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Tsiami F, Lago C, Pozza N, Piccioni F, Zhao X, Lülsberg F, Root DE, Tiberi L, Kool M, Schittenhelm J, Bandopadhayay P, Segal RA, Tabatabai G, Merk DJ. Genome-wide CRISPR-Cas9 knockout screens identify DNMT1 as a druggable dependency in sonic hedgehog medulloblastoma. Acta Neuropathol Commun 2024; 12:125. [PMID: 39107797 PMCID: PMC11304869 DOI: 10.1186/s40478-024-01831-x] [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: 04/15/2024] [Accepted: 07/09/2024] [Indexed: 08/10/2024] Open
Abstract
Sonic hedgehog subgroup of medulloblastoma (SHH-MB) is characterized by aberrant activation of the SHH signaling pathway. An inhibition of the positive SHH regulator Smoothened (SMO) has demonstrated promising clinical efficacy. Yet, primary and acquired resistance to SMO inhibitors limit their efficacy. An understanding of underlying molecular mechanisms of resistance to therapy is warranted to bridge this unmet need. Here, we make use of genome-wide CRISPR-Cas9 knockout screens in murine SMB21 and human DAOY cells, in order to unravel genetic dependencies and drug-related genetic interactors that could serve as alternative therapeutic targets for SHH-MB. Our screens reinforce SMB21 cells as a faithful model system for SHH-MB, as opposed to DAOY cells, and identify members of the epigenetic machinery including DNA methyltransferase 1 (DNMT1) as druggable targets in SHH-dependent tumors. We show that Dnmt1 plays a crucial role in normal murine cerebellar development and is required for SHH-MB growth in vivo. Additionally, DNMT1 pharmacological inhibition alone and in combination with SMO inhibition effectively inhibits tumor growth in murine and human SHH-MB cell models and prolongs survival of SHH-MB mouse models by inhibiting SHH signaling output downstream of SMO. In conclusion, our data highlight the potential of inhibiting epigenetic regulators as a novel therapeutic avenue in SMO-inhibitor sensitive as well as resistant SHH-MBs.
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Affiliation(s)
- Foteini Tsiami
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, University Hospital Tübingen, Eberhard Karls University, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University, Tübingen, Germany
| | - Chiara Lago
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, CIBIO, Trento, Italy
| | - Noemi Pozza
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, CIBIO, Trento, Italy
| | - Federica Piccioni
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Merck Research Laboratories, Cambridge, MA, USA
| | - Xuesong Zhao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Fabienne Lülsberg
- Institute for Anatomy, Anatomy and Cell Biology, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - David E Root
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Luca Tiberi
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, CIBIO, Trento, Italy
| | - Marcel Kool
- Hopp Children's Cancer Center (KITZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Research Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jens Schittenhelm
- Department of Pathology and Neuropathology, Institute of Neuropathology, University Hospital Tübingen, Eberhard Karls University, Tübingen, Germany
- Comprehensive Cancer Center Tübingen Stuttgart, University Hospital Tübingen, Eberhard Karls University, Tübingen, Germany
| | - Pratiti Bandopadhayay
- Dana-Farber/Boston Children´S Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Rosalind A Segal
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Ghazaleh Tabatabai
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, University Hospital Tübingen, Eberhard Karls University, Tübingen, Germany
- Comprehensive Cancer Center Tübingen Stuttgart, University Hospital Tübingen, Eberhard Karls University, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University, Tübingen, Germany
- German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), Partner Site Tübingen, Heidelberg, Germany
| | - Daniel J Merk
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, University Hospital Tübingen, Eberhard Karls University, Tübingen, Germany.
- Cluster of Excellence iFIT (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University, Tübingen, Germany.
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2
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Alberca CD, Georgieff EI, Berardino BG, Ferroni NM, Fesser EA, Cantarelli VI, Ponzio MF, Cánepa ET, Chertoff M. Perinatal protein malnutrition alters maternal behavior and leads to maladaptive stress response, neurodevelopmental delay and disruption on DNA methylation machinery in female mice offspring. Horm Behav 2024; 164:105603. [PMID: 39029339 DOI: 10.1016/j.yhbeh.2024.105603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/21/2024] [Accepted: 07/09/2024] [Indexed: 07/21/2024]
Abstract
Deficiencies in maternal nutrition have long-term consequences affecting brain development of the progeny and its behavior. In the present work, female mice were exposed to a normal-protein or a low-protein diet during gestation and lactation. We analyzed behavioral and molecular consequences of malnutrition in dams and how it affects female offspring at weaning. We have observed that a low-protein diet during pregnancy and lactation leads to anxiety-like behavior and anhedonia in dams. Protein malnutrition during the perinatal period delays physical and neurological development of female pups. Glucocorticoid levels increased in the plasma of malnourished female offspring but not in dams when compared to the control group. Interestingly, the expression of glucocorticoid receptor (GR) was reduced in hippocampus and amygdala on both malnourished dams and female pups. In addition, malnourished pups exhibited a significant increase in the expression of Dnmt3b, Gadd45b, and Fkbp5 and a reduction in Bdnf VI variant mRNA in hippocampus. In contrast, a reduction on Dnmt3b has been observed on the amygdala of weaned mice. No changes have been observed on global methylation levels (5-methylcytosine) in hippocampal genomic DNA neither in dams nor female offspring. In conclusion, deregulated behaviors observed in malnourished dams might be mediated by a low expression of GR in brain regions associated with emotive behaviors. Additionally, low-protein diet differentially deregulates the expression of genes involved in DNA methylation/demethylation machinery in female offspring but not in dams, providing an insight into regional- and age-specific mechanisms due to protein malnutrition.
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Affiliation(s)
- Carolina D Alberca
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Erika I Georgieff
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Bruno G Berardino
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nadina M Ferroni
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Estefanía A Fesser
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Verónica I Cantarelli
- Instituto de Fisiología, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, e Instituto de Investigaciones en Ciencias de la Salud (INICSA; CONICET-UNC), Santa Rosa 1085, X5000ESU Córdoba, Argentina
| | - Marina F Ponzio
- Instituto de Fisiología, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, e Instituto de Investigaciones en Ciencias de la Salud (INICSA; CONICET-UNC), Santa Rosa 1085, X5000ESU Córdoba, Argentina
| | - Eduardo T Cánepa
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariela Chertoff
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina.
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3
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Zhang J, Tian Z, Qin C, Momeni MR. The effects of exercise on epigenetic modifications: focus on DNA methylation, histone modifications and non-coding RNAs. Hum Cell 2024; 37:887-903. [PMID: 38587596 DOI: 10.1007/s13577-024-01057-y] [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: 01/04/2024] [Accepted: 03/10/2024] [Indexed: 04/09/2024]
Abstract
Physical activity on a regular basis has been shown to bolster the overall wellness of an individual; research is now revealing that these changes are accompanied by epigenetic modifications. Regular exercise has been proven to make intervention plans more successful and prolong adherence to them. When it comes to epigenetic changes, there are four primary components. This includes changes to the DNA, histones, expression of particular non-coding RNAs and DNA methylation. External triggers, such as physical activity, can lead to modifications in the epigenetic components, resulting in changes in the transcription process. This report pays attention to the current knowledge that pertains to the epigenetic alterations that occur after exercise, the genes affected and the resulting characteristics.
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Affiliation(s)
- Junxiong Zhang
- Xiamen Academy of Art and Design, Fuzhou University, Xiamen, 361024, Fujian, China.
| | - Zhongxin Tian
- College of Physical Education, Taiyuan University of Technology, Taiyuan, 030024, Shanxi, China.
| | - Chao Qin
- College of Physical Education, Taiyuan University of Technology, Taiyuan, 030024, Shanxi, China
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4
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Lemes Dos Santos Sanna P, Bernardes Carvalho L, Cristina Dos Santos Afonso C, de Carvalho K, Aires R, Souza J, Rodrigues Ferreira M, Birbrair A, Martha Bernardi M, Latini A, Foganholi da Silva RA. Adora2A downregulation promotes caffeine neuroprotective effect against LPS-induced neuroinflammation in the hippocampus. Brain Res 2024; 1833:148866. [PMID: 38494098 DOI: 10.1016/j.brainres.2024.148866] [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: 01/16/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 03/19/2024]
Abstract
Caffeine has been extensively studied in the context of CNS pathologies as many researchers have shown that consuming it reduces pro-inflammatory biomarkers, potentially delaying the progression of neurodegenerative pathologies. Several lines of evidence suggest that adenosine receptors, especially A1 and A2A receptors, are the main targets of its neuroprotective action. We found that caffeine pretreatment 15 min before LPS administration reduced the expression of Il1b in the hippocampus and striatum. The harmful modulation of caffeine-induced inflammatory response involved the downregulation of the expression of A2A receptors, especially in the hippocampus. Caffeine treatment alone promoted the downregulation of the adenosinergic receptor Adora2A; however, this promotion effect was reversed by LPS. Although administering caffeine increased the expression of the enzymes DNA methyltransferases 1 and 3A and decreased the expression of the demethylase enzyme Tet1, this effect was reversed by LPS in the hippocampus of mice that were administered Caffeine + LPS, relative to the basal condition; no significant differences were observed in the methylation status of the promoter regions of adenosine receptors. Finally, the bioinformatics analysis of the expanded network demonstrated the following results: the Adora2B gene connects the extended networks of the adenosine receptors Adora1 and Adora2A; the Mapk3 and Esr1 genes connect the extended Adora1 network; the Mapk4 and Arrb2 genes connect the extended Adora2A network with the extended network of the proinflammatory cytokine Il1β. These results indicated that the anti-inflammatory effects of acute caffeine administration in the hippocampus may be mediated by a complex network of interdependencies between the Adora2B and Adora2A genes.
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Affiliation(s)
| | | | | | - Kassia de Carvalho
- Center for Epigenetic Study and Genic Regulation - CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University, São Paulo, São Paulo, Brazil
| | - Rogério Aires
- Center for Epigenetic Study and Genic Regulation - CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University, São Paulo, São Paulo, Brazil
| | - Jennyffer Souza
- Laboratory of Bioenergetics and Oxidative Stress - LABOX, Department of Biochemistry, Center for Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Marcel Rodrigues Ferreira
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unity, Botucatu Medical School, São Paulo State University, Brazil.
| | - Alexander Birbrair
- Department of Dermatology, University of Wisconsin-Madison, Madison, WI, USA
| | - Maria Martha Bernardi
- Center for Epigenetic Study and Genic Regulation - CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University, São Paulo, São Paulo, Brazil
| | - Alexandra Latini
- Laboratory of Bioenergetics and Oxidative Stress - LABOX, Department of Biochemistry, Center for Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Rodrigo A Foganholi da Silva
- Dentistry, University of Taubaté, Taubaté, São Paulo, São Paulo, Brazil; Center for Epigenetic Study and Genic Regulation - CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University, São Paulo, São Paulo, Brazil.
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5
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Cánepa ET, Berardino BG. Epigenetic mechanisms linking early-life adversities and mental health. Biochem J 2024; 481:615-642. [PMID: 38722301 DOI: 10.1042/bcj20230306] [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: 02/19/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/15/2024]
Abstract
Early-life adversities, whether prenatal or postnatal exposure, have been linked to adverse mental health outcomes later in life increasing the risk of several psychiatric disorders. Research on its neurobiological consequences demonstrated an association between exposure to adversities and persistent alterations in the structure, function, and connectivity of the brain. Consistent evidence supports the idea that regulation of gene expression through epigenetic mechanisms are involved in embedding the impact of early-life experiences in the genome and mediate between social environments and later behavioral phenotypes. In addition, studies from rodent models and humans suggest that these experiences and the acquired risk factors can be transmitted through epigenetic mechanisms to offspring and the following generations potentially contributing to a cycle of disease or disease risk. However, one of the important aspects of epigenetic mechanisms, unlike genetic sequences that are fixed and unchangeable, is that although the epigenetic markings are long-lasting, they are nevertheless potentially reversible. In this review, we summarize our current understanding of the epigenetic mechanisms involved in the mental health consequences derived from early-life exposure to malnutrition, maltreatment and poverty, adversities with huge and pervasive impact on mental health. We also discuss the evidence about transgenerational epigenetic inheritance in mammals and experimental data suggesting that suitable social and pharmacological interventions could reverse adverse epigenetic modifications induced by early-life negative social experiences. In this regard, these studies must be accompanied by efforts to determine the causes that promote these adversities and that result in health inequity in the population.
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Affiliation(s)
- Eduardo T Cánepa
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IQUIBICEN, CONICET, Buenos Aires, Argentina
| | - Bruno G Berardino
- Laboratorio de Neuroepigenética y Adversidades Tempranas, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IQUIBICEN, CONICET, Buenos Aires, Argentina
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6
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Li NN, Lun DX, Gong N, Meng G, Du XY, Wang H, Bao X, Li XY, Song JW, Hu K, Li L, Li SY, Liu W, Zhu W, Zhang Y, Li J, Yao T, Mou L, Han X, Hao F, Hu Y, Liu L, Zhu H, Wu Y, Liu B. Targeting the chromatin structural changes of antitumor immunity. J Pharm Anal 2024; 14:100905. [PMID: 38665224 PMCID: PMC11043877 DOI: 10.1016/j.jpha.2023.11.012] [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: 06/16/2023] [Revised: 09/28/2023] [Accepted: 11/21/2023] [Indexed: 04/28/2024] Open
Abstract
Epigenomic imbalance drives abnormal transcriptional processes, promoting the onset and progression of cancer. Although defective gene regulation generally affects carcinogenesis and tumor suppression networks, tumor immunogenicity and immune cells involved in antitumor responses may also be affected by epigenomic changes, which may have significant implications for the development and application of epigenetic therapy, cancer immunotherapy, and their combinations. Herein, we focus on the impact of epigenetic regulation on tumor immune cell function and the role of key abnormal epigenetic processes, DNA methylation, histone post-translational modification, and chromatin structure in tumor immunogenicity, and introduce these epigenetic research methods. We emphasize the value of small-molecule inhibitors of epigenetic modulators in enhancing antitumor immune responses and discuss the challenges of developing treatment plans that combine epigenetic therapy and immunotherapy through the complex interaction between cancer epigenetics and cancer immunology.
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Affiliation(s)
- Nian-nian Li
- Weifang People's Hospital, Weifang, Shandong, 261000, China
- School of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Deng-xing Lun
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Ningning Gong
- Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong, 261000, China
| | - Gang Meng
- Shaanxi Key Laboratory of Sericulture, Ankang University, Ankang, Shaanxi, 725000, China
| | - Xin-ying Du
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - He Wang
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xiangxiang Bao
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xin-yang Li
- Guizhou Education University, Guiyang, 550018, China
| | - Ji-wu Song
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Kewei Hu
- Weifang Traditional Chinese Medicine Hospital, Weifang, Shandong, 261000, China
| | - Lala Li
- Guizhou Normal University, Guiyang, 550025, China
| | - Si-ying Li
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Wenbo Liu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Wanping Zhu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yunlong Zhang
- School of Medical Imaging, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Jikai Li
- Department of Bone and Soft Tissue Oncology, Tianjin Hospital, Tianjin, 300299, China
| | - Ting Yao
- School of Life Sciences, Nankai University, Tianjin, 300071, China
- Teda Institute of Biological Sciences & Biotechnology, Nankai University, Tianjin, 300457, China
| | - Leming Mou
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Xiaoqing Han
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Furong Hao
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yongcheng Hu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Lin Liu
- School of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Hongguang Zhu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
| | - Yuyun Wu
- Xinqiao Hospital of Army Military Medical University, Chongqing, 400038, China
| | - Bin Liu
- Weifang People's Hospital, Weifang, Shandong, 261000, China
- School of Life Sciences, Nankai University, Tianjin, 300071, China
- Teda Institute of Biological Sciences & Biotechnology, Nankai University, Tianjin, 300457, China
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7
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Kupke J, Klimmt J, Mudlaff F, Schwab M, Lutsik P, Plass C, Sticht C, Oliveira AMM. Dnmt3a1 regulates hippocampus-dependent memory via the downstream target Nrp1. Neuropsychopharmacology 2024:10.1038/s41386-024-01843-0. [PMID: 38499720 DOI: 10.1038/s41386-024-01843-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/04/2024] [Accepted: 03/04/2024] [Indexed: 03/20/2024]
Abstract
Epigenetic factors are well-established players in memory formation. Specifically, DNA methylation is necessary for the formation of long-term memory in multiple brain regions including the hippocampus. Despite the demonstrated role of DNA methyltransferases (Dnmts) in memory formation, it is unclear whether individual Dnmts have unique or redundant functions in long-term memory formation. Furthermore, the downstream processes controlled by Dnmts during memory consolidation have not been investigated. In this study, we demonstrated that Dnmt3a1, the predominant Dnmt in the adult brain, is required for long-term spatial object recognition and contextual fear memory. Using RNA sequencing, we identified an activity-regulated Dnmt3a1-dependent genomic program in which several genes were associated with functional and structural plasticity. Furthermore, we found that some of the identified genes are selectively dependent on Dnmt3a1, but not its isoform Dnmt3a2. Specifically, we identified Neuropilin 1 (Nrp1) as a downstream target of Dnmt3a1 and further demonstrated the involvement of Nrp1 in hippocampus-dependent memory formation. Importantly, we found that Dnmt3a1 regulates hippocampus-dependent memory via Nrp1. In contrast, Nrp1 overexpression did not rescue memory impairments triggered by reduced Dnmt3a2 levels. Taken together, our study uncovered a Dnmt3a-isoform-specific mechanism in memory formation, identified a novel regulator of memory, and further highlighted the complex and highly regulated functions of distinct epigenetic regulators in brain function.
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Affiliation(s)
- Janina Kupke
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120, Heidelberg, Germany
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, 1081 HV, Amsterdam, the Netherlands
| | - Julien Klimmt
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120, Heidelberg, Germany
- Institute for Stroke and Dementia Research, University Hospital, Ludwig-Maximilians-University Munich, 81377, Munich, Germany
| | - Franziska Mudlaff
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120, Heidelberg, Germany
- Integrated Program in Neuroscience, McGill University, Montreal, QC, H3A 2B4, Canada
- Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, Montreal, QC, H3G 1A4, Canada
| | - Maximilian Schwab
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Carsten Sticht
- Next Generation Sequencing Core Facility, Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
| | - Ana M M Oliveira
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, 69120, Heidelberg, Germany.
- Department of Molecular and Cellular Cognition Research, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany.
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8
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Ghosh K, Zhou JJ, Shao JY, Chen SR, Pan HL. DNA demethylation in the hypothalamus promotes transcription of Agtr1a and Slc12a2 and hypertension development. J Biol Chem 2024; 300:105597. [PMID: 38160798 PMCID: PMC10830874 DOI: 10.1016/j.jbc.2023.105597] [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: 09/27/2023] [Revised: 12/09/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024] Open
Abstract
Increased expression of angiotensin II AT1A receptor (encoded by Agtr1a) and Na+-K+-Cl- cotransporter-1 (NKCC1, encoded by Slc12a2) in the hypothalamic paraventricular nucleus (PVN) contributes to hypertension development. However, little is known about their transcriptional control in the PVN in hypertension. DNA methylation is a critical epigenetic mechanism that regulates gene expression. Here, we determined whether transcriptional activation of Agtr1a and Slc12a2 results from altered DNA methylation in spontaneously hypertensive rats (SHR). Methylated DNA immunoprecipitation and bisulfite sequencing-PCR showed that CpG methylation at Agtr1a and Slc12a2 promoters in the PVN was progressively diminished in SHR compared with normotensive Wistar-Kyoto rats (WKY). Chromatin immunoprecipitation-quantitative PCR revealed that enrichment of DNA methyltransferases (DNMT1 and DNMT3A) and methyl-CpG binding protein 2, a DNA methylation reader protein, at Agtr1a and Slc12a2 promoters in the PVN was profoundly reduced in SHR compared with WKY. By contrast, the abundance of ten-eleven translocation enzymes (TET1-3) at Agtr1a and Slc12a2 promoters in the PVN was much greater in SHR than in WKY. Furthermore, microinjecting of RG108, a selective DNMT inhibitor, into the PVN of WKY increased arterial blood pressure and correspondingly potentiated Agtr1a and Slc12a2 mRNA levels in the PVN. Conversely, microinjection of C35, a specific TET inhibitor, into the PVN of SHR markedly reduced arterial blood pressure, accompanied by a decrease in Agtr1a and Slc12a2 mRNA levels in the PVN. Collectively, our findings suggest that DNA hypomethylation resulting from the DNMT/TET switch at gene promoters in the PVN promotes transcription of Agtr1a and Slc12a2 and hypertension development.
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Affiliation(s)
- Krishna Ghosh
- Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jing-Jing Zhou
- Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jian-Ying Shao
- Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shao-Rui Chen
- Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hui-Lin Pan
- Center for Neuroscience and Pain Research, Department of Anesthesiology and Perioperative Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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9
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Shi J, Wang Z, Wang Z, Shao G, Li X. Epigenetic regulation in adult neural stem cells. Front Cell Dev Biol 2024; 12:1331074. [PMID: 38357000 PMCID: PMC10864612 DOI: 10.3389/fcell.2024.1331074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024] Open
Abstract
Neural stem cells (NSCs) exhibit self-renewing and multipotential properties. Adult NSCs are located in two neurogenic regions of adult brain: the ventricular-subventricular zone (V-SVZ) of the lateral ventricle and the subgranular zone of the dentate gyrus in the hippocampus. Maintenance and differentiation of adult NSCs are regulated by both intrinsic and extrinsic signals that may be integrated through expression of some key factors in the adult NSCs. A number of transcription factors have been shown to play essential roles in transcriptional regulation of NSC cell fate transitions in the adult brain. Epigenetic regulators have also emerged as key players in regulation of NSCs, neural progenitor cells and their differentiated progeny via epigenetic modifications including DNA methylation, histone modifications, chromatin remodeling and RNA-mediated transcriptional regulation. This minireview is primarily focused on epigenetic regulations of adult NSCs during adult neurogenesis, in conjunction with transcriptional regulation in these processes.
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Affiliation(s)
- Jiajia Shi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zilin Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhijun Wang
- Zhenhai Lianhua Hospital, Ningbo City, Zhejiang, China
| | - Guofeng Shao
- Department of Cardiothoracic Surgery, Lihuili Hospital Affiliated to Ningbo University, Ningbo City, Zhejiang, China
| | - Xiajun Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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10
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Yoshikawa C, Ariyani W, Kohno D. DNA Methylation in the Hypothalamic Feeding Center and Obesity. J Obes Metab Syndr 2023; 32:303-311. [PMID: 38124554 PMCID: PMC10786209 DOI: 10.7570/jomes23073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/28/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023] Open
Abstract
Obesity rates have been increasing worldwide for decades, mainly due to environmental factors, such as diet, nutrition, and exercise. However, the molecular mechanisms through which environmental factors induce obesity remain unclear. Several mechanisms underlie the body's response to environmental factors, and one of the main mechanisms involves epigenetic modifications, such as DNA methylation. The pattern of DNA methylation is influenced by environmental factors, and altered DNA methylation patterns can affect gene expression profiles and phenotypes. DNA methylation may mediate the development of obesity caused by environmental factors. Similar to the factors governing obesity, DNA methylation is influenced by nutrients and metabolites. Notably, DNA methylation is associated with body size and weight programming. The DNA methylation levels of proopiomelanocortin (Pomc) and neuropeptide Y (Npy) in the hypothalamic feeding center, a key region controlling systemic energy balance, are affected by diet. Conditional knockout mouse studies of epigenetic enzymes have shown that DNA methylation in the hypothalamic feeding center plays an indispensable role in energy homeostasis. In this review, we discuss the role of DNA methylation in the hypothalamic feeding center as a potential mechanism underlying the development of obesity induced by environmental factors.
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Affiliation(s)
- Chiharu Yoshikawa
- Metabolic Signal Research Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Winda Ariyani
- Metabolic Signal Research Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Daisuke Kohno
- Metabolic Signal Research Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
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11
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Valvassori SS, da Rosa RT, Dal-Pont GC, Varela RB, Mastella GA, Daminelli T, Fries GR, Quevedo J, Zugno AI. Haloperidol alters neurotrophic factors and epigenetic parameters in an animal model of schizophrenia induced by ketamine. Int J Dev Neurosci 2023; 83:691-702. [PMID: 37635268 DOI: 10.1002/jdn.10296] [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: 04/10/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
This study aimed to evaluate Haloperidol's (Hal) effects on the behavioral, neurotrophic factors, and epigenetic parameters in an animal model of schizophrenia (SCZ) induced by ketamine (Ket). Injections of Ket or saline were administered intraperitoneal (once a day) between the 1st and 14th days of the experiment. Water or Hal was administered via gavage between the 8th and 14th experimental days. Thirty minutes after the last injection, the animals were subjected to behavioral analysis. The activity of DNA methyltransferase (DNMT), histone deacetylase (HDAC), and histone acetyltransferase and levels of brain-derived neurotrophic factor (BDNF), nerve growth factor (NGF), neurotrophin-3 (NT-3), and glial-derived neurotrophic factor (GDNF) were evaluated in the frontal cortex, hippocampus, and striatum. Ket increased the covered distance and time spent in the central area of the open field, and Hal did not reverse these behavioral alterations. Significant increases in the DNMT and HDAC activities were detected in the frontal cortex and striatum from rats that received Ket, Hal, or a combination thereof. Besides, Hal per se increased the activity of DNMT and HDAC in the hippocampus of rats. Hal per se or the association of Ket plus Hal decreased BDNF, NGF, NT-3, and GDNF, depending on the brain region and treatment regimen. The administration of Hal can alter the levels of neurotrophic factors and the activity of epigenetic enzymes, which can be a factor in the development of effect collateral in SCZ patients. However, the precise mechanisms involved in these alterations are still unclear.
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Affiliation(s)
- Samira S Valvassori
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, Santa Catarina, Brazil
| | - Richard T da Rosa
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, Santa Catarina, Brazil
| | - Gustavo C Dal-Pont
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, Santa Catarina, Brazil
| | - Roger B Varela
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, Santa Catarina, Brazil
| | - Gustavo A Mastella
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, Santa Catarina, Brazil
| | - Thiani Daminelli
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, Santa Catarina, Brazil
| | - Gabriel R Fries
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA
- Center of Excellence on Mood Disorders, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA
| | - João Quevedo
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, Santa Catarina, Brazil
- Translational Psychiatry Program, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA
- Center of Excellence on Mood Disorders, Faillace Department of Psychiatry and Behavioral Sciences, McGovern Medical School, University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, USA
- Neuroscience Graduate Program, University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Alexandra I Zugno
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, Santa Catarina, Brazil
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12
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Beard DC, Zhang X, Wu DY, Martin JR, Erickson A, Boua JV, Hamagami N, Swift RG, McCullough KB, Ge X, Bell-Hensley A, Zheng H, Palmer CW, Fuhler NA, Lawrence AB, Hill CA, Papouin T, Noguchi KK, McAlinden A, Garbow JR, Dougherty JD, Maloney SE, Gabel HW. Distinct disease mutations in DNMT3A result in a spectrum of behavioral, epigenetic, and transcriptional deficits. Cell Rep 2023; 42:113411. [PMID: 37952155 PMCID: PMC10843706 DOI: 10.1016/j.celrep.2023.113411] [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: 02/28/2023] [Revised: 09/06/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023] Open
Abstract
Phenotypic heterogeneity in monogenic neurodevelopmental disorders can arise from differential severity of variants underlying disease, but how distinct alleles drive variable disease presentation is not well understood. Here, we investigate missense mutations in DNA methyltransferase 3A (DNMT3A), a DNA methyltransferase associated with overgrowth, intellectual disability, and autism, to uncover molecular correlates of phenotypic heterogeneity. We generate a Dnmt3aP900L/+ mouse mimicking a mutation with mild to moderate severity and compare phenotypic and epigenomic effects with a severe R878H mutation. P900L mutants exhibit core growth and behavioral phenotypes shared across models but show subtle epigenomic changes, while R878H mutants display extensive disruptions. We identify mutation-specific dysregulated genes that may contribute to variable disease severity. Shared transcriptomic disruption identified across mutations overlaps dysregulation observed in other developmental disorder models and likely drives common phenotypes. Together, our findings define central drivers of DNMT3A disorders and illustrate how variable epigenomic disruption contributes to phenotypic heterogeneity in neurodevelopmental disease.
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Affiliation(s)
- Diana C Beard
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiyun Zhang
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dennis Y Wu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jenna R Martin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alyssa Erickson
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jane Valeriane Boua
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicole Hamagami
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Raylynn G Swift
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine B McCullough
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xia Ge
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Austin Bell-Hensley
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63110, USA; Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hongjun Zheng
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Cory W Palmer
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicole A Fuhler
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Austin B Lawrence
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Cheryl A Hill
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Thomas Papouin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kevin K Noguchi
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Audrey McAlinden
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joel R Garbow
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph D Dougherty
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susan E Maloney
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA.
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13
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Motamed Nezhad A, Behroozi Z, Kookli K, Ghadaksaz A, Fazeli SM, Moshiri A, Ramezani F, Shooshtari MG, Janzadeh A. Evaluation of photobiomodulation therapy (117 and 90s) on pain, regeneration, and epigenetic factors (HDAC 2, DNMT3a) expression following spinal cord injury in a rat model. Photochem Photobiol Sci 2023; 22:2527-2540. [PMID: 37787959 DOI: 10.1007/s43630-023-00467-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/05/2023] [Indexed: 10/04/2023]
Abstract
BACKGROUND Photobiomodulation therapy (PBMT), due to its anti-inflammatory, analgesic effects, and most importantly as a non-invasive procedure, has currently gained a special setting in pain relief and the treatment of Spinal cord injuries (SCI). However, the mechanism of action of the PBM is not yet completely understood. METHODS In this study, SCI is induced by an aneurysm clip, and PBM therapy was applied by a continuous-wave (CW) laser with a wavelength of 660 nm. Adult male rats were divided into four groups: Control, SCI, SCI + PBMT 90s, and SCI + PBMT 117s. After 7 weeks, hyperalgesia, allodynia, and functional recovery were assessed. Fibroblasts infiltrating the spinal cord were counted after H&E staining. The expression of epigenetic factors (HDAC2, DNMT3a), protein relevant for pain (GAD65), and astrocytes marker (GFAP) after 4 weeks of daily PBMT (90 and 117s) was probed by western blotting. RESULTS Both PBMTs (90 and 117s) significantly improved the pain and ability to move and fibroblast invasion was reduced. SCI + PBMT 90s, increased GAD65, HDAC2, and DNMT3a expression. However, PBMT 117s decreased GFAP, HDAC2, and DNMT3a. CONCLUSION PBMT 90 and 117s improved the pain, and functional recovery equally. The regulation of epigenetic mechanisms appears to be a significant effect of PBMT117s, which emphasizes on impact of radiation duration and accumulative energy.
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Affiliation(s)
- Ali Motamed Nezhad
- College of Veterinary Medicine, Islamic Azad University, Karaj, Alborz, Iran
| | - Zahra Behroozi
- Physiology Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Keihan Kookli
- International Campus, Iran University of Medical Sciences, Tehran, Iran
- Cancer Control Research Center, Cancer Control Foundation, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Ghadaksaz
- Department of Biophysics, Medical School, University of Pécs, Pécs, 7622, Hungary
| | - Seyedalireza Moghaddas Fazeli
- International Campus, Iran University of Medical Sciences, Tehran, Iran
- Cancer Control Research Center, Cancer Control Foundation, Iran University of Medical Sciences, Tehran, Iran
| | | | - Fatemeh Ramezani
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.
- Radiation Biology Research Center (RBRC), Iran University of Medical Sciences (IUMS), Tehran, Iran.
| | | | - Atousa Janzadeh
- Radiation Biology Research Center (RBRC), Iran University of Medical Sciences (IUMS), Tehran, Iran.
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14
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Massri AJ, Fitzpatrick M, Cunny H, Li JL, Harry GJ. Differential gene expression profiling implicates altered network development in rat postnatal day 4 cortex following 4-Methylimidazole (4-MeI) induced maternal seizures. Neurotoxicol Teratol 2023; 100:107301. [PMID: 37783441 PMCID: PMC10843020 DOI: 10.1016/j.ntt.2023.107301] [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: 06/23/2023] [Revised: 08/31/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023]
Abstract
Compromised maternal health leading to maternal seizures can have adverse effects on the healthy development of offspring. This may be the result of inflammation, hypoxia-ischemia, and altered GABA signaling. The current study examined cortical tissue from F2b (2nd litter of the 2nd generation) postnatal day 4 (PND4) offspring of female Harlan SD rats chronically exposed to the seizuregenic compound, 4-Methylimidazole (0, 750, or 2500 ppm 4-MeI). Maternal seizures were evident only at 2500 ppm 4-MeI. GABA related gene expression as examined by qRT-PCR and whole genome microarray showed no indication of disrupted GABA or glutamatergic signaling. Canonical pathway hierarchical clustering and multi-omics combinatory genomic (CNet) plots of differentially expressed genes (DEG) showed alterations in genes associated with regulatory processes of cell development including neuronal differentiation and synaptogenesis. Functional enrichment analysis showed a similarity of cellular processes across the two exposure groups however, the genes comprising each cluster were primarily unique rather than shared and often showed different directionality. A dose-related induction of cytokine signaling was indicated however, pathways associated with individual cytokine signaling were not elevated, suggesting an alternative involvement of cytokine signaling. Pathways related to growth process and cell signaling showed a negative activation supporting an interpretation of disruption or delay in developmental processes at the 2500 ppm 4-MeI exposure level with maternal seizures. Thus, while GABA signaling was not altered as has been observed with maternal seizures, the pattern of DEG suggested a potential for alteration in neuronal network formation.
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Affiliation(s)
- Abdull J Massri
- Integrative Bioinformatics, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Mackenzie Fitzpatrick
- Mechanistic Toxicology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Helen Cunny
- Office of the Scientific Director, Division of Translational Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Jian-Liang Li
- Integrative Bioinformatics, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - G Jean Harry
- Mechanistic Toxicology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA.
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15
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Zuzina AB, Vinarskaya AK, Balaban PM. DNA Methylation Inhibition Reversibly Impairs the Long-Term Context Memory Maintenance in Helix. Int J Mol Sci 2023; 24:14068. [PMID: 37762369 PMCID: PMC10531757 DOI: 10.3390/ijms241814068] [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: 08/16/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
This work aims to study the epigenetic mechanisms of regulating long-term context memory in the gastropod mollusk: Helix. We have shown that RG108, an inhibitor of DNA methyltransferase (DNMT), impaired long-term context memory in snails, and this impairment can be reversed within a limited time window: no more than 48 h. Research on the mechanisms through which the long-term context memory impaired by DNMT inhibition could be reinstated demonstrated that this effect depends on several biochemical mechanisms: nitric oxide synthesis, protein synthesis, and activity of the serotonergic system. Memory recovery did not occur if at least one of these mechanisms was impaired. The need for the joint synergic activity of several biochemical systems for a successful memory rescue confirms the assumption that the memory recovery process depends on the process of active reconsolidation, and is not simply a passive weakening of the effect of RG108 over time. Finally, we showed that the reactivation of the impaired memory by RG108, followed by administration of histone deacetylase inhibitor sodium butyrate, led to memory recovery only within a narrow time window: no more than 48 h after memory disruption.
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Affiliation(s)
| | | | - Pavel M. Balaban
- Cellular Neurobiology of Learning Lab, Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, 5A Butlerova St., Moscow 117485, Russia; (A.B.Z.); (A.K.V.)
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16
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Martin S, Poppe D, Olova N, O'Leary C, Ivanova E, Pflueger J, Dechka J, Simmons RK, Cooper HM, Reik W, Lister R, Wolvetang EJ. Embryonic Stem Cell-Derived Neurons as a Model System for Epigenome Maturation during Development. Genes (Basel) 2023; 14:genes14050957. [PMID: 37239317 DOI: 10.3390/genes14050957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/16/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
DNA methylation in neurons is directly linked to neuronal genome regulation and maturation. Unlike other tissues, vertebrate neurons accumulate high levels of atypical DNA methylation in the CH sequence context (mCH) during early postnatal brain development. Here, we investigate to what extent neurons derived in vitro from both mouse and human pluripotent stem cells recapitulate in vivo DNA methylation patterns. While human ESC-derived neurons did not accumulate mCH in either 2D culture or 3D organoid models even after prolonged culture, cortical neurons derived from mouse ESCs acquired in vivo levels of mCH over a similar time period in both primary neuron cultures and in vivo development. mESC-derived neuron mCH deposition was coincident with a transient increase in Dnmt3a, preceded by the postmitotic marker Rbfox3 (NeuN), was enriched at the nuclear lamina, and negatively correlated with gene expression. We further found that methylation patterning subtly differed between in vitro mES-derived and in vivo neurons, suggesting the involvement of additional noncell autonomous processes. Our findings show that mouse ESC-derived neurons, in contrast to those of humans, can recapitulate the unique DNA methylation landscape of adult neurons in vitro over experimentally tractable timeframes, which allows their use as a model system to study epigenome maturation over development.
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Affiliation(s)
- Sally Martin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Daniel Poppe
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Nelly Olova
- Epigenetics ISP, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Conor O'Leary
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Elena Ivanova
- Epigenetics ISP, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Jahnvi Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Jennifer Dechka
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Rebecca K Simmons
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Helen M Cooper
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Wolf Reik
- Epigenetics ISP, The Babraham Institute, Cambridge CB22 3AT, UK
- The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Ernst J Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
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17
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Patricia da Silva E, da Silva Feltran G, Alexandre Alcântara Dos Santos S, Cardoso de Oliveira R, Assis RIF, Antônio Justulin Junior L, Carleto Andia D, Zambuzzi WF, Latini A, Foganholi da Silva RA. Hyperglycemic microenvironment compromises the homeostasis of communication between the bone-brain axis by the epigenetic repression of the osteocalcin receptor, Gpr158 in the hippocampus. Brain Res 2023; 1803:148234. [PMID: 36634900 DOI: 10.1016/j.brainres.2023.148234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/05/2023] [Accepted: 01/07/2023] [Indexed: 01/11/2023]
Abstract
Diabetes mellitus (DM) is a chronic metabolic disease, mainly characterized by increased blood glucose and insulin dysfunction. In response to the persistent systemic hyperglycemic state, numerous metabolic and physiological complications have already been well characterized. However, its relationship to bone fragility, cognitive deficits and increased risk of dementia still needs to be better understood. The impact of chronic hyperglycemia on bone physiology and architecture was assessed in a model of chronic hyperglycemia induced by a single intraperitoneal administration of streptozotocin (STZ; 55 mg/kg) in Wistar rats. In addition, the bone-to-brain communication was investigated by analyzing the gene expression and methylation status of genes that encode the main osteokines released by the bone [Fgf23 (fibroblast growth factor 23), Bglap (bone gamma-carboxyglutamate protein) and Lcn2 (lipocalin 2) and their receptors in both, the bone and the brain [Fgfr1 (fibroblast growth factor receptor 1), Gpr6A (G-protein coupled receptor family C group 6 member A), Gpr158 (G protein-coupled receptor 158) and Slc22a17 (Solute carrier family 22 member 17)]. It was observed that chronic hyperglycemia negatively impacted on bone biology and compromised the balance of the bone-brain endocrine axis. Ultrastructural disorganization was accompanied by global DNA hypomethylation and changes in gene expression of DNA-modifying enzymes that were accompanied by changes in the methylation status of the osteokine promoter region Bglap and Lcn2 (lipocalin 2) in the femur. Additionally, the chronic hyperglycemic state was accompanied by modulation of gene expression of the osteokines Fgf23 (fibroblast growth factor 23), Bglap (bone gamma-carboxyglutamate protein) and Lcn2 (lipocalin 2) in the different brain regions. However, transcriptional regulation mediated by DNA methylation was observed only for the osteokine receptors, Fgfr1(fibroblast growth factor receptor 1) in the striatum and Gpr158 (G protein-coupled receptor 158) in the hippocampus. This is a pioneer study demonstrating that the chronic hyperglycemic state compromises the crosstalk between bone tissue and the brain, mainly affecting the hippocampus, through transcriptional silencing of the Bglap receptor by hypermethylation of Gpr158 gene.
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Affiliation(s)
- Ericka Patricia da Silva
- CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University - UNIP, São Paulo, São Paulo, Brazil
| | - Geórgia da Silva Feltran
- Laboratory of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil
| | | | - Rodrigo Cardoso de Oliveira
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo -FOB, Bauru, São Paulo, Brazil
| | - Rahyza I F Assis
- Department of Clinical Dentistry, Federal University of Espírito Santo, Vitória, ES, Brazil
| | - Luis Antônio Justulin Junior
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil
| | - Denise Carleto Andia
- School of Dentistry, Health Science Institute, Paulista University - UNIP, São Paulo, São Paulo, Brazil
| | - Willian F Zambuzzi
- Laboratory of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University - UNESP, Botucatu, São Paulo, Brazil
| | - Alexandra Latini
- LABOX, Department of Biochemistry, Center for Biological Sciences, Federal University of Santa Catarina - UFSC, Florianopolis, Brazil.
| | - Rodrigo A Foganholi da Silva
- CEEpiRG, Program in Environmental and Experimental Pathology, Paulista University - UNIP, São Paulo, São Paulo, Brazil; Department of Dentistry, University of Taubaté - UNITAU, Taubaté, São Paulo, Brazil.
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18
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Moazeny M, Dehbashi M, Hojati Z, Esmaeili F. Investigating neural differentiation of mouse P19 embryonic stem cells in a time-dependent manner by bioinformatic, microscopic and transcriptional analyses. Mol Biol Rep 2023; 50:2183-2194. [PMID: 36565416 DOI: 10.1007/s11033-022-08166-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 09/23/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND As an available cell line, mouse pluripotent P19 has been widely employed for neuronal differentiation studies. In this research, by applying the in vitro differentiation of this cell line into neuron-like cells through retinoic acid (RA) treatment, the roles of some genes including DNMT3B, ICAM1, IRX3, JAK2, LHX1, SOX9, TBX3 and THY1 in neural differentiation was investigated. METHODS AND RESULTS Bioinformatics, microscopic, and transcriptional studies were conducted in a time-dependent manner after RA-induced neural differentiation. According to bioinformatics studies, we determined the engagement of the metabolic and developmental super-pathways and pathways in neural cell differentiation, particularly focusing on the considered genes. According to our qRT-PCR analyses, JAK2, SOX9, TBX3, LHX1 and IRX3 genes were found to be significantly overexpressed in a time-dependent manner (p < 0.05). In addition, the significant downregulation of THY1, DNMT3B and ICAM1 genes was observed during the experiment (p < 0.05). The optical microscopic investigation showed that the specialized extensions of the neuron-like cells were revealed on day 8 after RA treatment. CONCLUSION Accordingly, the neural differentiation of P19 cell line and the role of the considered genes during the differentiation were proved. However, our results warrant further in vivo studies.
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Affiliation(s)
- Marzieh Moazeny
- Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, 81746-73441, Isfahan, Iran
| | - Moein Dehbashi
- Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, 81746-73441, Isfahan, Iran
| | - Zohreh Hojati
- Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, 81746-73441, Isfahan, Iran.
| | - Fariba Esmaeili
- Division of Animal Sciences, Department of Plant and Animal Biology, Faculty of Biological Science and Technology, University of Isfahan, 81746-73441, Isfahan, Iran
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19
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Beard DC, Zhang X, Wu DY, Martin JR, Hamagami N, Swift RG, McCullough KB, Ge X, Bell-Hensley A, Zheng H, Lawrence AB, Hill CA, Papouin T, McAlinden A, Garbow JR, Dougherty JD, Maloney SE, Gabel HW. Distinct disease mutations in DNMT3A result in a spectrum of behavioral, epigenetic, and transcriptional deficits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530041. [PMID: 36909558 PMCID: PMC10002657 DOI: 10.1101/2023.02.27.530041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Phenotypic heterogeneity is a common feature of monogenic neurodevelopmental disorders that can arise from differential severity of missense variants underlying disease, but how distinct alleles impact molecular mechanisms to drive variable disease presentation is not well understood. Here, we investigate missense mutations in the DNA methyltransferase DNMT3A associated with variable overgrowth, intellectual disability, and autism, to uncover molecular correlates of phenotypic heterogeneity in neurodevelopmental disease. We generate a DNMT3A P900L/+ mouse model mimicking a disease mutation with mild-to-moderate severity and compare phenotypic and epigenomic effects with a severe R878H mutation. We show that the P900L mutation leads to disease-relevant overgrowth, obesity, and social deficits shared across DNMT3A disorder models, while the R878H mutation causes more extensive epigenomic disruption leading to differential dysregulation of enhancers elements. We identify distinct gene sets disrupted in each mutant which may contribute to mild or severe disease, and detect shared transcriptomic disruption that likely drives common phenotypes across affected individuals. Finally, we demonstrate that core gene dysregulation detected in DNMT3A mutant mice overlaps effects in other developmental disorder models, highlighting the importance of DNMT3A-deposited methylation in neurodevelopment. Together, these findings define central drivers of DNMT3A disorders and illustrate how variable disruption of transcriptional mechanisms can drive the spectrum of phenotypes in neurodevelopmental disease.
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Affiliation(s)
- Diana C. Beard
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiyun Zhang
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dennis Y. Wu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jenna R. Martin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicole Hamagami
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Raylynn G. Swift
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine B. McCullough
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xia Ge
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Austin Bell-Hensley
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63110, USA
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hongjun Zheng
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Austin B. Lawrence
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Cheryl A. Hill
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Thomas Papouin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Audrey McAlinden
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joel R. Garbow
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph D. Dougherty
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susan E. Maloney
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Harrison W. Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
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20
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Smith AR, Richards DM, Lunnon K, Schapira AHV, Migdalska-Richards A. DNA Methylation of α-Synuclein Intron 1 Is Significantly Decreased in the Frontal Cortex of Parkinson's Individuals with GBA1 Mutations. Int J Mol Sci 2023; 24:ijms24032687. [PMID: 36769009 PMCID: PMC9917152 DOI: 10.3390/ijms24032687] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Parkinson's disease (PD) is a common movement disorder, estimated to affect 4% of individuals by the age of 80. Mutations in the glucocerebrosidase 1 (GBA1) gene represent the most common genetic risk factor for PD, with at least 7-10% of non-Ashkenazi PD individuals carrying a GBA1 mutation (PD-GBA1). Although similar to idiopathic PD, the clinical presentation of PD-GBA1 includes a slightly younger age of onset, a higher incidence of neuropsychiatric symptoms, and a tendency to earlier, more prevalent and more significant cognitive impairment. The pathophysiological mechanisms underlying PD-GBA1 are incompletely understood, but, as in idiopathic PD, α-synuclein accumulation is thought to play a key role. It has been hypothesized that this overexpression of α-synuclein is caused by epigenetic modifications. In this paper, we analyze DNA methylation levels at 17 CpG sites located within intron 1 and the promoter of the α-synuclein (SNCA) gene in three different brain regions (frontal cortex, putamen and substantia nigra) in idiopathic PD, PD-GBA1 and elderly non-PD controls. In all three brain regions we find a tendency towards a decrease in DNA methylation within an eight CpG region of intron 1 in both idiopathic PD and PD-GBA1. The trend towards a reduction in DNA methylation was more pronounced in PD-GBA1, with a significant decrease in the frontal cortex. This suggests that PD-GBA1 and idiopathic PD have distinct epigenetic profiles, and highlights the importance of separating idiopathic PD and PD-GBA1 cases. This work also provides initial evidence that different genetic subtypes might exist within PD, each characterized by its own pathological mechanism. This may have important implications for how PD is diagnosed and treated.
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Affiliation(s)
- Adam R. Smith
- Faculty of Health and Life Sciences, University of Exeter, Exeter EX2 5DW, UK
| | - David M. Richards
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
- Department of Physics and Astronomy, University of Exeter, Exeter EX4 4QD, UK
| | - Katie Lunnon
- Faculty of Health and Life Sciences, University of Exeter, Exeter EX2 5DW, UK
| | - Anthony H. V. Schapira
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London NW3 2PF, UK
| | - Anna Migdalska-Richards
- Faculty of Health and Life Sciences, University of Exeter, Exeter EX2 5DW, UK
- Correspondence:
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21
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Iannone C, Kainov Y, Zhuravskaya A, Hamid F, Nojima T, Makeyev EV. PTBP1-activated co-transcriptional splicing controls epigenetic status of pluripotent stem cells. Mol Cell 2023; 83:203-218.e9. [PMID: 36626906 DOI: 10.1016/j.molcel.2022.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 11/15/2022] [Accepted: 12/12/2022] [Indexed: 01/11/2023]
Abstract
Many spliceosomal introns are excised from nascent transcripts emerging from RNA polymerase II (RNA Pol II). The extent of cell-type-specific regulation and possible functions of such co-transcriptional events remain poorly understood. We examined the role of the RNA-binding protein PTBP1 in this process using an acute depletion approach followed by the analysis of chromatin- and RNA Pol II-associated transcripts. We show that PTBP1 activates the co-transcriptional excision of hundreds of introns, a surprising effect given that this protein is known to promote intron retention. Importantly, some co-transcriptionally activated introns fail to complete their splicing without PTBP1. In a striking example, retention of a PTBP1-dependent intron triggers nonsense-mediated decay of transcripts encoding DNA methyltransferase DNMT3B. We provide evidence that this regulation facilitates the natural decline in DNMT3B levels in developing neurons and protects differentiation-specific genes from ectopic methylation. Thus, PTBP1-activated co-transcriptional splicing is a widespread phenomenon mediating epigenetic control of cellular identity.
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Affiliation(s)
- Camilla Iannone
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Yaroslav Kainov
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Anna Zhuravskaya
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Fursham Hamid
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK
| | - Takayuki Nojima
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK.
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22
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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: 12] [Impact Index Per Article: 12.0] [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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23
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Kunert S, Linhard V, Weirich S, Choudalakis M, Osswald F, Krämer L, Köhler AR, Bröhm A, Wollenhaupt J, Schwalbe H, Jeltsch A. The MECP2-TRD domain interacts with the DNMT3A-ADD domain at the H3-tail binding site. Protein Sci 2023; 32:e4542. [PMID: 36519786 PMCID: PMC9798253 DOI: 10.1002/pro.4542] [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: 10/22/2022] [Revised: 12/01/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
The DNMT3A DNA methyltransferase and MECP2 methylation reader are highly expressed in neurons. Both proteins interact via their DNMT3A-ADD and MECP2-TRD domains, and the MECP2 interaction regulates the activity and subnuclear localization of DNMT3A. Here, we mapped the interface of both domains using peptide SPOT array binding, protein pull-down, equilibrium peptide binding assays, and structural analyses. The region D529-D531 on the surface of the ADD domain was identified as interaction point with the TRD domain. This includes important residues of the histone H3 N-terminal tail binding site to the ADD domain, explaining why TRD and H3 binding to the ADD domain is competitive. On the TRD domain, residues 214-228 containing K219 and K223 were found to be essential for the ADD interaction. This part represents a folded patch within the otherwise largely disordered TRD domain. A crystal structure analysis of ADD revealed that the identified H3/TDR lysine binding pocket is occupied by an arginine residue from a crystallographic neighbor in the ADD apoprotein structure. Finally, we show that mutations in the interface of ADD and TRD domains disrupt the cellular interaction of both proteins in NIH3T3 cells. In summary, our data show that the H3 peptide binding cleft of the ADD domain also mediates the interaction with the MECP2-TRD domain suggesting that this binding site may have a broader role also in the interaction of DNMT3A with other proteins leading to complex regulation options by competitive and PTM specific binding.
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Affiliation(s)
- Stefan Kunert
- Institute of Biochemistry and Technical BiochemistryUniversity of StuttgartStuttgartGermany
| | - Verena Linhard
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical BiologyGoethe UniversityFrankfurtGermany
| | - Sara Weirich
- Institute of Biochemistry and Technical BiochemistryUniversity of StuttgartStuttgartGermany
| | - Michel Choudalakis
- Institute of Biochemistry and Technical BiochemistryUniversity of StuttgartStuttgartGermany
| | - Florian Osswald
- Institute of Biochemistry and Technical BiochemistryUniversity of StuttgartStuttgartGermany
| | - Lisa Krämer
- Institute of Biochemistry and Technical BiochemistryUniversity of StuttgartStuttgartGermany
| | - Anja R. Köhler
- Institute of Biochemistry and Technical BiochemistryUniversity of StuttgartStuttgartGermany
| | - Alexander Bröhm
- Institute of Biochemistry and Technical BiochemistryUniversity of StuttgartStuttgartGermany
| | - Jan Wollenhaupt
- Macromolecular Crystallography GroupHelmholtz‐Zentrum BerlinBerlinGermany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical BiologyGoethe UniversityFrankfurtGermany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical BiochemistryUniversity of StuttgartStuttgartGermany
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24
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Shen XY, Shi SH, Li H, Wang CC, Zhang Y, Yu H, Li YB, Liu B. The role of Gadd45b in neurologic and neuropsychiatric disorders: An overview. Front Mol Neurosci 2022; 15:1021207. [PMID: 36311022 PMCID: PMC9606402 DOI: 10.3389/fnmol.2022.1021207] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/21/2022] [Indexed: 11/26/2022] Open
Abstract
Growth arrest and DNA damage-inducible beta (Gadd45b) is directly intertwined with stress-induced DNA repair, cell cycle arrest, survival, and apoptosis. Previous research on Gadd45b has focused chiefly on non-neuronal cells. Gadd45b is extensively expressed in the nervous system and plays a critical role in epigenetic DNA demethylation, neuroplasticity, and neuroprotection, according to accumulating evidence. This article provided an overview of the preclinical and clinical effects of Gadd45b, as well as its hypothesized mechanisms of action, focusing on major psychosis, depression, autism, stroke, seizure, dementia, Parkinson’s disease, and autoimmune diseases of the nervous system.
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Affiliation(s)
- Xiao-yue Shen
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, China
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Shu-han Shi
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Heng Li
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Cong-cong Wang
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Yao Zhang
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Hui Yu
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Yan-bin Li
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, China
- Yan-bin Li,
| | - Bin Liu
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, China
- *Correspondence: Bin Liu,
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25
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Qian S, Shi C, Huang S, Yang C, Luo Y. DNA methyltransferase activity in the basolateral amygdala is critical for reconsolidation of a heroin reward memory. Front Mol Neurosci 2022; 15:1002139. [PMID: 36176958 PMCID: PMC9513049 DOI: 10.3389/fnmol.2022.1002139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
The persistence of drug memory contributes to relapse to drug seeking. The association between repeated drug exposure and drug-related cues leads to cravings triggered by drug-paired cues. The erasure of drug memories has been considered a promising way to inhibit cravings and prevent relapse. The re-exposure to drug-related cues destabilizes well-consolidated drug memories, during which a de novo protein synthesis-dependent process termed “reconsolidation” occurs to restabilize the reactivated drug memory. Disrupting reconsolidation of drug memories leads to the attenuation of drug-seeking behavior in both animal models and people with addictions. Additionally, epigenetic mechanisms regulated by DNA methyltransferase (DNMT) are involved in the reconsolidation of fear and cocaine reward memory. In the present study, we investigated the role of DNMT in the reconsolidation of heroin reward memory. In the heroin self-administration model in rats, we tested the effects of DNMT inhibition during the reconsolidation process on cue-induced reinstatement, heroin-priming-induced reinstatement, and spontaneous recovery of heroin-seeking behavior. We found that the bilateral infusion of 5-azacytidine (5-AZA) inhibiting DNMT into the basolateral amygdala (BLA) immediately after heroin reward memory retrieval, but not delayed 6 h after retrieval or without retrieval, decreased subsequent cue-induced and heroin-priming-induced reinstatement of heroin-seeking behavior. These findings demonstrate that inhibiting the activity of DNMT in BLA during the reconsolidation of heroin reward memory attenuates heroin-seeking behavior, which may provide a potential strategy for the therapeutic of heroin addiction.
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Affiliation(s)
- Shuyi Qian
- Department of Nephrology and Laboratory of Kidney Disease, Hunan Provincial People’s Hospital, Hunan Normal University, Changsha, China
| | - Cuijie Shi
- Hunan Province People’s Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Shihao Huang
- National Institute on Drug Dependence, Beijing Key Laboratory of Drug Dependence, Peking University, Beijing, China
| | - Chang Yang
- Hunan Province People’s Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Yixiao Luo
- Hunan Province People’s Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha, China
- *Correspondence: Yixiao Luo,
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26
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The Role of DNA Methylation in Stroke Recovery. Int J Mol Sci 2022; 23:ijms231810373. [PMID: 36142283 PMCID: PMC9499691 DOI: 10.3390/ijms231810373] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022] Open
Abstract
Epigenetic alterations affect the onset of ischemic stroke, brain injury after stroke, and mechanisms of poststroke recovery. In particular, DNA methylation can be dynamically altered by maintaining normal brain function or inducing abnormal brain damage. DNA methylation is regulated by DNA methyltransferase (DNMT), which promotes methylation, DNA demethylase, which removes methyl groups, and methyl-cytosine–phosphate–guanine-binding domain (MBD) protein, which binds methylated DNA and inhibits gene expression. Investigating the effects of modulating DNMT, TET, and MBD protein expression on neuronal cell death and neurorepair in ischemic stroke and elucidating the underlying mechanisms can facilitate the formulation of therapeutic strategies for neuroprotection and promotion of neuronal recovery after stroke. In this review, we summarize the role of DNA methylation in neuroprotection and neuronal recovery after stroke according to the current knowledge regarding the effects of DNA methylation on excitotoxicity, oxidative stress, apoptosis, neuroinflammation, and recovery after ischemic stroke. This review of the literature regarding the role of DNA methylation in neuroprotection and functional recovery after stroke may contribute to the development and application of novel therapeutic strategies for stroke.
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27
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Anier K, Somelar K, Jaako K, Alttoa M, Sikk K, Kokassaar R, Kisand K, Kalda A. Psychostimulant-induced aberrant DNA methylation in an in vitro model of human peripheral blood mononuclear cells. Clin Epigenetics 2022; 14:89. [PMID: 35842682 PMCID: PMC9288712 DOI: 10.1186/s13148-022-01303-w] [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: 01/28/2022] [Accepted: 06/30/2022] [Indexed: 11/14/2022] Open
Abstract
Background Several reports have provided crucial evidence in animal models that epigenetic modifications, such as DNA methylation, may be involved in psychostimulant-induced stable changes at the cellular level in the brain. Epigenetic editors DNA methyltransferases (DNMTs) and ten-eleven translocation enzymes (TETs) coordinate expression of gene networks, which then manifest as long-term behavioural changes. However, the extent to which aberrant DNA methylation is involved in the mechanisms of substance use disorder in humans is unclear. We previously demonstrated that cocaine modifies gene transcription, via DNA methylation, throughout the brain and in peripheral blood cells in mice. Results We treated human peripheral blood mononuclear cells (PBMCs) from healthy male donors (n = 18) in vitro with psychostimulants (amphetamine, cocaine). After treatment, we assessed mRNA levels and enzymatic activities of TETs and DNMTs, conducted genome-wide DNA methylation assays and next-generation sequencing. We found that repeated exposure to psychostimulants decreased mRNA levels and enzymatic activity of TETs and 5-hydroxymethylation levels in PBMCs. These data were in line with observed hyper- and hypomethylation and mRNA expression of marker genes (IL-10, ATP2B4). Additionally, we evaluated whether the effects of cocaine on epigenetic editors (DNMTs and TETs) and cytokines interleukin-6 (IL-6) and IL-10 could be reversed by the DNMT inhibitor decitabine. Indeed, decitabine eliminated cocaine’s effect on the activity of TETs and DNMTs and decreased cytokine levels, whereas cocaine increased IL-6 and decreased IL-10. Conclusions Our data suggest that repeated psychostimulant exposure decreases TETs’ enzymatic activity in PBMCs. Co-treatment with decitabine reversed TETs’ levels and modulated immune response after repeated cocaine exposure. Further investigation is needed to clarify if TET could represent a putative biomarker of psychostimulant use and if DNMT inhibition could have therapeutic potential. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01303-w.
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Affiliation(s)
- Kaili Anier
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, 50411, Tartu, Estonia
| | - Kelli Somelar
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, 50411, Tartu, Estonia.
| | - Külli Jaako
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, 50411, Tartu, Estonia
| | - Margret Alttoa
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, 50411, Tartu, Estonia
| | - Kerli Sikk
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, 50411, Tartu, Estonia
| | - Raul Kokassaar
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, 50411, Tartu, Estonia
| | - Kai Kisand
- Department of Molecular Pathology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, 50411, Tartu, Estonia
| | - Anti Kalda
- Department of Pharmacology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, 50411, Tartu, Estonia
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Yan N, Li Y, Xing Y, Wu J, Li J, Liang Y, Tang Y, Wang Z, Song H, Wang H, Xiao S, Lu M. Developmental arsenic exposure impairs cognition, directly targets DNMT3A, and reduces DNA methylation. EMBO Rep 2022; 23:e54147. [PMID: 35373418 PMCID: PMC9171692 DOI: 10.15252/embr.202154147] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 03/10/2022] [Accepted: 03/16/2022] [Indexed: 12/21/2022] Open
Abstract
Developmental arsenic exposure has been associated with cognitive deficits in epidemiological studies, but the underlying mechanisms remain poorly understood. Here, we establish a mouse model of developmental arsenic exposure exhibiting deficits of recognition and spatial memory in the offspring. These deficits are associated with genome-wide DNA hypomethylation and abnormal expression of cognition-related genes in the hippocampus. Arsenic atoms directly bind to the cysteine-rich ADD domain of DNA methyltransferase 3A (DNMT3A), triggering ubiquitin- and proteasome-mediated degradation of DNMT3A in different cellular contexts. DNMT3A degradation leads to genome-wide DNA hypomethylation in mouse embryonic fibroblasts but not in non-embryonic cell lines. Treatment with metformin, a first-line antidiabetic agent reported to increase DNA methylation, ameliorates the behavioral deficits and normalizes the aberrant expression of cognition-related genes and DNA methylation in the hippocampus of arsenic-exposed offspring. Our study establishes a DNA hypomethylation effect of developmental arsenic exposure and proposes a potential treatment against cognitive deficits in the offspring of pregnant women in arsenic-contaminated areas.
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Affiliation(s)
- Ni Yan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuntong Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yangfei Xing
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiale Wu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiabing Li
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Liang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yigang Tang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhengyuan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huaxin Song
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haoyu Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shujun Xiao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Min Lu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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29
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Asada M, Hayashi H, Takagi N. Possible Involvement of DNA Methylation and Protective Effect of Zebularine on Neuronal Cell Death after Glutamate Excitotoxity. Biol Pharm Bull 2022; 45:770-779. [PMID: 35650104 DOI: 10.1248/bpb.b22-00147] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Neuronal cell death after cerebral ischemia consists various steps including glutamate excitotoxity. Excessive Ca2+ influx through the N-methyl-D-aspartate (NMDA) receptor, which is one of the ionotropic glutamate receptors, plays a central role in neuronal cell death after cerebral ischemia. We previously reported that DNA methylation is transiently increased in neurons during ischemic injury and that this aberrant DNA methylation is accompanied by neuronal cell death. Therefore, we performed the present experiments on glutamate excitotoxicity to gain further insight into DNA methylation involvement in the neuronal cell death. We demonstrated that knockdown of DNA methyltransferase (DNMT)1, DNMT3a, or DNMT3b gene in Neuro2a cells was performed to examine which DNMTs were more important for neuronal cell death after glutamate excitotoxicity. Although we confirmed a decrease in the levels of the target DNMT protein after small interfering RNA (siRNA) transfection, the Neuro2a cells were not protected from injury by transfection with siRNA for each DNMT. We next revealed that the pharmacological inhibitor of DNMTs protected against glutamate excitotoxicity in Neuro2a cells and also in primary cultured cortical neurons. This protective effect was associated with a decrease in the number of 5-methylcytosine (5 mC)-positive cells under glutamate excitotoxicity. In addition, the increased level of cleaved caspase-3 was also reduced by a DNMT inhibitor. Our results suggest the possibility that at least 2 or all DNMTs functionally would cooperate to activate DNA methylation after glutamate excitotoxicity and that inhibition of DNA methylation in neurons after cerebral ischemia might become a strategy to reduce the neuronal injury.
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Affiliation(s)
- Mayumi Asada
- Department of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences
| | - Hideki Hayashi
- Department of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences
| | - Norio Takagi
- Department of Applied Biochemistry, Tokyo University of Pharmacy and Life Sciences
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30
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Croizier S, Bouret SG. Molecular Control of the Development of Hypothalamic Neurons Involved in Metabolic Regulation. J Chem Neuroanat 2022; 123:102117. [DOI: 10.1016/j.jchemneu.2022.102117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/03/2022] [Accepted: 06/03/2022] [Indexed: 10/18/2022]
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31
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The disordered N-terminal domain of DNMT3A recognizes H2AK119ub and is required for postnatal development. Nat Genet 2022; 54:625-636. [PMID: 35534561 PMCID: PMC9295050 DOI: 10.1038/s41588-022-01063-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/28/2022] [Indexed: 02/03/2023]
Abstract
DNA methyltransferase 3a (DNMT3A) plays a crucial role during mammalian development. Two isoforms of DNMT3A are differentially expressed from stem cells to somatic tissues, but their individual functions remain largely uncharacterized. Here we report that the long isoform DNMT3A1, but not the short DNMT3A2, is essential for mouse postnatal development. DNMT3A1 binds to and regulates bivalent neurodevelopmental genes in the brain. Strikingly, Dnmt3a1 knockout perinatal lethality could be partially rescued by DNMT3A1 restoration in the nervous system. We further show that the intrinsically disordered N terminus of DNMT3A1 is required for normal development and DNA methylation at DNMT3A1-enriched regions. Mechanistically, a ubiquitin-interacting motif embedded in a putative α-helix within the N terminus binds to mono-ubiquitinated histone H2AK119, probably mediating recruitment of DNMT3A1 to Polycomb-regulated regions. These data demonstrate an isoform-specific role for DNMT3A1 in mouse postnatal development and reveal the N terminus as a necessary regulatory domain for DNMT3A1 chromatin occupancy and functions in the nervous system.
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32
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Luo L, Li R, Wang G, Chen J, Chen L, Qin LQ, Yu Z, Wan Z. Age-dependent effects of a high-fat diet combined with dietary advanced glycation end products on cognitive function and protection with voluntary exercise. Food Funct 2022; 13:4445-4458. [PMID: 35342920 DOI: 10.1039/d1fo03241k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
To determine whether a high fat diet (HFD) combined with an advanced glycation end products (AGEs) diet will induce worse cognitive impairment than a HFD alone and to investigate whether voluntary exercise is capable of improving cognitive function after the combined diet, young and middle-aged male C57BL/6J mice were randomly assigned to four groups, i.e., control, HFD, combined diet, and combined diet treated with voluntary exercise. Compared to HFD, combined diet induced worse memory abilities only in middle-aged mice, as exhibited by the reduced number of crossings and reduced distance in the target zone during a probe trial. Exercise reversed combined-diet-induced cognitive impairment for both ages of mice. For young mice, the neuro-protective effects of exercise were mainly associated with inhibition of NLRP3, Dnmt3a, Dnmt3b, and H3K9me2 and elevation of OST48; it also elevated Bacilli and reduced Epsilonproteobacteria, Campylobacterales, and Helicobacter. For middle-aged mice, exercise elevated Tet2, inhibited NF-κB and NLRP3, and rebalanced circadian clock proteins and the RAGE-OST48 axis; also, exercise elevated Coriobacteriia/Coriobacteriaceae, Erysipelotrichaceae, and Allobaculum and restored intestinal permeability.
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Affiliation(s)
- Lan Luo
- Department of Nutrition and Food Hygiene, School of Public Health, Soochow University, 199 Ren'ai Road, Suzhou, 215123, China.
| | - Rui Li
- Department of Nutrition and Food Hygiene, School of Public Health, Soochow University, 199 Ren'ai Road, Suzhou, 215123, China.
| | - Guiping Wang
- Laboratory Animal Center, Medical College of Soochow University, 199 Ren'ai Road, Suzhou, China
| | - Jingsi Chen
- Department of Nutrition and Food Hygiene, School of Public Health, Soochow University, 199 Ren'ai Road, Suzhou, 215123, China.
| | - Liangkai Chen
- Department of Nutrition and Food Hygiene, Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Li-Qiang Qin
- Department of Nutrition and Food Hygiene, School of Public Health, Soochow University, 199 Ren'ai Road, Suzhou, 215123, China.
| | - Zengli Yu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Zhongxiao Wan
- Department of Nutrition and Food Hygiene, School of Public Health, Soochow University, 199 Ren'ai Road, Suzhou, 215123, China.
- College of Public Health, Zhengzhou University, Zhengzhou 450001, Henan, China
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33
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Kaplan G, Xu H, Abreu K, Feng J. DNA Epigenetics in Addiction Susceptibility. Front Genet 2022; 13:806685. [PMID: 35145550 PMCID: PMC8821887 DOI: 10.3389/fgene.2022.806685] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/06/2022] [Indexed: 12/22/2022] Open
Abstract
Addiction is a chronically relapsing neuropsychiatric disease that occurs in some, but not all, individuals who use substances of abuse. Relatively little is known about the mechanisms which contribute to individual differences in susceptibility to addiction. Neural gene expression regulation underlies the pathogenesis of addiction, which is mediated by epigenetic mechanisms, such as DNA modifications. A growing body of work has demonstrated distinct DNA epigenetic signatures in brain reward regions that may be associated with addiction susceptibility. Furthermore, factors that influence addiction susceptibility are also known to have a DNA epigenetic basis. In the present review, we discuss the notion that addiction susceptibility has an underlying DNA epigenetic basis. We focus on major phenotypes of addiction susceptibility and review evidence of cell type-specific, time dependent, and sex biased effects of drug use. We highlight the role of DNA epigenetics in these diverse processes and propose its contribution to addiction susceptibility differences. Given the prevalence and lack of effective treatments for addiction, elucidating the DNA epigenetic mechanism of addiction vulnerability may represent an expeditious approach to relieving the addiction disease burden.
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Plaza-Diaz J, Izquierdo D, Torres-Martos Á, Baig AT, Aguilera CM, Ruiz-Ojeda FJ. Impact of Physical Activity and Exercise on the Epigenome in Skeletal Muscle and Effects on Systemic Metabolism. Biomedicines 2022; 10:biomedicines10010126. [PMID: 35052805 PMCID: PMC8773693 DOI: 10.3390/biomedicines10010126] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 12/30/2021] [Accepted: 01/04/2022] [Indexed: 02/05/2023] Open
Abstract
Exercise and physical activity induces physiological responses in organisms, and adaptations in skeletal muscle, which is beneficial for maintaining health and preventing and/or treating most chronic diseases. These adaptations are mainly instigated by transcriptional responses that ensue in reaction to each individual exercise, either resistance or endurance. Consequently, changes in key metabolic, regulatory, and myogenic genes in skeletal muscle occur as both an early and late response to exercise, and these epigenetic modifications, which are influenced by environmental and genetic factors, trigger those alterations in the transcriptional responses. DNA methylation and histone modifications are the most significant epigenetic changes described in gene transcription, linked to the skeletal muscle transcriptional response to exercise, and mediating the exercise adaptations. Nevertheless, other alterations in the epigenetics markers, such as epitranscriptomics, modifications mediated by miRNAs, and lactylation as a novel epigenetic modification, are emerging as key events for gene transcription. Here, we provide an overview and update of the impact of exercise on epigenetic modifications, including the well-described DNA methylations and histone modifications, and the emerging modifications in the skeletal muscle. In addition, we describe the effects of exercise on epigenetic markers in other metabolic tissues; also, we provide information about how systemic metabolism or its metabolites influence epigenetic modifications in the skeletal muscle.
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Affiliation(s)
- Julio Plaza-Diaz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain; (D.I.); (C.M.A.)
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain;
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada;
- Correspondence: (J.P.-D.); (F.J.R.-O.); Tel.: +34-9-5824-1000 (ext. 20314) (F.J.R.-O.)
| | - David Izquierdo
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain; (D.I.); (C.M.A.)
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain;
| | - Álvaro Torres-Martos
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain;
| | - Aiman Tariq Baig
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada;
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 85M, Canada
| | - Concepción M. Aguilera
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain; (D.I.); (C.M.A.)
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain;
- Center of Biomedical Research, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Avda. del Conocimiento s/n., 18016 Granada, Spain
- CIBEROBN (CIBER Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Francisco Javier Ruiz-Ojeda
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain; (D.I.); (C.M.A.)
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain;
- RG Adipocytes and Metabolism, Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz, Center Munich, Neuherberg, 85764 Munich, Germany
- Correspondence: (J.P.-D.); (F.J.R.-O.); Tel.: +34-9-5824-1000 (ext. 20314) (F.J.R.-O.)
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35
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Guo X, Zhang G, Cai W, Huang F, Qin J, Song X. Long non-coding RNA rhabdomyosarcoma 2-associated transcript contributes to neuropathic pain by recruiting HuR to stabilize DNA methyltransferase 3 alpha mRNA expression in dorsal root ganglion neuron. Front Mol Neurosci 2022; 15:1027063. [PMID: 36911851 PMCID: PMC9992530 DOI: 10.3389/fnmol.2022.1027063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/16/2022] [Indexed: 02/24/2023] Open
Abstract
Introduction Long non-coding RNAs (lncRNAs) act as key regulators in multiple human diseases. In particular, the dysfunction of lncRNAs in dorsal root ganglion (DRG) contributes to the pathogenesis of neuropathic pain (NP). Nevertheless, the role and mechanism of most lncRNAs in NP remain unclear. Methods Two classic chronic NP models, including L4 spinal nerve ligation (SNL) model and chronic constriction injury (CCI) of the sciatic nerve, were performed. Mechanical allodynia and heat hyperalgesia were used to evaluate neuropathic pain. DRG microinjection was used to deliver agents into DRG. qRT-PCR, immunofluorescence, immunoprecipitation, western blotting, siRNA transfection, AAV transduction were performed to investigate the phenotypes and molecular basis. Results Here, we discovered that Rmst as a lncRNA was specifically expressed in Atf3 + injured DRG neurons and significantly upregulated following peripheral nerve damage. Rmst overexpression by direct DRG injection of AAV5-Rmst causes neuropathic symptoms in the absence of nerve damage. Conversely, blocking Rmst expression in injured DRGs alleviated nerve injury-induced pain hypersensitivities and downregulated Dnmt3a expression. Furthermore, we found peripheral nerve damage induced Rmst increase could interact with RNA-binding protein HuR to stabilize the Dnmt3a mRNA. Conclusion Our findings reveal a crucial role of Rmst in damaged DRG neurons under NP condition and provide a novel target for drug development against NP.
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Affiliation(s)
- Xinying Guo
- Department of Anesthesiology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Gaolong Zhang
- Department of Anesthesiology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Weihua Cai
- Department of Anesthesia, McGill University, Montreal, QC, Canada
| | - Fa Huang
- Department of Anesthesiology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Jingwen Qin
- Department of Anesthesiology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Xingrong Song
- Department of Anesthesiology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
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36
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Sheehy RN, Quintanilla LJ, Song J. Epigenetic regulation in the neurogenic niche of the adult dentate gyrus. Neurosci Lett 2022; 766:136343. [PMID: 34774980 PMCID: PMC8691367 DOI: 10.1016/j.neulet.2021.136343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/06/2021] [Accepted: 11/08/2021] [Indexed: 01/03/2023]
Abstract
The adult dentate gyrus (DG) of the hippocampal formation is a specialized region of the brain that creates new adult-born neurons from a pool of resident adult neural stem and progenitor cells (aNSPCs) throughout life. These aNSPCs undergo epigenetic and epitranscriptomic regulation, including 3D genome interactions, histone modifications, DNA modifications, noncoding RNA mechanisms, and RNA modifications, to precisely control the neurogenic process. Furthermore, the specialized neurogenic niche also uses epigenetic mechanisms in mature neurons and glial cells to communicate signals to direct the behavior of the aNSPCs. Here, we review recent advances of epigenetic regulation in aNSPCs and their surrounding niche cells within the adult DG.
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Affiliation(s)
- Ryan N. Sheehy
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Pharmacology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Luis J. Quintanilla
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Neuroscience Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Juan Song
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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37
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Yildiz CB, Zimmer-Bensch G. Role of DNMTs in the Brain. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:363-394. [DOI: 10.1007/978-3-031-11454-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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38
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Li J, Li L, Wang Y, Huang G, Li X, Xie Z, Zhou Z. Insights Into the Role of DNA Methylation in Immune Cell Development and Autoimmune Disease. Front Cell Dev Biol 2021; 9:757318. [PMID: 34790667 PMCID: PMC8591242 DOI: 10.3389/fcell.2021.757318] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/07/2021] [Indexed: 12/26/2022] Open
Abstract
To date, nearly 100 autoimmune diseases have been an area of focus, and these diseases bring health challenges to approximately 5% of the population worldwide. As a type of disease caused by tolerance breakdown, both environmental and genetic risk factors contribute to autoimmune disease development. However, in most cases, there are still gaps in our understanding of disease pathogenesis, diagnosis, and treatment. Therefore, more detailed knowledge of disease pathogenesis and potential therapies is indispensable. DNA methylation, which does not affect the DNA sequence, is one of the key epigenetic silencing mechanisms and has been indicated to play a key role in gene expression regulation and to participate in the development of certain autoimmune diseases. Potential epigenetic regulation via DNA methylation has garnered more attention as a disease biomarker in recent years. In this review, we clarify the basic function and distribution of DNA methylation, evaluate its effects on gene expression and discuss related key enzymes. In addition, we summarize recent aberrant DNA methylation modifications identified in the most important cell types related to several autoimmune diseases and then provide potential directions for better diagnosing and monitoring disease progression driven by epigenetic control, which may broaden our understanding and contribute to further epigenetic research in autoimmune diseases.
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Affiliation(s)
- Jiaqi Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Lifang Li
- Department of Ultrasound, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yimeng Wang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
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Epigenetic Mechanisms in Memory and Cognitive Decline Associated with Aging and Alzheimer's Disease. Int J Mol Sci 2021; 22:ijms222212280. [PMID: 34830163 PMCID: PMC8618067 DOI: 10.3390/ijms222212280] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/21/2022] Open
Abstract
Epigenetic mechanisms, which include DNA methylation, a variety of post-translational modifications of histone proteins (acetylation, phosphorylation, methylation, ubiquitination, sumoylation, serotonylation, dopaminylation), chromatin remodeling enzymes, and long non-coding RNAs, are robust regulators of activity-dependent changes in gene transcription. In the brain, many of these epigenetic modifications have been widely implicated in synaptic plasticity and memory formation. Dysregulation of epigenetic mechanisms has been reported in the aged brain and is associated with or contributes to memory decline across the lifespan. Furthermore, alterations in the epigenome have been reported in neurodegenerative disorders, including Alzheimer’s disease. Here, we review the diverse types of epigenetic modifications and their role in activity- and learning-dependent synaptic plasticity. We then discuss how these mechanisms become dysregulated across the lifespan and contribute to memory loss with age and in Alzheimer’s disease. Collectively, the evidence reviewed here strongly supports a role for diverse epigenetic mechanisms in memory formation, aging, and neurodegeneration in the brain.
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Allison J, Kaliszewska A, Uceda S, Reiriz M, Arias N. Targeting DNA Methylation in the Adult Brain through Diet. Nutrients 2021; 13:nu13113979. [PMID: 34836233 PMCID: PMC8618930 DOI: 10.3390/nu13113979] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 02/07/2023] Open
Abstract
Metabolism and nutrition have a significant role in epigenetic modifications such as DNA methylation, which can influence gene expression. Recently, it has been suggested that bioactive nutrients and gut microbiota can alter DNA methylation in the central nervous system (CNS) through the gut-brain axis, playing a crucial role in modulating CNS functions and, finally, behavior. Here, we will focus on the effect of metabolic signals in shaping brain DNA methylation during adulthood. We will provide an overview of potential interactions among diet, gastrointestinal microbiome and epigenetic alterations on brain methylation and behavior. In addition, the impact of different diet challenges on cytosine methylation dynamics in the adult brain will be discussed. Finally, we will explore new ways to modulate DNA hydroxymethylation, which is particularly abundant in neural tissue, through diet.
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Affiliation(s)
- Joseph Allison
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Denmark Hill, London SE5 8AF, UK; (J.A.); (A.K.)
| | - Aleksandra Kaliszewska
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Denmark Hill, London SE5 8AF, UK; (J.A.); (A.K.)
| | - Sara Uceda
- BRABE Group, Department of Psychology, Faculty of Life and Natural Sciences, University of Nebrija, C/del Hostal, 28248 Madrid, Spain; (S.U.); (M.R.)
| | - Manuel Reiriz
- BRABE Group, Department of Psychology, Faculty of Life and Natural Sciences, University of Nebrija, C/del Hostal, 28248 Madrid, Spain; (S.U.); (M.R.)
| | - Natalia Arias
- BRABE Group, Department of Psychology, Faculty of Life and Natural Sciences, University of Nebrija, C/del Hostal, 28248 Madrid, Spain; (S.U.); (M.R.)
- Institute of Neurosciences of the Principality of Asturias (INEUROPA), 33003 Oviedo, Spain
- Health Research Institute of the Principality of Asturias—ISPA, 33011 Oviedo, Spain
- Correspondence: ; Tel.: +34-91-452-1101
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41
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Reichard J, Zimmer-Bensch G. The Epigenome in Neurodevelopmental Disorders. Front Neurosci 2021; 15:776809. [PMID: 34803599 PMCID: PMC8595945 DOI: 10.3389/fnins.2021.776809] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/04/2021] [Indexed: 12/26/2022] Open
Abstract
Neurodevelopmental diseases (NDDs), such as autism spectrum disorders, epilepsy, and schizophrenia, are characterized by diverse facets of neurological and psychiatric symptoms, differing in etiology, onset and severity. Such symptoms include mental delay, cognitive and language impairments, or restrictions to adaptive and social behavior. Nevertheless, all have in common that critical milestones of brain development are disrupted, leading to functional deficits of the central nervous system and clinical manifestation in child- or adulthood. To approach how the different development-associated neuropathologies can occur and which risk factors or critical processes are involved in provoking higher susceptibility for such diseases, a detailed understanding of the mechanisms underlying proper brain formation is required. NDDs rely on deficits in neuronal identity, proportion or function, whereby a defective development of the cerebral cortex, the seat of higher cognitive functions, is implicated in numerous disorders. Such deficits can be provoked by genetic and environmental factors during corticogenesis. Thereby, epigenetic mechanisms can act as an interface between external stimuli and the genome, since they are known to be responsive to external stimuli also in cortical neurons. In line with that, DNA methylation, histone modifications/variants, ATP-dependent chromatin remodeling, as well as regulatory non-coding RNAs regulate diverse aspects of neuronal development, and alterations in epigenomic marks have been associated with NDDs of varying phenotypes. Here, we provide an overview of essential steps of mammalian corticogenesis, and discuss the role of epigenetic mechanisms assumed to contribute to pathophysiological aspects of NDDs, when being disrupted.
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Affiliation(s)
- Julia Reichard
- Functional Epigenetics in the Animal Model, Institute for Biology II, RWTH Aachen University, Aachen, Germany
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany
| | - Geraldine Zimmer-Bensch
- Functional Epigenetics in the Animal Model, Institute for Biology II, RWTH Aachen University, Aachen, Germany
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, Aachen, Germany
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42
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Thomas KT, Zakharenko SS. MicroRNAs in the Onset of Schizophrenia. Cells 2021; 10:2679. [PMID: 34685659 PMCID: PMC8534348 DOI: 10.3390/cells10102679] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/30/2021] [Accepted: 10/02/2021] [Indexed: 12/14/2022] Open
Abstract
Mounting evidence implicates microRNAs (miRNAs) in the pathology of schizophrenia. These small noncoding RNAs bind to mRNAs containing complementary sequences and promote their degradation and/or inhibit protein synthesis. A single miRNA may have hundreds of targets, and miRNA targets are overrepresented among schizophrenia-risk genes. Although schizophrenia is a neurodevelopmental disorder, symptoms usually do not appear until adolescence, and most patients do not receive a schizophrenia diagnosis until late adolescence or early adulthood. However, few studies have examined miRNAs during this critical period. First, we examine evidence that the miRNA pathway is dynamic throughout adolescence and adulthood and that miRNAs regulate processes critical to late neurodevelopment that are aberrant in patients with schizophrenia. Next, we examine evidence implicating miRNAs in the conversion to psychosis, including a schizophrenia-associated single nucleotide polymorphism in MIR137HG that is among the strongest known predictors of age of onset in patients with schizophrenia. Finally, we examine how hemizygosity for DGCR8, which encodes an obligate component of the complex that synthesizes miRNA precursors, may contribute to the onset of psychosis in patients with 22q11.2 microdeletions and how animal models of this disorder can help us understand the many roles of miRNAs in the onset of schizophrenia.
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Affiliation(s)
- Kristen T. Thomas
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Stanislav S. Zakharenko
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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43
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Abstract
Epigenetic mechanisms such as DNA methylation (DNAm) have been associated with stress responses and increased vulnerability to depression. Abnormal DNAm is observed in stressed animals and depressed individuals. Antidepressant treatment modulates DNAm levels and regulates gene expression in diverse tissues, including the brain and the blood. Therefore, DNAm could be a potential therapeutic target in depression. Here, we reviewed the current knowledge about the involvement of DNAm in the behavioural and molecular changes associated with stress exposure and depression. We also evaluated the possible use of DNAm changes as biomarkers of depression. Finally, we discussed current knowledge limitations and future perspectives.
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Kausar S, Abbas MN, Cui H. A review on the DNA methyltransferase family of insects: Aspect and prospects. Int J Biol Macromol 2021; 186:289-302. [PMID: 34237376 DOI: 10.1016/j.ijbiomac.2021.06.205] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/22/2021] [Accepted: 06/30/2021] [Indexed: 12/11/2022]
Abstract
The DNA methyltransferase family contains a conserved set of DNA-modifying enzymatic proteins. They are responsible for epigenetic gene modulation, such as transcriptional silencing, transcription activation, and post-transcriptional modulation. Recent research has revealed that the canonical DNA methyltransferases (DNMTs) biological roles go beyond their traditional functions of establishing and maintaining DNA methylation patterns. Although a complete DNA methylation toolkit is absent in most insect orders, recent evidence indicates the de novo DNA methylation and maintenance function remain conserved. Studies using various molecular approaches provided evidence that DNMTs are multi-functional proteins. However, still in-depth studies on their biological role lack due to the least studied area in insects. Here, we review the DNA methylation toolkit of insects, focusing on recent research on various insect orders, which exhibit DNA methylation at different levels, and for which DNMTs functional studies have become available in recent years. We survey research on the potential roles of DNMTs in the regulation of gene transcription in insect species. DNMTs participate in different physiological processes by interacting with other epigenetic factors. Future studies on insect's DNMTs will benefit to understand developmental processes, responses to various stimuli, and adaptability of insects to different environmental conditions.
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Affiliation(s)
- Saima Kausar
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Muhammad Nadeem Abbas
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China.
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Piotrowska M, Gliwiński M, Trzonkowski P, Iwaszkiewicz-Grzes D. Regulatory T Cells-Related Genes Are under DNA Methylation Influence. Int J Mol Sci 2021; 22:7144. [PMID: 34281195 PMCID: PMC8267835 DOI: 10.3390/ijms22137144] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022] Open
Abstract
Regulatory T cells (Tregs) exert a highly suppressive function in the immune system. Disturbances in their function predispose an individual to autoimmune dysregulation, with a predominance of the pro-inflammatory environment. Besides Foxp3, which is a master regulator of these cells, other genes (e.g., Il2ra, Ctla4, Tnfrsf18, Ikzf2, and Ikzf4) are also involved in Tregs development and function. Multidimensional Tregs suppression is determined by factors that are believed to be crucial in the action of Tregs-related genes. Among them, epigenetic changes, such as DNA methylation, tend to be widely studied over the past few years. DNA methylation acts as a repressive mark, leading to diminished gene expression. Given the role of increased CpG methylation upon Tregs imprinting and functional stability, alterations in the methylation pattern can cause an imbalance in the immune response. Due to the fact that epigenetic changes can be reversible, so-called epigenetic modifiers are broadly used in order to improve Tregs performance. In this review, we place emphasis on the role of DNA methylation of the genes that are key regulators of Tregs function. We also discuss disease settings that have an impact on the methylation status of Tregs and systematize the usefulness of epigenetic drugs as factors able to influence Tregs functions.
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Affiliation(s)
| | | | | | - Dorota Iwaszkiewicz-Grzes
- Department of Medical Immunology, Medical University of Gdansk, 80-210 Gdańsk, Poland; (M.P.); (M.G.); (P.T.)
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46
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Hyeon JW, Kim AH, Yano H. Epigenetic regulation in Huntington's disease. Neurochem Int 2021; 148:105074. [PMID: 34038804 DOI: 10.1016/j.neuint.2021.105074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/23/2021] [Accepted: 05/17/2021] [Indexed: 12/25/2022]
Abstract
Huntington's disease (HD) is a devastating and fatal monogenic neurodegenerative disorder characterized by progressive loss of selective neurons in the brain and is caused by an abnormal expansion of CAG trinucleotide repeats in a coding exon of the huntingtin (HTT) gene. Progressive gene expression changes that begin at premanifest stages are a prominent feature of HD and are thought to contribute to disease progression. Increasing evidence suggests the critical involvement of epigenetic mechanisms in abnormal transcription in HD. Genome-wide alterations of a number of epigenetic modifications, including DNA methylation and multiple histone modifications, are associated with HD, suggesting that mutant HTT causes complex epigenetic abnormalities and chromatin structural changes, which may represent an underlying pathogenic mechanism. The causal relationship of specific epigenetic changes to early transcriptional alterations and to disease pathogenesis require further investigation. In this article, we review recent studies on epigenetic regulation in HD with a focus on DNA and histone modifications. We also discuss the contribution of epigenetic modifications to HD pathogenesis as well as potential mechanisms linking mutant HTT and epigenetic alterations. Finally, we discuss the therapeutic potential of epigenetic-based treatments.
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Affiliation(s)
- Jae Wook Hyeon
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hiroko Yano
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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Acupuncture alleviates chronic pain and comorbid conditions in a mouse model of neuropathic pain: the involvement of DNA methylation in the prefrontal cortex. Pain 2021; 162:514-530. [PMID: 32796318 PMCID: PMC7808350 DOI: 10.1097/j.pain.0000000000002031] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/13/2020] [Indexed: 12/12/2022]
Abstract
ABSTRACT Chronic pain reduces life quality and is an important clinical problem associated with emotional and cognitive dysfunction. Epigenetic regulation of DNA methylation is involved in the induction of abnormal behaviors and pathological gene expression. We examined whether acupuncture can restore epigenetic changes caused by chronic pain, and identified the underlying mechanisms in neuropathic pain mice. Acupuncture treatment for 6 months (3 days/week) improved mechanical/cold allodynia and the emotional/cognitive dysfunction caused by left partial sciatic nerve ligation (PSNL)-induced neuropathic pain. The effects of acupuncture were associated with global DNA methylation recovery in the prefrontal cortex (PFC). Analysis of DNA methylation patterns in PFC indicated that 1364 overlapping genes among 4442 and 4416 methylated genes in the PSNL vs sham and PSNL vs acupuncture points groups, respectively, were highly associated with the DNA methylation process. Acupuncture restored the reduced expression of 5-methylcytosine, methyl-cytosine-phospho-guanine binding protein 2, and DNA methyltransferase family enzymes induced by PSNL in PFC. Methylation levels of Nr4a1 and Chkb associated with mitochondrial dysfunction were decreased in PFC of the PSNL mice, and increased by acupuncture. By contrast, high expression of Nr4a1 and Chkb mRNA in PSNL mice decreased after acupuncture. We also found that acupuncture inhibited the expression of Ras pathway-related genes such as Rasgrp1 and Rassf1. Finally, the expression of Nr4a1, Rasgrp1, Rassf1, and Chkb mRNA increased in the neuronal cells treated with Mecp2 small interfering RNA. These results suggest that acupuncture can relieve chronic pain-induced comorbid conditions by altering DNA methylation of Nr4a1, Rasgrp1, Rassf1, and Chkb in the PFC.
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48
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Implications of Extended Inhibitory Neuron Development. Int J Mol Sci 2021; 22:ijms22105113. [PMID: 34066025 PMCID: PMC8150951 DOI: 10.3390/ijms22105113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 12/23/2022] Open
Abstract
A prolonged developmental timeline for GABA (γ-aminobutyric acid)-expressing inhibitory neurons (GABAergic interneurons) is an amplified trait in larger, gyrencephalic animals. In several species, the generation, migration, and maturation of interneurons take place over several months, in some cases persisting after birth. The late integration of GABAergic interneurons occurs in a region-specific pattern, especially during the early postnatal period. These changes can contribute to the formation of functional connectivity and plasticity, especially in the cortical regions responsible for higher cognitive tasks. In this review, we discuss GABAergic interneuron development in the late gestational and postnatal forebrain. We propose the protracted development of interneurons at each stage (neurogenesis, neuronal migration, and network integration), as a mechanism for increased complexity and cognitive flexibility in larger, gyrencephalic brains. This developmental feature of interneurons also provides an avenue for environmental influences to shape neural circuit formation.
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49
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Pfeifer GP. DNA repair in neurons and its possible link to the epigenetic machinery at enhancers. Epigenomics 2021; 13:913-917. [PMID: 33942660 DOI: 10.2217/epi-2021-0129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Gerd P Pfeifer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
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50
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Swahari V, Nakamura A, Hollville E, Stroud H, Simon JM, Ptacek TS, Beck MV, Flowers C, Guo J, Plestant C, Liang J, Kurtz CL, Kanke M, Hammond SM, He YW, Anton ES, Sethupathy P, Moy SS, Greenberg ME, Deshmukh M. MicroRNA-29 is an essential regulator of brain maturation through regulation of CH methylation. Cell Rep 2021; 35:108946. [PMID: 33826889 PMCID: PMC8103628 DOI: 10.1016/j.celrep.2021.108946] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/09/2020] [Accepted: 03/14/2021] [Indexed: 11/27/2022] Open
Abstract
Although embryonic brain development and neurodegeneration have received considerable attention, the events that govern postnatal brain maturation are less understood. Here, we identify the miR-29 family to be strikingly induced during the late stages of brain maturation. Brain maturation is associated with a transient, postnatal period of de novo non-CG (CH) DNA methylation mediated by DNMT3A. We examine whether an important function of miR-29 during brain maturation is to restrict the period of CH methylation via its targeting of Dnmt3a. Deletion of miR-29 in the brain, or knockin mutations preventing miR-29 to specifically target Dnmt3a, result in increased DNMT3A expression, higher CH methylation, and repression of genes associated with neuronal activity and neuropsychiatric disorders. These mouse models also develop neurological deficits and premature lethality. Our results identify an essential role for miR-29 in restricting CH methylation in the brain and illustrate the importance of CH methylation regulation for normal brain maturation.
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Affiliation(s)
- Vijay Swahari
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA.
| | - Ayumi Nakamura
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Neurobiology Curriculum, University of North Carolina, Chapel Hill, NC, USA
| | - Emilie Hollville
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - Hume Stroud
- Department of Neurobiology, Harvard University, Boston, MA, USA
| | - Jeremy M Simon
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA
| | - Travis S Ptacek
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA
| | - Matthew V Beck
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - Cornelius Flowers
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | - Jiami Guo
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
| | | | - Jie Liang
- Department of Immunology, Duke University, Durham, NC, USA
| | - C Lisa Kurtz
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Matt Kanke
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Scott M Hammond
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - You-Wen He
- Department of Immunology, Duke University, Durham, NC, USA
| | - E S Anton
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Neurobiology Curriculum, University of North Carolina, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA
| | - Praveen Sethupathy
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA; Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA
| | - Sheryl S Moy
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA
| | | | - Mohanish Deshmukh
- Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA; Neurobiology Curriculum, University of North Carolina, Chapel Hill, NC, USA; Carolina Institute for Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, USA.
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