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Erlitzki N, Kohli RM. An Overview of Global, Local, and Base-Resolution Methods for the Detection of 5-Hydroxymethylcytosine in Genomic DNA. Methods Mol Biol 2024; 2842:325-352. [PMID: 39012604 DOI: 10.1007/978-1-0716-4051-7_17] [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] [Indexed: 07/17/2024]
Abstract
The discovery of 5-hydroxymethylcytosine (5hmC) as a common DNA modification in mammalian genomes has ushered in new areas of inquiry regarding the dynamic epigenome. The balance between 5hmC and its precursor, 5-methylcytosine (5mC), has emerged as a determinant of key processes including cell fate specification, and alterations involving these bases have been implicated in the pathogenesis of various diseases. The identification of 5hmC separately from 5mC initially posed a challenge given that legacy epigenetic sequencing technologies could not discriminate between these two most abundant modifications, a significant blind spot considering their potentially functionally opposing roles. The growing interest in 5hmC, as well as in the Ten-Eleven Translocation (TET) family enzymes that catalyze its generation and further oxidation to 5-formylcytosine (5fC) and 5-carboxycytosine (5caC), has spurred the development of versatile methods for 5hmC detection. These methods enable the quantification and localization of 5hmC in diverse biological samples and, in some cases, at the resolution of individual nucleotides. However, navigating this growing toolbox of methods for 5hmC detection can be challenging. Here, we detail existing and emerging methods for the detection, quantification, and localization of 5hmC at global, locus-specific, and base resolution levels. These methods are discussed in the context of their advantages and limitations, with the goal of providing a framework to help guide researchers in choosing the level of resolution and the associated method that could be most suitable for specific needs.
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Affiliation(s)
- Noa Erlitzki
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
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Kaplánek R, Kejík Z, Hajduch J, Veselá K, Kučnirová K, Skaličková M, Venhauerová A, Hosnedlová B, Hromádka R, Dytrych P, Novotný P, Abramenko N, Antonyová V, Hoskovec D, Babula P, Masařík M, Martásek P, Jakubek M. TET protein inhibitors: Potential and limitations. Biomed Pharmacother 2023; 166:115324. [PMID: 37598475 DOI: 10.1016/j.biopha.2023.115324] [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: 04/25/2023] [Revised: 07/31/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023] Open
Abstract
TET proteins (methylcytosine dioxygenases) play an important role in the regulation of gene expression. Dysregulation of their activity is associated with many serious pathogenic states such as oncological diseases. Regulation of their activity by specific inhibitors could represent a promising therapeutic strategy. Therefore, this review describes various types of TET protein inhibitors in terms of their inhibitory mechanism and possible applicability. The potential and possible limitations of this approach are thoroughly discussed in the context of TET protein functionality in living systems. Furthermore, possible therapeutic strategies based on the inhibition of TET proteins are presented and evaluated, especially in the field of oncological diseases.
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Affiliation(s)
- Robert Kaplánek
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Zdeněk Kejík
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Jan Hajduch
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Kateřina Veselá
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Kateřina Kučnirová
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Markéta Skaličková
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Anna Venhauerová
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Božena Hosnedlová
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Róbert Hromádka
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Petr Dytrych
- 1st Department of Surgery-Department of Abdominal, Thoracic Surgery and Traumatology, First Faculty of Medicine, Charles University and General University Hospital, U Nemocnice 2, 121 08 Prague, Czech Republic
| | - Petr Novotný
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Nikita Abramenko
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - Veronika Antonyová
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
| | - David Hoskovec
- 1st Department of Surgery-Department of Abdominal, Thoracic Surgery and Traumatology, First Faculty of Medicine, Charles University and General University Hospital, U Nemocnice 2, 121 08 Prague, Czech Republic
| | - Petr Babula
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Michal Masařík
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Pavel Martásek
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic.
| | - Milan Jakubek
- BIOCEV, First Faculty of Medicine, Charles University, Průmyslová 595, 252 50 Vestec, Czech Republic; Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic.
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Liu J, Li T, Zhong G, Pan Y, Gao M, Su S, Liang Y, Ma C, Liu Y, Wang Q, Shi Q. Exploring the therapeutic potential of natural compounds for Alzheimer's disease: Mechanisms of action and pharmacological properties. Biomed Pharmacother 2023; 166:115406. [PMID: 37659206 DOI: 10.1016/j.biopha.2023.115406] [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: 07/18/2023] [Revised: 08/26/2023] [Accepted: 08/28/2023] [Indexed: 09/04/2023] Open
Abstract
Alzheimer's Disease (AD) is a global public health priority characterized by high mortality rates in adults and an increasing prevalence in aging populations worldwide. Despite significant advancements in comprehending the pathogenesis of AD since its initial report in 1907, there remains a lack of effective curative or preventive measures for the disease. In recent years, natural compounds sourced from diverse origins have garnered considerable attention as potential therapeutic agents for AD, owing to their anti-inflammatory, antioxidant, and neuroprotective properties. This review aims to consolidate the therapeutic effects of natural compounds on AD, specifically targeting the reduction of β-amyloid (Aβ) overproduction, anti-apoptosis, autophagy, neuroinflammation, oxidative stress, endoplasmic reticulum (ER) stress, and mitochondrial dysfunction. Notably, the identified compounds exhibiting these effects predominantly originate from plants. This review provides valuable insights into the potential of natural compounds as a reservoir of novel therapeutic agents for AD, thereby stimulating further research and contributing to the development of efficacious treatments for this devastating disease.
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Affiliation(s)
- Jinman Liu
- Affiliated Jiangmen TCM Hospital of Ji'nan University, Jiangmen 529099, China
| | - Tianyao Li
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Guangcheng Zhong
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Yaru Pan
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Minghuang Gao
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Shijie Su
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Yong Liang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Cuiru Ma
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Yuanyue Liu
- Department of Neurology, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210017, China
| | - Qi Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China.
| | - Qing Shi
- Affiliated Jiangmen TCM Hospital of Ji'nan University, Jiangmen 529099, China.
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Wang E, Wang M, Guo L, Fullard JF, Micallef C, Bendl J, Song WM, Ming C, Huang Y, Li Y, Yu K, Peng J, Bennett DA, De Jager PL, Roussos P, Haroutunian V, Zhang B. Genome-wide methylomic regulation of multiscale gene networks in Alzheimer's disease. Alzheimers Dement 2023; 19:3472-3495. [PMID: 36811307 PMCID: PMC10440222 DOI: 10.1002/alz.12969] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/19/2022] [Indexed: 02/24/2023]
Abstract
INTRODUCTION Recent studies revealed the association of abnormal methylomic changes with Alzheimer's disease (AD) but there is a lack of systematic study of the impact of methylomic alterations over the molecular networks underlying AD. METHODS We profiled genome-wide methylomic variations in the parahippocampal gyrus from 201 post mortem control, mild cognitive impaired, and AD brains. RESULTS We identified 270 distinct differentially methylated regions (DMRs) associated with AD. We quantified the impact of these DMRs on each gene and each protein as well as gene and protein co-expression networks. DNA methylation had a profound impact on both AD-associated gene/protein modules and their key regulators. We further integrated the matched multi-omics data to show the impact of DNA methylation on chromatin accessibility, which further modulates gene and protein expression. DISCUSSION The quantified impact of DNA methylation on gene and protein networks underlying AD identified potential upstream epigenetic regulators of AD. HIGHLIGHTS A cohort of DNA methylation data in the parahippocampal gyrus was developed from 201 post mortem control, mild cognitive impaired, and Alzheimer's disease (AD) brains. Two hundred seventy distinct differentially methylated regions (DMRs) were found to be associated with AD compared to normal control. A metric was developed to quantify methylation impact on each gene and each protein. DNA methylation was found to have a profound impact on not only the AD-associated gene modules but also key regulators of the gene and protein networks. Key findings were validated in an independent multi-omics cohort in AD. The impact of DNA methylation on chromatin accessibility was also investigated by integrating the matched methylomic, epigenomic, transcriptomic, and proteomic data.
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Affiliation(s)
- Erming Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Lei Guo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - John F Fullard
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Courtney Micallef
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Jaroslav Bendl
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Won-min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Chen Ming
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Yong Huang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Yuxin Li
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Kaiwen Yu
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology and the Taub Institute, Columbia University Medical Center, New York, New York, USA
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY 10468, USA
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Vahram Haroutunian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, 130 West Kingsbridge Road, Bronx, NY 10468, USA
- The Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, One Gustave L Levy Place, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
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Donato L, Mordà D, Scimone C, Alibrandi S, D'Angelo R, Sidoti A. How Many Alzheimer-Perusini's Atypical Forms Do We Still Have to Discover? Biomedicines 2023; 11:2035. [PMID: 37509674 PMCID: PMC10377159 DOI: 10.3390/biomedicines11072035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Alzheimer-Perusini's (AD) disease represents the most spread dementia around the world and constitutes a serious problem for public health. It was first described by the two physicians from whom it took its name. Nowadays, we have extensively expanded our knowledge about this disease. Starting from a merely clinical and histopathologic description, we have now reached better molecular comprehension. For instance, we passed from an old conceptualization of the disease based on plaques and tangles to a more modern vision of mixed proteinopathy in a one-to-one relationship with an alteration of specific glial and neuronal phenotypes. However, no disease-modifying therapies are yet available. It is likely that the only way to find a few "magic bullets" is to deepen this aspect more and more until we are able to draw up specific molecular profiles for single AD cases. This review reports the most recent classifications of AD atypical variants in order to summarize all the clinical evidence using several discrimina (for example, post mortem neurofibrillary tangle density, cerebral atrophy, or FDG-PET studies). The better defined four atypical forms are posterior cortical atrophy (PCA), logopenic variant of primary progressive aphasia (LvPPA), behavioral/dysexecutive variant and AD with corticobasal degeneration (CBS). Moreover, we discuss the usefulness of such classifications before outlining the molecular-genetic aspects focusing on microglial activity or, more generally, immune system control of neuroinflammation and neurodegeneration.
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Affiliation(s)
- Luigi Donato
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy
- Department of Biomolecular Strategies, Genetics, Cutting-Edge Therapies, Euro-Mediterranean Institute of Science and Technology, Via Michele Miraglia, 98139 Palermo, Italy
| | - Domenico Mordà
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy
- Department of Biomolecular Strategies, Genetics, Cutting-Edge Therapies, Euro-Mediterranean Institute of Science and Technology, Via Michele Miraglia, 98139 Palermo, Italy
| | - Concetta Scimone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy
- Department of Biomolecular Strategies, Genetics, Cutting-Edge Therapies, Euro-Mediterranean Institute of Science and Technology, Via Michele Miraglia, 98139 Palermo, Italy
| | - Simona Alibrandi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy
| | - Rosalia D'Angelo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy
| | - Antonina Sidoti
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Via Consolare Valeria 1, 98125 Messina, Italy
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Hernaiz A, Sentre S, Betancor M, López-Pérez Ó, Salinas-Pena M, Zaragoza P, Badiola JJ, Toivonen JM, Bolea R, Martín-Burriel I. 5-Methylcytosine and 5-Hydroxymethylcytosine in Scrapie-Infected Sheep and Mouse Brain Tissues. Int J Mol Sci 2023; 24:ijms24021621. [PMID: 36675131 PMCID: PMC9864596 DOI: 10.3390/ijms24021621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Scrapie is a neurodegenerative disorder belonging to the group of transmissible spongiform encephalopathies or prion diseases, which are caused by an infectious isoform of the innocuous cellular prion protein (PrPC) known as PrPSc. DNA methylation, one of the most studied epigenetic mechanisms, is essential for the proper functioning of the central nervous system. Recent findings point to possible involvement of DNA methylation in the pathogenesis of prion diseases, but there is still a lack of knowledge about the behavior of this epigenetic mechanism in such neurodegenerative disorders. Here, we evaluated by immunohistochemistry the 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) levels in sheep and mouse brain tissues infected with scrapie. Expression analysis of different gene coding for epigenetic regulatory enzymes (DNMT1, DNMT3A, DNMT3B, HDAC1, HDAC2, TET1, and TET2) was also carried out. A decrease in 5mC levels was observed in scrapie-affected sheep and mice compared to healthy animals, whereas 5hmC displayed opposite patterns between the two models, demonstrating a decrease in 5hmC in scrapie-infected sheep and an increase in preclinical mice. 5mC correlated with prion-related lesions in mice and sheep, but 5hmC was associated with prion lesions only in sheep. Differences in the expression changes of epigenetic regulatory genes were found between both disease models, being differentially expressed Dnmt3b, Hdac1, and Tet1 in mice and HDAC2 in sheep. Our results support the evidence that DNA methylation in both forms, 5mC and 5hmC, and its associated epigenetic enzymes, take part in the neurodegenerative course of prion diseases.
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Affiliation(s)
- Adelaida Hernaiz
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
| | - Sara Sentre
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
| | - Marina Betancor
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes (CEETE), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
| | - Óscar López-Pérez
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
| | - Mónica Salinas-Pena
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
| | - Pilar Zaragoza
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, 28029 Madrid, Spain
| | - Juan José Badiola
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes (CEETE), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
| | - Janne Markus Toivonen
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, 28029 Madrid, Spain
| | - Rosa Bolea
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes (CEETE), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
| | - Inmaculada Martín-Burriel
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes (CEETE), Facultad de Veterinaria, Universidad de Zaragoza, IA2, IIS Aragón, 50013 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-976-761662
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Raval M, Mishra S, Tiwari AK. Epigenetic regulons in Alzheimer's disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:185-247. [DOI: 10.1016/bs.pmbts.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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8
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Zhao J, Huai J. Role of primary aging hallmarks in Alzheimer´s disease. Theranostics 2023; 13:197-230. [PMID: 36593969 PMCID: PMC9800733 DOI: 10.7150/thno.79535] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease, which severely threatens the health of the elderly and causes significant economic and social burdens. The causes of AD are complex and include heritable but mostly aging-related factors. The primary aging hallmarks include genomic instability, telomere wear, epigenetic changes, and loss of protein stability, which play a dominant role in the aging process. Although AD is closely associated with the aging process, the underlying mechanisms involved in AD pathogenesis have not been well characterized. This review summarizes the available literature about primary aging hallmarks and their roles in AD pathogenesis. By analyzing published literature, we attempted to uncover the possible mechanisms of aberrant epigenetic markers with related enzymes, transcription factors, and loss of proteostasis in AD. In particular, the importance of oxidative stress-induced DNA methylation and DNA methylation-directed histone modifications and proteostasis are highlighted. A molecular network of gene regulatory elements that undergoes a dynamic change with age may underlie age-dependent AD pathogenesis, and can be used as a new drug target to treat AD.
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9
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Ma Y, Li W, Fan C, Wang Y, Jiang H, Yang W. Comprehensive Analysis of Long Non-Coding RNAs N4-Acetylcytidine in Alzheimer's Disease Mice Model Using High-Throughput Sequencing. J Alzheimers Dis 2022; 90:1659-1675. [PMID: 36314201 DOI: 10.3233/jad-220564] [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] [Indexed: 12/24/2022]
Abstract
BACKGROUND N4-acetylcytidine (ac4C), an important posttranscriptional modification, is involved in various disease processes. Long noncoding RNAs (lncRNAs) regulate gene expression mainly through epigenetic modification, transcription, and posttranscriptional modification. Alzheimer's disease (AD) is a neurodegenerative disease characterized by amyloidosis of the brain. However, the role of lncRNA ac4C modification in AD remains unclear. OBJECTIVE In this study, we investigated the association between ac4C modification and AD, and the underlying mechanisms of ac4C modification in AD. METHODS The male 9-month-old APP/PS1 double transgenic mice, age- and sex-matched wild type (WT) mice were used in this study. Then, ac4C-RIP-seq and RNA-seq were used to comprehensively analyze lncRNA ac4C modification in AD mice. The lncRNA-miRNA-mRNA regulatory networks using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed the regulatory relationships among these three lncRNAs and AD. RESULTS The results showed that there were 120 significantly different ac4C peaks located on 102 lncRNAs in AD, of which 55 were hyperacetylated and 47 were hypoacetylated. Simultaneously, 231 differentially expressed lncRNAs were identified, including 138 upregulated lncRNAs and 93 downregulated lncRNAs. Moreover, 3 lncRNAs, lncRNA Gm26508, lncRNA A430046D13Rik, and lncRNA 9530059O14Rik, showed significant changes in both the ac4C and RNA levels using conjoint analysis. CONCLUSION The abundance of lncRNA ac4C modification is significantly different in AD and indicates that lncRNA ac4C is associated with the occurrence and development of AD, which could provide a basis for further exploration of the related regulatory mechanisms.
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Affiliation(s)
- Yanzhen Ma
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Weizu Li
- Department of Pharmacology, Basic Medicine College, Key Laboratory of Anti-inflammatory and Immunopharmacology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China
| | - Chang Fan
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Yongzhong Wang
- Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, Anhui, China.,Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Hui Jiang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China.,Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Wenming Yang
- Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, Anhui, China.,Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
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10
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Epigenetic Changes in Prion and Prion-like Neurodegenerative Diseases: Recent Advances, Potential as Biomarkers, and Future Perspectives. Int J Mol Sci 2022; 23:ijms232012609. [PMID: 36293477 PMCID: PMC9604074 DOI: 10.3390/ijms232012609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/09/2022] [Accepted: 10/18/2022] [Indexed: 12/01/2022] Open
Abstract
Prion diseases are transmissible spongiform encephalopathies (TSEs) caused by a conformational conversion of the native cellular prion protein (PrPC) to an abnormal, infectious isoform called PrPSc. Amyotrophic lateral sclerosis, Alzheimer’s, Parkinson’s, and Huntington’s diseases are also known as prion-like diseases because they share common features with prion diseases, including protein misfolding and aggregation, as well as the spread of these misfolded proteins into different brain regions. Increasing evidence proposes the involvement of epigenetic mechanisms, namely DNA methylation, post-translational modifications of histones, and microRNA-mediated post-transcriptional gene regulation in the pathogenesis of prion-like diseases. Little is known about the role of epigenetic modifications in prion diseases, but recent findings also point to a potential regulatory role of epigenetic mechanisms in the pathology of these diseases. This review highlights recent findings on epigenetic modifications in TSEs and prion-like diseases and discusses the potential role of such mechanisms in disease pathology and their use as potential biomarkers.
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11
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Chen Z, Wu M, Lai Q, Zhou W, Wen X, Yin X. Epigenetic regulation of synaptic disorder in Alzheimer’s disease. Front Neurosci 2022; 16:888014. [PMID: 35992921 PMCID: PMC9382295 DOI: 10.3389/fnins.2022.888014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/15/2022] [Indexed: 01/15/2023] Open
Abstract
Synapses are critical structures involved in neurotransmission and neuroplasticity. Their activity depends on their complete structure and function, which are the basis of learning, memory, and cognitive function. Alzheimer’s disease (AD) is neuropathologically characterized by synaptic loss, synaptic disorder, and plasticity impairment. AD pathogenesis is characterized by complex interactions between genetic and environmental factors. Changes in various receptors on the postsynaptic membrane, synaptic components, and dendritic spines lead to synaptic disorder. Changes in epigenetic regulation, including DNA methylation, RNA interference, and histone modification, are closely related to AD. These can affect neuronal and synaptic functions by regulating the structure and expression of neuronal genes. Some drugs have ameliorated synaptic and neural dysfunction in AD models via epigenetic regulation. We reviewed the recent progress on pathological changes and epigenetic mechanisms of synaptic dysregulation in AD to provide a new perspective on this disease.
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Affiliation(s)
- Zhiying Chen
- Department of Neurology, Affiliated Hospital of Jiujiang University, Jiujiang, China
- Jiujiang Clinical Precision Medicine Research Center, Jiujiang, China
| | - Moxin Wu
- Jiujiang Clinical Precision Medicine Research Center, Jiujiang, China
- Department of Medical Laboratory, Affiliated Hospital of Jiujiang University, Jiujiang, China
| | - Qin Lai
- Department of Neurology, Affiliated Hospital of Jiujiang University, Jiujiang, China
| | - Weixin Zhou
- Jiujiang Clinical Precision Medicine Research Center, Jiujiang, China
| | - Xiaoqing Wen
- Department of Neurology, Affiliated Hospital of Jiujiang University, Jiujiang, China
| | - Xiaoping Yin
- Department of Neurology, Affiliated Hospital of Jiujiang University, Jiujiang, China
- Jiujiang Clinical Precision Medicine Research Center, Jiujiang, China
- *Correspondence: Xiaoping Yin,
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12
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He X, Pei S, Meng X, Hua Q, Zhang T, Wang Y, Zhang Z, Zhu X, Liu R, Guo Y, Chen L, Li D. Punicalagin Attenuates Neuronal Apoptosis by Upregulating 5-Hydroxymethylcytosine in the Diabetic Mouse Brain. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4995-5004. [PMID: 35412829 DOI: 10.1021/acs.jafc.2c00863] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Punicalagin exerts neuroprotective activity by improving AMP-activated kinase (AMPK) and mitochondrial Krebs cycle. AMPK and Krebs cycle metabolites regulate 5-hydroxymethylcytosine (5hmC) via acting on ten-eleven translocation (TET) enzymes. Therefore, we hypothesized that punicalagin inhibits diabetes-related neuronal apoptosis by upregulating 5hmC in the diabetic mouse brain. C57BL/6J mice aged 8 weeks were randomly separated into five groups (n = 10), normal control (NC), diabetes mellitus (DM), resveratrol (RES), low-dose punicalagin (LPU), and high-dose punicalagin (HPU). Compared with other groups, the neuronal apoptosis rate was significantly higher and the 5hmC level of the cerebral cortex was significantly lower in the DM group. The levels of TET2 and P-AMPKα/AMPKα were significantly lower in the DM group than in both LPU and HPU groups. The ratio of (succinic acid + fumaric acid)/α-ketoglutarate was significantly higher in the DM group than in other groups. The present results suggest that punicalagin upregulates 5hmC via activating AMPK and maintaining Krebs cycle homeostasis, thus inhibiting neuronal apoptosis in the diabetic mouse brain.
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Affiliation(s)
- Xin He
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Shengjie Pei
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Xiangyuan Meng
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Qinglian Hua
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Tianyu Zhang
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Yan Wang
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Zhizhao Zhang
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Xinyu Zhu
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Run Liu
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Yurong Guo
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710062, China
| | - Lei Chen
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Duo Li
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
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13
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Chen L, Shen Q, Xu S, Yu H, Pei S, Zhang Y, He X, Wang Q, Li D. 5-Hydroxymethylcytosine Signatures in Circulating Cell-Free DNA as Diagnostic Biomarkers for Late-Onset Alzheimer's Disease. J Alzheimers Dis 2021; 85:573-585. [PMID: 34864677 DOI: 10.3233/jad-215217] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND 5-Hydroxymethylcytosine (5hmC) is an epigenetic DNA modification that is highly abundant in central nervous system. It has been reported that DNA 5hmC dysregulation play a critical role in Alzheimer's disease (AD) pathology. Changes in 5hmC signatures can be detected in circulating cell-free DNA (cfDNA), which has shown potential as a non-invasive liquid biopsy material. OBJECTIVE However, the genome-wide profiling of 5hmC in cfDNA and its potential for the diagnosis of AD has not been reported to date. METHODS We carried out a case-control study and used a genome-wide chemical capture followed by high-throughput sequencing to detect the genome-wide profiles of 5hmC in human cfDNA and identified differentially hydroxymethylated regions (DhMRs) in late-onset AD patients and the control. RESULTS We discovered significant differences of 5hmC enrichment in gene bodies which were linked to multiple AD pathogenesis-associated signaling pathways in AD patients compared with cognitively normal controls, indicating they can be well distinguished from normal controls by DhMRs in cfDNA. Specially, we identified 7 distinct genes (RABEP1, CPNE4, DNAJC15, REEP3, ROR1, CAMK1D, and RBFOX1) with predicting diagnostic potential based on their significant correlations with MMSE and MoCA scores of subjects. CONCLUSION The present results suggest that 5hmC markers derived from plasma cfDNA can served as an effective, minimally invasive biomarkers for clinical auxiliary diagnosis of late-onset AD.
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Affiliation(s)
- Lei Chen
- Institute of Nutrition & Health, Qingdao University, Qingdao, China.,School of Public health, Qingdao University, Qingdao, China
| | - Qianqian Shen
- Institute of Nutrition & Health, Qingdao University, Qingdao, China.,School of Public health, Qingdao University, Qingdao, China
| | - Shunliang Xu
- Department of Neurology, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hongzhuan Yu
- Weifang Hospital of Traditional Chinese Medicine, Weifang, China
| | - Shengjie Pei
- Institute of Nutrition & Health, Qingdao University, Qingdao, China.,School of Public health, Qingdao University, Qingdao, China
| | - Yangting Zhang
- Institute of Nutrition & Health, Qingdao University, Qingdao, China.,School of Public health, Qingdao University, Qingdao, China
| | - Xin He
- Institute of Nutrition & Health, Qingdao University, Qingdao, China.,School of Public health, Qingdao University, Qingdao, China
| | - QiuZhen Wang
- Institute of Nutrition & Health, Qingdao University, Qingdao, China.,School of Public health, Qingdao University, Qingdao, China
| | - Duo Li
- Institute of Nutrition & Health, Qingdao University, Qingdao, China.,School of Public health, Qingdao University, Qingdao, China
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14
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de Sousa MML, Ye J, Luna L, Hildrestrand G, Bjørås K, Scheffler K, Bjørås M. Impact of Oxidative DNA Damage and the Role of DNA Glycosylases in Neurological Dysfunction. Int J Mol Sci 2021; 22:12924. [PMID: 34884729 PMCID: PMC8657561 DOI: 10.3390/ijms222312924] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 11/16/2022] Open
Abstract
The human brain requires a high rate of oxygen consumption to perform intense metabolic activities, accounting for 20% of total body oxygen consumption. This high oxygen uptake results in the generation of free radicals, including reactive oxygen species (ROS), which, at physiological levels, are beneficial to the proper functioning of fundamental cellular processes. At supraphysiological levels, however, ROS and associated lesions cause detrimental effects in brain cells, commonly observed in several neurodegenerative disorders. In this review, we focus on the impact of oxidative DNA base lesions and the role of DNA glycosylase enzymes repairing these lesions on brain function and disease. Furthermore, we discuss the role of DNA base oxidation as an epigenetic mechanism involved in brain diseases, as well as potential roles of DNA glycosylases in different epigenetic contexts. We provide a detailed overview of the impact of DNA glycosylases on brain metabolism, cognition, inflammation, tissue loss and regeneration, and age-related neurodegenerative diseases based on evidence collected from animal and human models lacking these enzymes, as well as post-mortem studies on patients with neurological disorders.
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Affiliation(s)
- Mirta Mittelstedt Leal de Sousa
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7028 Trondheim, Norway; (J.Y.); (K.B.)
| | - Jing Ye
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7028 Trondheim, Norway; (J.Y.); (K.B.)
| | - Luisa Luna
- Department of Microbiology, Oslo University Hospital, University of Oslo, Rikshospitalet, 0424 Oslo, Norway; (L.L.); (G.H.)
| | - Gunn Hildrestrand
- Department of Microbiology, Oslo University Hospital, University of Oslo, Rikshospitalet, 0424 Oslo, Norway; (L.L.); (G.H.)
| | - Karine Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7028 Trondheim, Norway; (J.Y.); (K.B.)
| | - Katja Scheffler
- Department of Neurology, St. Olavs Hospital, 7006 Trondheim, Norway;
- Department of Laboratory Medicine, St. Olavs Hospital, 7006 Trondheim, Norway
- Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7028 Trondheim, Norway; (J.Y.); (K.B.)
- Department of Microbiology, Oslo University Hospital, University of Oslo, Rikshospitalet, 0424 Oslo, Norway; (L.L.); (G.H.)
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15
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Ao C, Gao L, Yu L. Research progress in predicting DNA methylation modifications and the relation with human diseases. Curr Med Chem 2021; 29:822-836. [PMID: 34533438 DOI: 10.2174/0929867328666210917115733] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/05/2021] [Accepted: 07/11/2021] [Indexed: 11/22/2022]
Abstract
DNA methylation is an important mode of regulation in epigenetic mechanisms, and it is one of the research foci in the field of epigenetics. DNA methylation modification affects a series of biological processes, such as eukaryotic cell growth, differentiation and transformation mechanisms, by regulating gene expression. In this review, we systematically summarized the DNA methylation databases, prediction tools for DNA methylation modification, machine learning algorithms for predicting DNA methylation modification, and the relationship between DNA methylation modification and diseases such as hypertension, Alzheimer's disease, diabetic nephropathy, and cancer. An in-depth understanding of DNA methylation mechanisms can promote accurate prediction of DNA methylation modifications and the treatment and diagnosis of related diseases.
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Affiliation(s)
- Chunyan Ao
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Liang Yu
- School of Computer Science and Technology, Xidian University, Xi'an, China
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16
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Sharma VK, Mehta V, Singh TG. Alzheimer's Disorder: Epigenetic Connection and Associated Risk Factors. Curr Neuropharmacol 2021; 18:740-753. [PMID: 31989902 PMCID: PMC7536832 DOI: 10.2174/1570159x18666200128125641] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 11/26/2019] [Accepted: 01/27/2020] [Indexed: 12/13/2022] Open
Abstract
The gene based therapeutics and drug targets have shown incredible and appreciable advances in alleviating human sufferings and complexities. Epigenetics simply means above genetics or which controls the organism beyond genetics. At present it is very clear that all characteristics of an individual are not determined by DNA alone, rather the environment, stress, life style and nutrition play a vital part in determining the response of an organism. Thus, nature (genetic makeup) and nurture (exposure) play equally important roles in the responses observed, both at the cellular and organism levels. Epigenetics influence plethora of complications at cellular and molecular levels that includes cancer, metabolic and cardiovascular complications including neurological (psychosis) and neurodegenerative disorders (Alzheimer’s disease, Parkinson disease etc.). The epigenetic mechanisms include DNA methylation, histone modification and non coding RNA which have substantial impact on progression and pathways linked to Alzheimer’s disease. The epigenetic mechanism gets deregulated in Alzheimer’s disease and is characterized by DNA hyper methylation, deacetylation of histones and general repressed chromatin state which alter gene expression at the transcription level by upregulation, downregulation or silencing of genes. Thus, the processes or modulators of these epigenetic processes have shown vast potential as a therapeutic target in Alzheimer’s disease.
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Affiliation(s)
| | - Vineet Mehta
- Govt. College of Pharmacy, Rohru, District Shimla, Himachal Pradesh-171207, India
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17
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High Methionine Diet-Induced Alzheimer's Disease like Symptoms Are Accompanied by 5-Methylcytosine Elevated Levels in the Brain. Behav Neurol 2021; 2021:6683318. [PMID: 33880134 PMCID: PMC8046555 DOI: 10.1155/2021/6683318] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/16/2021] [Accepted: 03/23/2021] [Indexed: 01/09/2023] Open
Abstract
Background Excessive or insufficient intake of methionine (Met) causes neuronal dysfunction, neurodegeneration, cerebrovascular dysfunction, vascular leakage, and short-term memory loss, which result in the occurrence of Alzheimer's disease- (AD-) like symptoms. Objective To determine the relationship between high methionine diets (HMD) induced AD-like symptoms and 5-methylcytosine (5-mC) level. Methods C57BL/6J mice were randomly divided into two groups: the control group (Maintain diets) and the model group (2% HMD). Mice were fed with 2% HMD for 9 weeks. Animals were weighed and food intake was recorded weekly. Open field test, nesting ability test, Y maze test, new object recognition test, and Morris water maze test were used to detect the motor, learning, and memory ability. Hematoxylin-eosin (HE) staining was used to observe the damage of cells in hippocampus and cortex. Immunofluorescence (IF) staining was used to detect the expression and distribution of amyloid-β 1-40 (Aβ1-40), amyloid-β 1-42 (Aβ1-42), and 5-methylcytosine (5-mC) in hippocampus and cortex. Western blotting (WB) was used to determine the expression of Aβ and DNA methyltransferases- (DNMTs-) related proteins in the cortex. Enzyme-linked immunosorbent assay (ELISA) was performed to detect homocysteine (Hcy) level (ELISA). Results Feeding of HMD decreased the body weight and food intake of mice. Behavioral testing revealed that HMD caused learning, memory, and motor ability impairment in the mice. HE staining results showed that HMD feeding caused damage of hippocampal and cortical neurons, along with disordered cell arrangement, and loss of neurons. Furthermore, HMD increased the contents of Aβ1-40, Aβ1-42, and 5-mC in the hippocampus and cortex. WB results showed that HMD increased the expression of Aβ production-related proteins, such as amyloid precursor protein (APP) and beta-secretase 1 (BACE1), and decreased the expression of Aβ metabolism-related protein in the cortex, including insulin-degrading enzyme (IDE) and neprilysin (NEP). Additionally, the decreased expression of DNA methyltransferase1 (DNMT1) was observed in HMD-treated mice, but there was no significant change of DNMT3a level. ELISA results showed that HMD increased the levels of Hcy in serum. Conclusion Our result suggested that the HMD can cause neurotoxicity, leading to AD-like symptoms in mice, which may be related to 5-mC elevated.
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Mallik S, Zhao Z. Detecting methylation signatures in neurodegenerative disease by density-based clustering of applications with reducing noise. Sci Rep 2020; 10:22164. [PMID: 33335112 PMCID: PMC7747741 DOI: 10.1038/s41598-020-78463-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022] Open
Abstract
There have been numerous genetic and epigenetic datasets generated for the study of complex disease including neurodegenerative disease. However, analysis of such data often suffers from detecting the outliers of the samples, which subsequently affects the extraction of the true biological signals involved in the disease. To address this critical issue, we developed a novel framework for identifying methylation signatures using consecutive adaptation of a well-known outlier detection algorithm, density based clustering of applications with reducing noise (DBSCAN) followed by hierarchical clustering. We applied the framework to two representative neurodegenerative diseases, Alzheimer's disease (AD) and Down syndrome (DS), using DNA methylation datasets from public sources (Gene Expression Omnibus, GEO accession ID: GSE74486). We first applied DBSCAN algorithm to eliminate outliers, and then used Limma statistical method to determine differentially methylated genes. Next, hierarchical clustering technique was applied to detect gene modules. Our analysis identified a methylation signature comprising 21 genes for AD and a methylation signature comprising 89 genes for DS, respectively. Our evaluation indicated that these two signatures could lead to high classification accuracy values (92% and 70%) for these two diseases. In summary, this framework will be useful to better detect outlier-free genetic and epigenetic signatures in various complex diseases and their developmental stages.
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Affiliation(s)
- Saurav Mallik
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
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Abstract
Finding early disease markers using non-invasive and widely available methods is essential to develop a successful therapy for Alzheimer’s Disease. Few studies to date have examined urine, the most readily available biofluid. Here we report the largest study to date using comprehensive metabolic phenotyping platforms (NMR spectroscopy and UHPLC-MS) to probe the urinary metabolome in-depth in people with Alzheimer’s Disease and Mild Cognitive Impairment. Feature reduction was performed using metabolomic Quantitative Trait Loci, resulting in the list of metabolites associated with the genetic variants. This approach helps accuracy in identification of disease states and provides a route to a plausible mechanistic link to pathological processes. Using these mQTLs we built a Random Forests model, which not only correctly discriminates between people with Alzheimer’s Disease and age-matched controls, but also between individuals with Mild Cognitive Impairment who were later diagnosed with Alzheimer’s Disease and those who were not. Further annotation of top-ranking metabolic features nominated by the trained model revealed the involvement of cholesterol-derived metabolites and small-molecules that were linked to Alzheimer’s pathology in previous studies.
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20
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Epigenomic analysis of Parkinson's disease neurons identifies Tet2 loss as neuroprotective. Nat Neurosci 2020; 23:1203-1214. [PMID: 32807949 DOI: 10.1038/s41593-020-0690-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 07/07/2020] [Indexed: 01/08/2023]
Abstract
Parkinson's disease (PD) pathogenesis may involve the epigenetic control of enhancers that modify neuronal functions. Here, we comprehensively examine DNA methylation at enhancers, genome-wide, in neurons of patients with PD and of control individuals. We find a widespread increase in cytosine modifications at enhancers in PD neurons, which is partly explained by elevated hydroxymethylation levels. In particular, patients with PD exhibit an epigenetic and transcriptional upregulation of TET2, a master-regulator of cytosine modification status. TET2 depletion in a neuronal cell model results in cytosine modification changes that are reciprocal to those observed in PD neurons. Moreover, Tet2 inactivation in mice fully prevents nigral dopaminergic neuronal loss induced by previous inflammation. Tet2 loss also attenuates transcriptional immune responses to an inflammatory trigger. Thus, widespread epigenetic dysregulation of enhancers in PD neurons may, in part, be mediated by increased TET2 expression. Decreased Tet2 activity is neuroprotective, in vivo, and may be a new therapeutic target for PD.
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Wang T, Zhang J, Xu Y. Epigenetic Basis of Lead-Induced Neurological Disorders. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17134878. [PMID: 32645824 PMCID: PMC7370007 DOI: 10.3390/ijerph17134878] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/01/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023]
Abstract
Environmental lead (Pb) exposure is closely associated with pathogenesis of a range of neurological disorders, including Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), attention deficit/hyperactivity disorder (ADHD), etc. Epigenetic machinery modulates neural development and activities, while faulty epigenetic regulation contributes to the diverse forms of CNS (central nervous system) abnormalities and diseases. As a potent epigenetic modifier, lead is thought to cause neurological disorders through modulating epigenetic mechanisms. Specifically, increasing evidence linked aberrant DNA methylations, histone modifications as well as ncRNAs (non-coding RNAs) with AD cases, among which circRNA (circular RNA) stands out as a new and promising field for association studies. In 23-year-old primates with developmental lead treatment, Zawia group discovered a variety of epigenetic changes relating to AD pathogenesis. This is a direct evidence implicating epigenetic basis in lead-induced AD animals with an entire lifespan. Additionally, some epigenetic molecules associated with AD etiology were also known to respond to chronic lead exposure in comparable disease models, indicating potentially interlaced mechanisms with respect to the studied neurotoxic and pathological events. Of note, epigenetic molecules acted via globally or selectively influencing the expression of disease-related genes. Compared to AD, the association of lead exposure with other neurological disorders were primarily supported by epidemiological survey, with fewer reports connecting epigenetic regulators with lead-induced pathogenesis. Some pharmaceuticals, such as HDAC (histone deacetylase) inhibitors and DNA methylation inhibitors, were developed to deal with CNS disease by targeting epigenetic components. Still, understandings are insufficient regarding the cause–consequence relations of epigenetic factors and neurological illness. Therefore, clear evidence should be provided in future investigations to address detailed roles of novel epigenetic factors in lead-induced neurological disorders, and efforts of developing specific epigenetic therapeutics should be appraised.
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Affiliation(s)
| | | | - Yi Xu
- Correspondence: ; Tel.: +86-183-2613-5046
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22
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Antonyová V, Kejík Z, Brogyányi T, Kaplánek R, Pajková M, Talianová V, Hromádka R, Masařík M, Sýkora D, Mikšátková L, Martásek P, Jakubek M. Role of mtDNA disturbances in the pathogenesis of Alzheimer's and Parkinson's disease. DNA Repair (Amst) 2020; 91-92:102871. [PMID: 32502755 DOI: 10.1016/j.dnarep.2020.102871] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/08/2020] [Accepted: 05/09/2020] [Indexed: 12/11/2022]
Abstract
Neurodegenerative diseases (e.g. Alzheimer's and Parkinson's disease) are becoming increasingly problematic to healthcare systems. Therefore, their underlying mechanisms are trending topics of study in medicinal research. Numerous studies have evidenced a strong association between mitochondrial DNA disturbances (e.g. oxidative damage, mutations, and methylation shifts) and the initiation and progression of neurodegenerative diseases. Therefore, this review discusses the risk and development of neurodegenerative diseases in terms of disturbances in mitochondrial DNA and as a part of a complex ecosystem that includes other important mechanisms (e.g. neuroinflammation and the misfolding and aggregation of amyloid-β peptides, α-synuclein, and tau proteins). In addition, the influence of individual mitochondrial DNA haplogroups on the risk and development of neurodegenerative diseases is also described and discussed.
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Affiliation(s)
- Veronika Antonyová
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Zdeněk Kejík
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Kateřinská 32, 121 08 Prague 2, Czech Republic; Department of Analytical Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Dejvice, Czech Republic
| | - Tereza Brogyányi
- Depertment of Pathological Physiology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 2, 121 00 Prague 2, Czech Republic
| | - Robert Kaplánek
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Kateřinská 32, 121 08 Prague 2, Czech Republic; BIOCEV, First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic; Department of Analytical Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Dejvice, Czech Republic
| | - Martina Pajková
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Kateřinská 32, 121 08 Prague 2, Czech Republic; BIOCEV, First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Veronika Talianová
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Kateřinská 32, 121 08 Prague 2, Czech Republic; BIOCEV, First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Róbert Hromádka
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Michal Masařík
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Kateřinská 32, 121 08 Prague 2, Czech Republic; BIOCEV, First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - David Sýkora
- BIOCEV, First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic; Department of Analytical Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Dejvice, Czech Republic
| | - Lucie Mikšátková
- BIOCEV, First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic; Department of Analytical Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Dejvice, Czech Republic
| | - Pavel Martásek
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Kateřinská 32, 121 08 Prague 2, Czech Republic.
| | - Milan Jakubek
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Kateřinská 32, 121 08 Prague 2, Czech Republic; BIOCEV, First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic; Department of Analytical Chemistry, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague 6, Dejvice, Czech Republic.
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23
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Pei H, Ma L, Cao Y, Wang F, Li Z, Liu N, Liu M, Wei Y, Li H. Traditional Chinese Medicine for Alzheimer's Disease and Other Cognitive Impairment: A Review. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2020; 48:487-511. [PMID: 32329645 DOI: 10.1142/s0192415x20500251] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Cognitive impairment (CI) refers to the dysfunction of memory, language, visual space, execution, calculation, understanding, and judgment in one or more aspects. With global aging, CI will become prevalent worldwide. At present, there is no effective cure for CI. However, Nobel laureate Tu Youyou's research on artemisinin has inspired Chinese researchers to focus on traditional Chinese herbs (TCHs) for the treatment of CI. Traditional Chinese Medicine (TCM) has led to a theory for an independent CI system. The pathogenesis of such impairment involves deficiency, phlegm, and stagnation and involves a range of organs, including the brain, kidneys, heart, liver, and spleen. Our current understanding of the etiology and pathogenesis of this condition has led to the realization that TCHs can improve cognitive dysfunction. Clinical research has shown that TCHs can improve the neuropsychological scale score of patients, the TCM symptom score, and the patient's quality of life. Research has also suggested that TCHs can retard Aβ deposits and tauopathy, regulate the metabolism of cholinergic neurotransmitters, and so on. However, due to their complexity, little is known of the safety and efficacy of TCHs in patients with CI. It is likely that we will be able to identify the precise mechanisms associated with the action of TCHs in such patients due to the integration of multiple technologies. This paper summarizes the pharmacokinetics, curative effect, and mechanisms of action of traditional Chinese herbs in order to provide a scientific basis for the improvement of cognitive dysfunction by TCHs.
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Affiliation(s)
- Hui Pei
- Institude of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, P. R. China
| | - Lina Ma
- Institude of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, P. R. China
| | - Yu Cao
- Institude of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, P. R. China
| | - Feixue Wang
- Traditional Chinese Medicine Department, Xuanwu Hospital Capital Medical University, Beijing 100053, P. R. China
| | - Zehui Li
- Institude of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, P. R. China
| | - Nanyang Liu
- Institude of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, P. R. China
| | - Meixia Liu
- Institude of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, P. R. China
| | - Yun Wei
- Institude of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, P. R. China
| | - Hao Li
- Institude of Geriatrics, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, P. R. China
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24
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Fessel J. The paradox of opposite directions of gene expressions in MCI and AD suggests possible therapy to prevent progression of MCI to AD. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2020; 6:e12003. [PMID: 32258360 PMCID: PMC7111579 DOI: 10.1002/trc2.12003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 12/26/2019] [Indexed: 01/06/2023]
Abstract
One of the puzzling observations concerning mild cognitive impairment (MCI) and Alzheimer's disease (AD), is that many gene expressions in MCI may be in the opposite direction of those seen in AD. Several examples of this paradox are provided. The likely explanation lies in in the control mechanisms of gene transcription. These mechanisms include (1) modification of DNA and histones by methylation or acetylation, affecting the balance between the Compass group of proteins that enhances mRNA formation, and the Polycomb group that suppresses it; (2) compensation for the loss of one gene's function by another gene with overlapping functions; (3) reduced control of the entire neural RNA production; and (4) response to microRNAs (miRNA). Although data are inadequate to exclude with certainty any one of the indicated mechanisms, the available evidence favors overall reduced control of neural mRNA production, including the effect of miRNA. The switch occurs at a specific stage, somewhere between Braak 0-1 and Braak 2-3, in the progression from MCI to AD, which reduces the number of its likely causes. Two strong but related candidates are the repressor element-1 silencing transcription factor (REST), which in adult neurons impairs plasticity; and a miRNA, for example, miRNA124, that represses REST. Another possible explanation is that only those patients with MCI who will not progress to AD are the ones that have gene expressions in the opposite direction as in AD. The solution to the paradox may have pragmatic value.
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25
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Zhou Y, Jiang W, Wu H, Liu F, Yin H, Lu N, Ai S. Amplified electrochemical immunoassay for 5-methylcytosine using a nanocomposite prepared from graphene oxide, magnetite nanoparticles and β-cyclodextrin. Mikrochim Acta 2019; 186:488. [DOI: 10.1007/s00604-019-3575-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 06/02/2019] [Indexed: 10/26/2022]
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26
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Hydrazones as novel epigenetic modulators: Correlation between TET 1 protein inhibition activity and their iron(II) binding ability. Bioorg Chem 2019; 88:102809. [DOI: 10.1016/j.bioorg.2019.02.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/16/2019] [Accepted: 02/15/2019] [Indexed: 02/06/2023]
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27
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Wang F, Chen D, Wu P, Klein C, Jin C. Formaldehyde, Epigenetics, and Alzheimer's Disease. Chem Res Toxicol 2019; 32:820-830. [PMID: 30964647 DOI: 10.1021/acs.chemrestox.9b00090] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Alzheimer's disease (AD) is the most common form of dementia. The accumulation of β-amyloid plaques and intracellular neurofibrillary tangles of hyperphosphorylated tau protein are two hallmarks of AD. The β-amyloid and tau proteins have been at the center of AD research and drug development for decades. However, most of the clinical trials targeting β-amyloid have failed. Whereas the safety and efficacy of most tau-targeting drugs have not yet been completely assessed, the first tau aggregation inhibitor, LMTX, failed in a late-stage trial, leading to further recognition of the complexities of AD and reconsideration of the amyloid hypothesis and perhaps the tau hypothesis as well. Multilevel complex interactions between genetic, epigenetic, and environmental factors contribute to the occurrence and progression of AD. Formaldehyde (FA) is a widespread environmental organic pollutant. It is also an endogenous metabolite in the human body. Recent studies suggest that elevation of FA in the body by endogenous and/or exogenous exposure may play important roles in AD development. We have demonstrated that FA reduces lysine acetylation of cytosolic histones, thereby compromising chromatin assembly and resulting in the loss of histone content in chromatin, a conserved feature of aging from yeast to humans. Aging is an important factor for AD progression. Therefore, FA-induced inhibition of chromatin assembly and the loss of histones may contribute to AD initiation and/or development. This review will briefly summarize current knowledge on mechanistic insights into AD, focusing on epigenetic alterations and the involvement of FA in AD development. The exploration of chemical exposures as contributing factors to AD may provide new insights into AD mechanisms and could identify potential novel therapeutic targets.
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Affiliation(s)
- Fei Wang
- School of Public Health , China Medical University , Shenyang 110122 , China
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28
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Román GC, Mancera-Páez O, Bernal C. Epigenetic Factors in Late-Onset Alzheimer's Disease: MTHFR and CTH Gene Polymorphisms, Metabolic Transsulfuration and Methylation Pathways, and B Vitamins. Int J Mol Sci 2019; 20:E319. [PMID: 30646578 PMCID: PMC6359124 DOI: 10.3390/ijms20020319] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/10/2019] [Accepted: 01/11/2019] [Indexed: 12/17/2022] Open
Abstract
DNA methylation and other epigenetic factors are important in the pathogenesis of late-onset Alzheimer's disease (LOAD). Methylenetetrahydrofolate reductase (MTHFR) gene mutations occur in most elderly patients with memory loss. MTHFR is critical for production of S-adenosyl-l-methionine (SAM), the principal methyl donor. A common mutation (1364T/T) of the cystathionine-γ-lyase (CTH) gene affects the enzyme that converts cystathionine to cysteine in the transsulfuration pathway causing plasma elevation of total homocysteine (tHcy) or hyperhomocysteinemia-a strong and independent risk factor for cognitive loss and AD. Other causes of hyperhomocysteinemia include aging, nutritional factors, and deficiencies of B vitamins. We emphasize the importance of supplementing vitamin B12 (methylcobalamin), vitamin B₉ (folic acid), vitamin B₆ (pyridoxine), and SAM to patients in early stages of LOAD.
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Affiliation(s)
- Gustavo C Román
- Department of Neurology, Methodist Neurological Institute, Institute for Academic Medicine Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX 77030, USA.
- Weill Cornell Medical College, Department of Neurology, Cornell University, New York, NY 10065, USA.
| | - Oscar Mancera-Páez
- Universidad Nacional de Colombia, Hospital Universitario Nacional, Faculty of Medicine, Department of Neurology, Bogotá ZC 57, Colombia.
- David Cabello International Alzheimer Disease Scholarship Fund, Houston Methodist Hospital, Houston, TX77030, USA.
| | - Camilo Bernal
- Universidad Nacional de Colombia, Hospital Universitario Nacional, Faculty of Medicine, Department of Neurology, Bogotá ZC 57, Colombia.
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29
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Wang ZT, Tan CC, Tan L, Yu JT. Systems biology and gene networks in Alzheimer’s disease. Neurosci Biobehav Rev 2019; 96:31-44. [DOI: 10.1016/j.neubiorev.2018.11.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 11/18/2018] [Accepted: 11/18/2018] [Indexed: 12/25/2022]
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30
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Stoccoro A, Coppedè F. Role of epigenetics in Alzheimer's disease pathogenesis. Neurodegener Dis Manag 2018; 8:181-193. [PMID: 29888987 DOI: 10.2217/nmt-2018-0004] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Advances in molecular biology technologies have allowed uncovering the role of epigenetic regulation in several complex diseases, such as cancer and neurodegenerative disorders. Although the role of epigenetic mechanisms in Alzheimer's disease is still little understood, recent findings clearly show that such mechanisms are dysregulated during disease progression, already in its early stages. However, it is not clear if the observed epigenetic changes represent a cause or a consequence of the disease. Promising results are emerging from studies performed in peripheral blood DNA that could provide early biomarkers of the pathology. Moreover, given the dynamic nature of the epigenetic marks, intense research is carried out to investigate the therapeutic efficacy of compounds exerting epigenetic properties.
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Affiliation(s)
- Andrea Stoccoro
- Department of Translational Research & New Technologies in Medicine & Surgery, Section of Medical Genetics, University of Pisa, Via Roma 55, 56126 Pisa, Italy.,Department of Medical Biotechnologies, Doctoral School in Genetics, Oncology & Clinical Medicine, University of Siena, Siena, Italy
| | - Fabio Coppedè
- Department of Translational Research & New Technologies in Medicine & Surgery, Section of Medical Genetics, University of Pisa, Via Roma 55, 56126 Pisa, Italy
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31
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Kovalchuk A, Ilnytskyy Y, Rodriguez-Juarez R, Shpyleva S, Melnyk S, Pogribny I, Katz A, Sidransky D, Kovalchuk O, Kolb B. Chemo brain or tumor brain - that is the question: the presence of extracranial tumors profoundly affects molecular processes in the prefrontal cortex of TumorGraft mice. Aging (Albany NY) 2018; 9:1660-1676. [PMID: 28758896 PMCID: PMC5559168 DOI: 10.18632/aging.101243] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 05/22/2017] [Indexed: 01/17/2023]
Abstract
Cancer chemotherapy causes numerous persistent central nervous system complications. This condition is known as chemo brain. Cognitive impairments occur even before treatment, and hence are referred to as cancer associated cognitive changes, or tumor brain. There is much yet to be learned about the mechanisms of both chemo brain and tumor brain. The frequency and timing of chemo brain and tumor brain occurrence and persistence strongly suggest they may be epigenetic in nature and associated with altered gene expression. Here we used TumorGraftTM models wherein part of a patient's tumor is removed and grafted into immune-deficient mice and conducted global gene expression and DNA methylation analysis. We show that malignant non-central nervous system tumor growth causes profound molecular alterations in the brain. Mice harbouring triple negative or progesterone positive breast cancer TumorGrafts exhibited altered gene expression, decreased levels of DNA methylation, increased levels of DNA hydroxymethylation, and oxidative stress in the prefrontal cortex. Interestingly, chemotherapy did not have any additional synergistic effects on the analyzed processes. The molecular changes observed in this study are known signs of neurodegeneration and brain aging. This study provides an important roadmap for future large-scale analysis of the molecular and cellular mechanisms of tumor brain.
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Affiliation(s)
- Anna Kovalchuk
- Department of Neuroscience, University of Lethbridge, Lethbridge, AB T1K 6T5, Canada.,Leaders in Medicine Program, Cumming School of Medicine, University of Calgary, Calgary, T2N 1N4, Canada
| | - Yaroslav Ilnytskyy
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 6T5, Canada
| | - Rocio Rodriguez-Juarez
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 6T5, Canada
| | - Svitlana Shpyleva
- Division of Biochemical Toxicology, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA.,Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Stepan Melnyk
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Igor Pogribny
- Division of Biochemical Toxicology, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA
| | - Amanda Katz
- Department of Oncology, Champions Oncology, Baltimore, MD 21205, USA
| | - David Sidransky
- Department of Oncology, Champions Oncology, Baltimore, MD 21205, USA
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 6T5, Canada
| | - Bryan Kolb
- Department of Neuroscience, University of Lethbridge, Lethbridge, AB T1K 6T5, Canada
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32
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Gao J, Cahill CM, Huang X, Roffman JL, Lamon-Fava S, Fava M, Mischoulon D, Rogers JT. S-Adenosyl Methionine and Transmethylation Pathways in Neuropsychiatric Diseases Throughout Life. Neurotherapeutics 2018; 15:156-175. [PMID: 29340929 PMCID: PMC5794704 DOI: 10.1007/s13311-017-0593-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
S-Adenosyl methionine (SAMe), as a major methyl donor, exerts its influence on central nervous system function through cellular transmethylation pathways, including the methylation of DNA, histones, protein phosphatase 2A, and several catecholamine moieties. Based on available evidence, this review focuses on the lifelong range of severe neuropsychiatric and neurodegenerative diseases and their associated neuropathologies, which have been linked to the deficiency/load of SAMe production or/and the disturbance in transmethylation pathways. Also included in this review are the present-day applications of SAMe in the treatment in these diseases in each age group.
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Affiliation(s)
- Jin Gao
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Clinical Psychology, Qilu Hospital of Shandong University, Qingdao, Shandong Province, China
| | - Catherine M Cahill
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Xudong Huang
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Joshua L Roffman
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Stefania Lamon-Fava
- Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA
| | - Maurizio Fava
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - David Mischoulon
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jack T Rogers
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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33
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Ellison EM, Bradley-Whitman MA, Lovell MA. Single-Base Resolution Mapping of 5-Hydroxymethylcytosine Modifications in Hippocampus of Alzheimer's Disease Subjects. J Mol Neurosci 2017; 63:185-197. [PMID: 28866733 PMCID: PMC5909840 DOI: 10.1007/s12031-017-0969-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/23/2017] [Indexed: 12/19/2022]
Abstract
Epigenetic modifications to cytosine have been shown to regulate transcription in cancer, embryonic development, and recently neurodegeneration. While cytosine methylation studies are now common in neurodegenerative research, hydroxymethylation studies are rare, particularly genome-wide mapping studies. As an initial study to analyze 5-hydroxymethylcytosine (5-hmC) in the Alzheimer's disease (AD) genome, reduced representation hydroxymethylation profiling (RRHP) was used to analyze more than 2 million sites of possible modification in hippocampal DNA of sporadic AD and normal control subjects. Genes with differentially hydroxymethylated regions were filtered based on previously published microarray data for altered gene expression in hippocampal DNA of AD subjects. Our data show significant pathways for altered levels of 5-hmC in the hippocampus of AD subjects compared to age-matched normal controls involved in signaling, energy metabolism, cell function, gene expression, protein degradation, and cell structure and stabilization. Overall, our data suggest a possible role for the dysregulation of epigenetic modifications to cytosine in late stage AD.
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Affiliation(s)
| | - Melissa A Bradley-Whitman
- Sanders-Brown Center on Aging, University of Kentucky, 135 Sanders-Brown Center on Aging, 800 South Limestone S, Lexington, KY, 40536, USA
| | - Mark A Lovell
- Department of Chemistry, University of Kentucky, Lexington, KY, USA.
- Sanders-Brown Center on Aging, University of Kentucky, 135 Sanders-Brown Center on Aging, 800 South Limestone S, Lexington, KY, 40536, USA.
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34
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Roubroeks JAY, Smith RG, van den Hove DLA, Lunnon K. Epigenetics and DNA methylomic profiling in Alzheimer's disease and other neurodegenerative diseases. J Neurochem 2017; 143:158-170. [PMID: 28805248 DOI: 10.1111/jnc.14148] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/13/2022]
Abstract
Recent studies have suggested a role for epigenetic mechanisms in the complex etiology of various neurodegenerative diseases. In this review, we discuss advances that have been made toward understanding the role of epigenetic processes in neurodegenerative disorders, with a particular focus on Alzheimer's disease, where the most extensive studies have been undertaken to date. We provide a brief overview of DNA modifications, followed by a summarization of studies of DNA modifications in Alzheimer's disease and other neurodegenerative diseases.
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Affiliation(s)
| | - Rebecca G Smith
- University of Exeter Medical School, University of Exeter, Devon, UK
| | - Daniel L A van den Hove
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, Maastricht, The Netherlands.,Laboratory of Translational Neuroscience, Division of Molecular Psychiatry, Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Katie Lunnon
- University of Exeter Medical School, University of Exeter, Devon, UK
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35
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Bayraktar G, Kreutz MR. Neuronal DNA Methyltransferases: Epigenetic Mediators between Synaptic Activity and Gene Expression? Neuroscientist 2017; 24:171-185. [PMID: 28513272 PMCID: PMC5846851 DOI: 10.1177/1073858417707457] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
DNMT3A and 3B are the main de novo DNA methyltransferases (DNMTs) in the brain that introduce new methylation marks to non-methylated DNA in postmitotic neurons. DNA methylation is a key epigenetic mark that is known to regulate important cellular processes in neuronal development and brain plasticity. Accumulating evidence disclosed rapid and dynamic changes in DNA methylation of plasticity-relevant genes that are important for learning and memory formation. To understand how DNMTs contribute to brain function and how they are regulated by neuronal activity is a prerequisite for a deeper appreciation of activity-dependent gene expression in health and disease. This review discusses the functional role of de novo methyltransferases and in particular DNMT3A1 in the adult brain with special emphasis on synaptic plasticity, memory formation, and brain disorders.
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Affiliation(s)
- Gonca Bayraktar
- 1 RG Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Michael R Kreutz
- 1 RG Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany.,2 Leibniz Group "Dendritic Organelles and Synaptic Function", ZMNH, Magdeburg, Germany
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