13/2022] Open
Abstract
Epigenetic mechanisms underlie differentiation of pluripotent stem cells into different lineages that contain identical genomes but express different sets of cell type-specific genes. Because of high discordance rates in monozygotic twins, epigenetic mechanisms are also implicated in development of neuropsychiatric disorders such as schizophrenia and autism. In support of this notion, increased levels of DNA methyltransferases (DNMTs), DNMT polymorphisms, and dysregulation of DNA methylation network were reported among schizophrenia patients. These results point to the importance of development of DNA methylation machinery-based models for studying the mechanism of abnormal neurogenesis due to certain DNMT alleles or dysregulated DNMTs. Achieving this goal is strongly confronted by embryonic lethality associated with altered levels of epigenetic machinery such as DNMT1 and expensive approaches in developing in vivo models. In light of literature evidence that embryonic stem cells (ESCs) are tolerant of DNMT mutations and advancement in the technology of gene targeting, it is now possible to introduce desired mutations in DNMT loci to generate suitable ESC lines that can help understand the underlying mechanisms by which abnormal levels of DNMTs or their specific mutations/alleles result in abnormal neurogenesis. In the future, these models can facilitate development of suitable drugs for treatment of neuropsychiatric disorders.
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Nasonkin IO, Merbs SL, Lazo K, Oliver VF, Brooks M, Patel K, Enke RA, Nellissery J, Jamrich M, Le YZ, Bharti K, Fariss RN, Rachel RA, Zack DJ, Rodriguez-Boulan EJ, Swaroop A. Conditional knockdown of DNA methyltransferase 1 reveals a key role of retinal pigment epithelium integrity in photoreceptor outer segment morphogenesis. Development 2013; 140:1330-41. [PMID: 23406904 DOI: 10.1242/dev.086603] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Dysfunction or death of photoreceptors is the primary cause of vision loss in retinal and macular degenerative diseases. As photoreceptors have an intimate relationship with the retinal pigment epithelium (RPE) for exchange of macromolecules, removal of shed membrane discs and retinoid recycling, an improved understanding of the development of the photoreceptor-RPE complex will allow better design of gene- and cell-based therapies. To explore the epigenetic contribution to retinal development we generated conditional knockout alleles of DNA methyltransferase 1 (Dnmt1) in mice. Conditional Dnmt1 knockdown in early eye development mediated by Rx-Cre did not produce lamination or cell fate defects, except in cones; however, the photoreceptors completely lacked outer segments despite near normal expression of phototransduction and cilia genes. We also identified disruption of RPE morphology and polarization as early as E15.5. Defects in outer segment biogenesis were evident with Dnmt1 exon excision only in RPE, but not when excision was directed exclusively to photoreceptors. We detected a reduction in DNA methylation of LINE1 elements (a measure of global DNA methylation) in developing mutant RPE as compared with neural retina, and of Tuba3a, which exhibited dramatically increased expression in mutant retina. These results demonstrate a unique function of DNMT1-mediated DNA methylation in controlling RPE apicobasal polarity and neural retina differentiation. We also establish a model to study the epigenetic mechanisms and signaling pathways that guide the modulation of photoreceptor outer segment morphogenesis by RPE during retinal development and disease.
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Affiliation(s)
- Igor O Nasonkin
- 1Neurobiology-Neurodegeneration and Repair Laboratory (N-NRL), National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Sheikh MA, Malik YS, Yu H, Lai M, Wang X, Zhu X. Epigenetic regulation of Dpp6 expression by Dnmt3b and its novel role in the inhibition of RA induced neuronal differentiation of P19 cells. PLoS One 2013; 8:e55826. [PMID: 23409053 PMCID: PMC3567024 DOI: 10.1371/journal.pone.0055826] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 01/02/2013] [Indexed: 12/05/2022] Open
Abstract
DNA methylation is an important mechanism of gene silencing in mammals catalyzed by a group of DNA methyltransferases including Dnmt1, Dnmt3a, and Dnmt3b which are required for the establishment of genomic methylation patterns during development and differentiation. In this report, we studied the role of DNA methyltransferases during retinoic acid induced neuronal differentiation of P19 cells. We observed an increase in the mRNA and protein level of Dnmt3b, whereas the expression of Dnmt1 and Dnmt3a was decreased after RA treatment of P19 cells which indicated that Dnmt3b is more important during neuronal differentiation of P19 cells. Dnmt3b enriched chromatin library from RA treated P19 cells identified dipeptidyl peptidase 6 (Dpp6) gene as a novel target of Dnmt3b. Further, quantitative ChIP analysis showed that the amount of Dnmt3b recruited on Dpp6 promoter was equal in both RA treated as well as untreated p19 cells. Bisulfite genomic sequencing, COBRA, and methylation specific PCR analysis revealed that Dpp6 promoter was heavily methylated in both RA treated and untreated P19 cells. Dnmt3b was responsible for transcriptional silencing of Dpp6 gene as depletion of Dnmt3b resulted in increased mRNA and protein expression of Dpp6. Consequently, the average methylation of Dpp6 gene promoter was reduced to half in Dnmt3b knockdown cells. In the absence of Dnmt3b, Dnmt3a was associated with Dpp6 gene promoter and regulated its expression and methylation in P19 cells. RA induced neuronal differentiation was inhibited upon ectopic expression of Dpp6 in P19 cells. Taken together, the present study described epigenetic silencing of Dpp6 expression by DNA methylation and established that its ectopic expression can act as negative signal during RA induced neuronal differentiation of P19 cells.
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Affiliation(s)
- Muhammad Abid Sheikh
- Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Yousra Saeed Malik
- Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Huali Yu
- Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Mingming Lai
- Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Xingzhi Wang
- Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Xiaojuan Zhu
- Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
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14
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D'Aiuto L, Di Maio R, Heath B, Raimondi G, Milosevic J, Watson AM, Bamne M, Parks WT, Yang L, Lin B, Miki T, Mich-Basso JD, Arav-Boger R, Sibille E, Sabunciyan S, Yolken R, Nimgaonkar V. Human induced pluripotent stem cell-derived models to investigate human cytomegalovirus infection in neural cells. PLoS One 2012; 7:e49700. [PMID: 23209593 PMCID: PMC3507916 DOI: 10.1371/journal.pone.0049700] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 10/12/2012] [Indexed: 11/18/2022] Open
Abstract
Human cytomegalovirus (HCMV) infection is one of the leading prenatal causes of congenital mental retardation and deformities world-wide. Access to cultured human neuronal lineages, necessary to understand the species specific pathogenic effects of HCMV, has been limited by difficulties in sustaining primary human neuronal cultures. Human induced pluripotent stem (iPS) cells now provide an opportunity for such research. We derived iPS cells from human adult fibroblasts and induced neural lineages to investigate their susceptibility to infection with HCMV strain Ad169. Analysis of iPS cells, iPS-derived neural stem cells (NSCs), neural progenitor cells (NPCs) and neurons suggests that (i) iPS cells are not permissive to HCMV infection, i.e., they do not permit a full viral replication cycle; (ii) Neural stem cells have impaired differentiation when infected by HCMV; (iii) NPCs are fully permissive for HCMV infection; altered expression of genes related to neural metabolism or neuronal differentiation is also observed; (iv) most iPS-derived neurons are not permissive to HCMV infection; and (v) infected neurons have impaired calcium influx in response to glutamate.
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Affiliation(s)
- Leonardo D'Aiuto
- Western Psychiatric Institute and Clinic, Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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15
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Kordi-Tamandani DM, Dahmardeh N, Torkamanzehi A. Evaluation of hypermethylation and expression pattern of GMR2, GMR5, GMR8, and GRIA3 in patients with schizophrenia. Gene 2012; 515:163-6. [PMID: 23149219 DOI: 10.1016/j.gene.2012.10.075] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Revised: 10/11/2012] [Accepted: 10/30/2012] [Indexed: 11/26/2022]
Abstract
UNLABELLED Emerging evidence suggests a role of dysfunction of glutamatergic neurotransmission and its receptors in the pathophysiology of schizophrenia (SCZ). This study evaluated whether the promoter hypermethylation and RNA expression pattern of GMR2 (glutamate metabotropic receptor), GMR5, GMR8, and GRIA3 (glutamate receptor, ionotropic alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) are associated with the risk of schizophrenia between schizophrenia patients and healthy controls. MATERIALS AND METHODS Methylation-specific polymerase chain reaction (MS-PCR) was used to estimate the promoter hypermethylation of GMR2, GMR5, GMR8, and GRIA3 genes on 81 isolated genomic DNA samples from the peripheral blood of individuals with schizophrenia and 71 healthy control subjects. In addition, real-time reverse transcription-PCR was used to estimate mRNA levels in 34 blood samples of healthy controls and cases. RESULTS The methylation of GRM2 and GRM5 greatly decreased the risk of schizophrenia in comparison to the reference unmethylated pattern [OR=0.38, 95% CI; 0.144-1.035, p=0.05; OR=0.06, 95% CI; 0.007-0.54.10, p=0.01], respectively. The methylation of GRIA3 highly increased the risk of schizophrenia, but non-significant (OR=2.3, 95% CI; 0.51-10.42). The outcomes of the expression analysis revealed a statistically significant difference between the cases (n=17) and healthy controls (n=17) regarding the relative gene expression of GRM2, GRM5, and GRIA3 (p=0.0001). CONCLUSION To the best of our knowledge, this is the first evidence showing that the promoter methylation of the GMR2 and GMR5 genes greatly decreased the risk of schizophrenia, and the expression level of the GRM2, GRM5, and GRIA3 genes increased significantly in patients in comparison to healthy controls. These outcomes suggest that there is a need for more attention to be paid to the effect of epigenetic variations in the development of SCZ in further investigations.
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