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Rocha GS, Freire MAM, Paiva KM, Oliveira RF, Morais PLAG, Santos JR, Cavalcanti JRLP. The neurobiological effects of senescence on dopaminergic system: A comprehensive review. J Chem Neuroanat 2024; 137:102415. [PMID: 38521203 DOI: 10.1016/j.jchemneu.2024.102415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/26/2024] [Accepted: 03/15/2024] [Indexed: 03/25/2024]
Abstract
Over time, the body undergoes a natural, multifactorial, and ongoing process named senescence, which induces changes at the molecular, cellular, and micro-anatomical levels in many body systems. The brain, being a highly complex organ, is particularly affected by this process, potentially impairing its numerous functions. The brain relies on chemical messengers known as neurotransmitters to function properly, with dopamine being one of the most crucial. This catecholamine is responsible for a broad range of critical roles in the central nervous system, including movement, learning, cognition, motivation, emotion, reward, hormonal release, memory consolidation, visual performance, sexual drive, modulation of circadian rhythms, and brain development. In the present review, we thoroughly examine the impact of senescence on the dopaminergic system, with a primary focus on the classic delimitations of the dopaminergic nuclei from A8 to A17. We provide in-depth information about their anatomy and function, particularly addressing how senescence affects each of these nuclei.
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Affiliation(s)
- Gabriel S Rocha
- Behavioral and Evolutionary Neurobiology Laboratory, Federal University of Sergipe (UFS), Itabaiana, Brazil
| | - Marco Aurelio M Freire
- Behavioral and Evolutionary Neurobiology Laboratory, Federal University of Sergipe (UFS), Itabaiana, Brazil
| | - Karina M Paiva
- Laboratory of Experimental Neurology, State University of Rio Grande do Norte (UERN), Mossoró, Brazil
| | - Rodrigo F Oliveira
- Laboratory of Experimental Neurology, State University of Rio Grande do Norte (UERN), Mossoró, Brazil
| | - Paulo Leonardo A G Morais
- Laboratory of Experimental Neurology, State University of Rio Grande do Norte (UERN), Mossoró, Brazil
| | - José Ronaldo Santos
- Behavioral and Evolutionary Neurobiology Laboratory, Federal University of Sergipe (UFS), Itabaiana, Brazil
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2
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Yazar V, Dawson VL, Dawson TM, Kang SU. DNA Methylation Signature of Aging: Potential Impact on the Pathogenesis of Parkinson's Disease. JOURNAL OF PARKINSON'S DISEASE 2023; 13:145-164. [PMID: 36710687 PMCID: PMC10041453 DOI: 10.3233/jpd-223517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Regulation of gene expression by epigenetic modifications means lasting and heritable changes in the function of genes without alterations in the DNA sequence. Of all epigenetic mechanisms identified thus far, DNA methylation has been of particular interest in both aging and age-related disease research over the last decade given the consistency of site-specific DNA methylation changes during aging that can predict future health and lifespan. An increasing line of evidence has implied the dynamic nature of DNA (de)methylation events that occur throughout the lifespan has a role in the pathophysiology of aging and age-associated neurodegenerative conditions, including Parkinson's disease (PD). In this regard, PD methylome shows, to some extent, similar genome-wide changes observed in the methylome of healthy individuals of matching age. In this review, we start by providing a brief overview of studies outlining global patterns of DNA methylation, then its mechanisms and regulation, within the context of aging and PD. Considering diverging lines of evidence from different experimental and animal models of neurodegeneration and how they combine to shape our current understanding of tissue-specific changes in DNA methylome in health and disease, we report a high-level comparison of the genomic methylation landscapes of brain, with an emphasis on dopaminergic neurons in PD and in natural aging. We believe this will be particularly useful for systematically dissecting overlapping genome-wide alterations in DNA methylation during PD and healthy aging, and for improving our knowledge of PD-specific changes in methylation patterns independent of aging process.
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Affiliation(s)
- Volkan Yazar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pharmacology and and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA
| | - Sung-Ung Kang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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3
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Liu Y, Shen Y, Wang H, Zhang Y, Zhu X. m5Cpred-XS: A New Method for Predicting RNA m5C Sites Based on XGBoost and SHAP. Front Genet 2022; 13:853258. [PMID: 35432446 PMCID: PMC9005994 DOI: 10.3389/fgene.2022.853258] [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: 01/12/2022] [Accepted: 02/16/2022] [Indexed: 11/13/2022] Open
Abstract
As one of the most important post-transcriptional modifications of RNA, 5-cytosine-methylation (m5C) is reported to closely relate to many chemical reactions and biological functions in cells. Recently, several computational methods have been proposed for identifying m5C sites. However, the accuracy and efficiency are still not satisfactory. In this study, we proposed a new method, m5Cpred-XS, for predicting m5C sites of H. sapiens, M. musculus, and A. thaliana. First, the powerful SHAP method was used to select the optimal feature subset from seven different kinds of sequence-based features. Second, different machine learning algorithms were used to train the models. The results of five-fold cross-validation indicate that the model based on XGBoost achieved the highest prediction accuracy. Finally, our model was compared with other state-of-the-art models, which indicates that m5Cpred-XS is superior to other methods. Moreover, we deployed the model on a web server that can be accessed through http://m5cpred-xs.zhulab.org.cn/, and m5Cpred-XS is expected to be a useful tool for studying m5C sites.
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Affiliation(s)
| | | | | | - Yong Zhang
- *Correspondence: Xiaolei Zhu, ; Yong Zhang,
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4
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Lima T, Li TY, Mottis A, Auwerx J. Pleiotropic effects of mitochondria in aging. NATURE AGING 2022; 2:199-213. [PMID: 37118378 DOI: 10.1038/s43587-022-00191-2] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/07/2022] [Indexed: 04/30/2023]
Abstract
Aging is typified by a progressive decline in mitochondrial activity and stress resilience. Here, we review how mitochondrial stress pathways have pleiotropic effects on cellular and systemic homeostasis, which can comprise protective or detrimental responses during aging. We describe recent evidence arguing that defects in these conserved adaptive pathways contribute to aging and age-related diseases. Signaling pathways regulating the mitochondrial unfolded protein response, mitochondrial membrane dynamics, and mitophagy are discussed, emphasizing how their failure contributes to heteroplasmy and de-regulation of key metabolites. Our current understanding of how these processes are controlled and interconnected explains how mitochondria can widely impact fundamental aspects of aging.
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Affiliation(s)
- Tanes Lima
- Laboratory of Integrative Systems Physiology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Terytty Yang Li
- Laboratory of Integrative Systems Physiology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Adrienne Mottis
- Laboratory of Integrative Systems Physiology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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5
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Yildiz CB, Zimmer-Bensch G. Role of DNMTs in the Brain. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:363-394. [DOI: 10.1007/978-3-031-11454-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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6
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Xu M, Zhu J, Liu XD, Luo MY, Xu NJ. Roles of physical exercise in neurodegeneration: reversal of epigenetic clock. Transl Neurodegener 2021; 10:30. [PMID: 34389067 PMCID: PMC8361623 DOI: 10.1186/s40035-021-00254-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/29/2021] [Indexed: 12/17/2022] Open
Abstract
The epigenetic clock is defined by the DNA methylation (DNAm) level and has been extensively applied to distinguish biological age from chronological age. Aging-related neurodegeneration is associated with epigenetic alteration, which determines the status of diseases. In recent years, extensive research has shown that physical exercise (PE) can affect the DNAm level, implying a reversal of the epigenetic clock in neurodegeneration. PE also regulates brain plasticity, neuroinflammation, and molecular signaling cascades associated with epigenetics. This review summarizes the effects of PE on neurodegenerative diseases via both general and disease-specific DNAm mechanisms, and discusses epigenetic modifications that alleviate the pathological symptoms of these diseases. This may lead to probing of the underpinnings of neurodegenerative disorders and provide valuable therapeutic references for cognitive and motor dysfunction.
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Affiliation(s)
- Miao Xu
- Department of Anatomy, Histology and Embryology, Kunming Medical University, Kunming, 650500, China.,Collaborative Innovation Center for Brain Science, Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - JiaYi Zhu
- Collaborative Innovation Center for Brain Science, Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Xian-Dong Liu
- Collaborative Innovation Center for Brain Science, Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ming-Ying Luo
- Department of Anatomy, Histology and Embryology, Kunming Medical University, Kunming, 650500, China
| | - Nan-Jie Xu
- Collaborative Innovation Center for Brain Science, Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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7
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Ravel-Godreuil C, Massiani-Beaudoin O, Mailly P, Prochiantz A, Joshi RL, Fuchs J. Perturbed DNA methylation by Gadd45b induces chromatin disorganization, DNA strand breaks and dopaminergic neuron death. iScience 2021; 24:102756. [PMID: 34278264 PMCID: PMC8264156 DOI: 10.1016/j.isci.2021.102756] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/14/2021] [Accepted: 06/17/2021] [Indexed: 12/13/2022] Open
Abstract
Age is a major risk factor for neurodegenerative diseases like Parkinson's disease, but few studies have explored the contribution of key hallmarks of aging, namely DNA methylation changes and heterochromatin destructuration, in the neurodegenerative process. Here, we investigated the consequences of viral overexpression of Gadd45b, a multifactorial protein involved in DNA demethylation, in the mouse midbrain. Gadd45b overexpression induced global and stable changes in DNA methylation, particularly in introns of genes related to neuronal functions, as well as on LINE-1 transposable elements. This was paralleled by disorganized heterochromatin, increased DNA damage, and vulnerability to oxidative stress. LINE-1 de-repression, a potential source of DNA damage, preceded Gadd45b-induced neurodegeneration, whereas prolonged Gadd45b expression deregulated expression of genes related to heterochromatin maintenance, DNA methylation, or Parkinson's disease. Our data indicates that aging-related alterations contribute to dopaminergic neuron degeneration with potential implications for Parkinson's disease.
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Affiliation(s)
- Camille Ravel-Godreuil
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Olivia Massiani-Beaudoin
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Philippe Mailly
- Orion Imaging Facility, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Labex Memolife, Université PSL, Paris, France
| | - Alain Prochiantz
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Rajiv L. Joshi
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Julia Fuchs
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
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8
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Lossow K, Kopp JF, Schwarz M, Finke H, Winkelbeiner N, Renko K, Meçi X, Ott C, Alker W, Hackler J, Grune T, Schomburg L, Haase H, Schwerdtle T, Kipp AP. Aging affects sex- and organ-specific trace element profiles in mice. Aging (Albany NY) 2020; 12:13762-13790. [PMID: 32620712 PMCID: PMC7377894 DOI: 10.18632/aging.103572] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/13/2020] [Indexed: 12/18/2022]
Abstract
A decline of immune responses and dynamic modulation of the redox status are observed during aging and are influenced by trace elements such as copper, iodine, iron, manganese, selenium, and zinc. So far, analytical studies have focused mainly on single trace elements. Therefore, we aimed to characterize age-specific profiles of several trace elements simultaneously in serum and organs of adult and old mice. This allows for correlating multiple trace element levels and to identify potential patterns of age-dependent alterations. In serum, copper and iodine concentrations were increased and zinc concentration was decreased in old as compared to adult mice. In parallel, decreased copper and elevated iron concentrations were observed in liver. The age-related reduction of hepatic copper levels was associated with reduced expression of copper transporters, whereas the increased hepatic iron concentrations correlated positively with proinflammatory mediators and Nrf2-induced ferritin H levels. Interestingly, the age-dependent inverse regulation of copper and iron was unique for the liver and not observed in any other organ. The physiological importance of alterations in the iron/copper ratio for liver function and the aging process needs to be addressed in further studies.
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Affiliation(s)
- Kristina Lossow
- Department of Molecular Nutritional Physiology, Institute of Nutritional Sciences, Friedrich Schiller University Jena, Jena, Germany.,Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany.,German Institute of Human Nutrition, Nuthetal, Germany.,TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany
| | - Johannes F Kopp
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany.,TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany
| | - Maria Schwarz
- Department of Molecular Nutritional Physiology, Institute of Nutritional Sciences, Friedrich Schiller University Jena, Jena, Germany.,TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany
| | - Hannah Finke
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - Nicola Winkelbeiner
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany.,TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany
| | - Kostja Renko
- Institute for Experimental Endocrinology, Charité University Medical School Berlin, Berlin, Germany.,German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Xheni Meçi
- Institute for Experimental Endocrinology, Charité University Medical School Berlin, Berlin, Germany
| | - Christiane Ott
- German Institute of Human Nutrition, Nuthetal, Germany.,DZHK German Centre for Cardiovascular Research, Berlin, Germany
| | - Wiebke Alker
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany.,Department of Food Chemistry and Toxicology, Technische Universität Berlin, Berlin, Germany
| | - Julian Hackler
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany.,Institute for Experimental Endocrinology, Charité University Medical School Berlin, Berlin, Germany
| | - Tilman Grune
- German Institute of Human Nutrition, Nuthetal, Germany
| | - Lutz Schomburg
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany.,Institute for Experimental Endocrinology, Charité University Medical School Berlin, Berlin, Germany
| | - Hajo Haase
- TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany.,Department of Food Chemistry and Toxicology, Technische Universität Berlin, Berlin, Germany
| | - Tanja Schwerdtle
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany.,TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany.,German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Anna P Kipp
- Department of Molecular Nutritional Physiology, Institute of Nutritional Sciences, Friedrich Schiller University Jena, Jena, Germany.,TraceAge-DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly, Potsdam-Berlin-Jena, Germany
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9
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Li Q, Cai M, Wang J, Gao Q, Guo X, Jia X, Xu S, Zhu H. Decreased ovarian function and autophagy gene methylation in aging rats. J Ovarian Res 2020; 13:12. [PMID: 32014030 PMCID: PMC6998822 DOI: 10.1186/s13048-020-0615-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/22/2020] [Indexed: 01/23/2023] Open
Abstract
Background Degeneration of ovarian function is an obvious feature of female aging. In addition, studies have shown that autophagy decreases with age, and DNA methylation is a hallmark epigenetic pattern during aging. However, it is not clear whether the expression and DNA methylation of autophagy genes are involved in the declines in ovarian function that occur during aging. Results Three groups of rats were used: 6-month-old (6 M) rats, 12-month-old (12 M) rats and 24-month-old (24 M) rats. Serum E2 levels and the mRNA and protein expression levels of Atg5, Atg12, Atg16L, Beclin1 and Lc3B were significantly decreased in aged rats. In addition, the methylation levels of the Atg5 gene were significantly increased in aged rats. The expression of the Dnmt1 and Dnmt2 genes decreased with aging; however, the expression of the Dnmt3A and Dnmt3B genes gradually increased with aging. Conclusions Decreased autophagic activity was involved in the declines in ovarian function in aging rats. Upregulation of the DNA methyltransferases Dnmt3A and Dnmt3B may have led to methylation of the autophagy genes Atg5 and Lc3B to ultimately cause the observed decreases in autophagic activity.
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Affiliation(s)
- Qiuyuan Li
- Department of Physiology, Harbin Medical University, Harbin, 150086, China
| | - Minghui Cai
- Department of Physiology, Harbin Medical University, Harbin, 150086, China
| | - Jiao Wang
- Department of Physiology, Harbin Medical University, Harbin, 150086, China
| | - Qiang Gao
- Department of Physiology, Harbin Medical University, Harbin, 150086, China
| | - Xiaocheng Guo
- Department of Physiology, Harbin Medical University, Harbin, 150086, China
| | - Xiaotong Jia
- Department of Physiology, Harbin Medical University, Harbin, 150086, China
| | - Shanshan Xu
- Department of Physiology, Harbin Medical University, Harbin, 150086, China
| | - Hui Zhu
- Department of Physiology, Harbin Medical University, Harbin, 150086, China.
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10
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Figueroa-Romero C, Guo K, Murdock BJ, Paez-Colasante X, Bassis CM, Mikhail KA, Pawlowski KD, Evans MC, Taubman GF, McDermott AJ, O'Brien PD, Savelieff MG, Hur J, Feldman EL. Temporal evolution of the microbiome, immune system and epigenome with disease progression in ALS mice. Dis Model Mech 2019; 13:dmm041947. [PMID: 31597644 PMCID: PMC6906635 DOI: 10.1242/dmm.041947] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/05/2019] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a terminal neurodegenerative disease. Genetic predisposition, epigenetic changes, aging and accumulated life-long environmental exposures are known ALS risk factors. The complex and dynamic interplay between these pathological influences plays a role in disease onset and progression. Recently, the gut microbiome has also been implicated in ALS development. In addition, immune cell populations are differentially expanded and activated in ALS compared to healthy individuals. However, the temporal evolution of both the intestinal flora and the immune system relative to symptom onset in ALS is presently not fully understood. To better elucidate the timeline of the various potential pathological factors, we performed a longitudinal study to simultaneously assess the gut microbiome, immunophenotype and changes in ileum and brain epigenetic marks relative to motor behavior and muscle atrophy in the mutant superoxide dismutase 1 (SOD1G93A) familial ALS mouse model. We identified alterations in the gut microbial environment early in the life of SOD1G93A animals followed by motor dysfunction and muscle atrophy, and immune cell expansion and activation, particularly in the spinal cord. Global brain cytosine hydroxymethylation was also altered in SOD1G93A animals at disease end-stage compared to control mice. Correlation analysis confirmed interrelationships with the microbiome and immune system. This study serves as a starting point to more deeply comprehend the influence of gut microorganisms and the immune system on ALS onset and progression. Greater insight may help pinpoint novel biomarkers and therapeutic interventions to improve diagnosis and treatment for ALS patients.This article has an associated First Person interview with the joint first authors of the paper.
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Affiliation(s)
| | - Kai Guo
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Benjamin J Murdock
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Christine M Bassis
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kristen A Mikhail
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Matthew C Evans
- Department of Pharmacology, University of Oxford, Oxford OX1 3QT, UK
| | | | - Andrew J McDermott
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Phillipe D O'Brien
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Masha G Savelieff
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Junguk Hur
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Eva L Feldman
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
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11
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Writers and Readers of DNA Methylation/Hydroxymethylation in Physiological Aging and Its Impact on Cognitive Function. Neural Plast 2019; 2019:5982625. [PMID: 31396272 PMCID: PMC6664507 DOI: 10.1155/2019/5982625] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/25/2019] [Accepted: 05/26/2019] [Indexed: 12/31/2022] Open
Abstract
The chromatin landscape has acquired deep attention from several fields ranging from cell biology to neurological and psychiatric diseases. The role that DNA modifications have on gene expression regulation has become apparent in several physiological processes, and numerous efforts have been performed to establish a relationship between DNA modifications and physiological conditions, such as cognitive performance and aging. DNA modifications are incorporated by specific sets of enzymes-the writers-and the modified DNA-interacting partners-the readers-are ultimately responsible for maintaining a functional epigenetic landscape. Therefore, understanding how these epigenetic mediators-writers and readers-are modulated in physiological aging will contribute to unraveling how aging-associated neuronal disturbances arise and contribute to the cognitive decline associated with this period of life. In this review, we focused on DNA modifications, writers and readers, highlighting that despite some methodological disparities, the evidence suggests a critical role for epigenetic mediators in the aging-associated neuronal dysfunction.
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12
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Gadecka A, Bielak-Zmijewska A. Slowing Down Ageing: The Role of Nutrients and Microbiota in Modulation of the Epigenome. Nutrients 2019; 11:nu11061251. [PMID: 31159371 PMCID: PMC6628342 DOI: 10.3390/nu11061251] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 12/13/2022] Open
Abstract
The human population is getting ageing. Both ageing and age-related diseases are correlated with an increased number of senescent cells in the organism. Senescent cells do not divide but are metabolically active and influence their environment by secreting many proteins due to a phenomenon known as senescence associated secretory phenotype (SASP). Senescent cells differ from young cells by several features. They possess more damaged DNA, more impaired mitochondria and an increased level of free radicals that cause the oxidation of macromolecules. However, not only biochemical and structural changes are related to senescence. Senescent cells have an altered chromatin structure, and in consequence, altered gene expression. With age, the level of heterochromatin decreases, and less condensed chromatin is more prone to DNA damage. On the one hand, some gene promoters are easily available for the transcriptional machinery; on the other hand, some genes are more protected (locally increased level of heterochromatin). The structure of chromatin is precisely regulated by the epigenetic modification of DNA and posttranslational modification of histones. The methylation of DNA inhibits transcription, histone methylation mostly leads to a more condensed chromatin structure (with some exceptions) and acetylation plays an opposing role. The modification of both DNA and histones is regulated by factors present in the diet. This means that compounds contained in daily food can alter gene expression and protect cells from senescence, and therefore protect the organism from ageing. An opinion prevailed for some time that compounds from the diet do not act through direct regulation of the processes in the organism but through modification of the physiology of the microbiome. In this review we try to explain the role of some food compounds, which by acting on the epigenetic level might protect the organism from age-related diseases and slow down ageing. We also try to shed some light on the role of microbiome in this process.
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Affiliation(s)
- Agnieszka Gadecka
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093 Warsaw, Poland.
| | - Anna Bielak-Zmijewska
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093 Warsaw, Poland.
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Unnikrishnan A, Hadad N, Masser DR, Jackson J, Freeman WM, Richardson A. Revisiting the genomic hypomethylation hypothesis of aging. Ann N Y Acad Sci 2018; 1418:69-79. [PMID: 29363785 DOI: 10.1111/nyas.13533] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/19/2017] [Accepted: 09/26/2017] [Indexed: 12/26/2022]
Abstract
The genomic hypomethylation hypothesis of aging proposes that an overall decrease in global DNA methylation occurs with age, and it has been argued that the decrease in global DNA methylation could be an important factor in aging, resulting in the relaxation of gene expression regulation and abnormal gene expression. Since it was initially observed that DNA methylation decreased with age in 1974, 16 articles have been published describing the effect of age on global DNA methylation in various tissues from rodents and humans. We critically reviewed the publications on the effect of age on DNA methylation and the expression of the enzymes involved in DNA methylation to evaluate the validity of the hypomethylation hypothesis of aging. On the basis of the current scientific literature, we conclude that a decrease in the global methylation of the genome occurs in most if not all tissues/cells as an animal ages. However, age-related changes in DNA methylation in specific regions or at specific sites in the genome occur even though the global DNA methylation does not change.
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Affiliation(s)
- Archana Unnikrishnan
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Niran Hadad
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Department of Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Dustin R Masser
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Jordan Jackson
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Willard M Freeman
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Arlan Richardson
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma.,Oklahoma City VA Medical Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
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Sjöholm LK, Ransome Y, Ekström TJ, Karlsson O. Evaluation of Post-Mortem Effects on Global Brain DNA Methylation and Hydroxymethylation. Basic Clin Pharmacol Toxicol 2017; 122:208-213. [PMID: 28834189 DOI: 10.1111/bcpt.12875] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/07/2017] [Indexed: 12/17/2022]
Abstract
The number of epigenetic studies on brain functions and diseases are dramatically increasing, but little is known about the impact of post-mortem intervals and post-sampling effects on DNA modifications such as 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Here, we examined post-mortem-induced changes in global brain 5mC and 5hmC levels at post-mortem intervals up to 540 min., and studied effects of tissue heat stabilization, using LUMA and ELISA. The global 5mC and 5hmC levels were generally higher in the cerebellum of adult rats than neonates. When measured by ELISA, the global 5mC content in adults, but not neonates, decreased with the post-mortem interval reaching a significantly lower level in cerebellum tissue at the post-mortem interval 540 min. (2.9 ± 0.7%; mean ± S.E.M.) compared to control (3.7 ± 0.6%). The global 5hmC levels increased with post-mortem interval reaching a significantly higher level at 540 min. (0.29 ± 0.06%) compared to control (0.19 ± 0.03%). This suggests that the post-mortem interval may confound 5mC and 5hmC analysis in human brain tissues as the post-mortem handling could vary substantially. The reactive oxygen species (ROS) level in cerebellum also increased over time, in particular in adults, and may be part of the mechanism that causes the observed post-mortem changes in 5mC and 5hmC. The global 5mC and 5hmC states were unaffected by heat stabilization, allowing analysis of tissues that are stabilized to preserve more labile analytes. Further studies in human samples are needed to confirm post-mortem effects on DNA methylation/hydroxymethylation and elucidate details of the underlying mechanisms.
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Affiliation(s)
- Louise K Sjöholm
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Yusuf Ransome
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Tomas J Ekström
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Oskar Karlsson
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden.,Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
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