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Ullah I, Zhao L, Uddin S, Zhou Y, Wang X, Li H. Nicotine-mediated therapy for Parkinson's disease in transgenic Caenorhabditis elegans model. Front Aging Neurosci 2024; 16:1358141. [PMID: 38813528 PMCID: PMC11135287 DOI: 10.3389/fnagi.2024.1358141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/30/2024] [Indexed: 05/31/2024] Open
Abstract
Parkinson's disease resultant in the degeneration of Dopaminergic neurons and accumulation of α-synuclein in the substantia nigra pars compacta. The synthetic therapeutics for Parkinson's disease have moderate symptomatic benefits but cannot prevent or delay disease progression. In this study, nicotine was employed by using transgenic Caenorhabditis elegans Parkinson's disease models to minimize the Parkinson's disease symptoms. The results showed that the nicotine at 100, 150, and 200 μM doses reduced degeneration of Dopaminergic neurons caused by 6-hydroxydopamine (14, 33, and 40%), lowered the aggregative toxicity of α-synuclein by 53, 56, and 78%, respectively. The reduction in food-sensing behavioral disabilities of BZ555 was observed to be 18, 49, and 86%, respectively, with nicotine concentrations of 100 μM, 150 μM, and 200 μM. Additionally, nicotine was found to enhance Daf-16 nuclear translocation by 14, 31, and 49%, and dose-dependently increased SOD-3 expression by 10, 19, and 23%. In summary, the nicotine might a promising therapy option for Parkinson's disease.
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Affiliation(s)
- Inam Ullah
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Longhe Zhao
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Shahab Uddin
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yangtao Zhou
- Department of Neurology, Clinical Center for Parkinson's Disease, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Xin Wang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Hongyu Li
- School of Life Sciences, Lanzhou University, Lanzhou, China
- School of Pharmacy, Lanzhou University, Lanzhou, China
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2
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Gao S, Wang Y, Li X, Liang Y, Jin Z, Yang B, Yuan TF, Tian H, Peng B, Rao Y. Dynamics of N6-methyladenosine modification during Alzheimer's disease development. Heliyon 2024; 10:e26911. [PMID: 38496847 PMCID: PMC10944207 DOI: 10.1016/j.heliyon.2024.e26911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/19/2024] Open
Abstract
N6-methyladenosine (m6A) modification is a common RNA modification in the central nervous system and has been linked to various neurological disorders, including Alzheimer's disease (AD). However, the dynamic of mRNA m6A modification and m6A enzymes during the development of AD are not well understood. Therefore, this study examined the expression profiles of m6A and its enzymes in the development of AD. The results showed that changes in the expression levels of m6A regulatory factors occur in the early stages of AD, indicating a potential role for m6A modification in the onset of the disease. Additionally, the analysis of mRNA m6A expression profiles using m6A-seq revealed significant differences in m6A modification between AD and control brains. The genes with differential methylation were found to be enriched in GO and KEGG terms related to processes such as inflammation response, immune system processes. And the differently expressed genes (DEGs) are negatively lryassociated with genes involved in microglia hemostasis, but positively associated with genes related to "disease-associated microglia" (DAM) associated genes. These findings suggest that dysregulation of mRNA m6A modification may contribute to the development of AD by affecting the function and gene expression of microglia.
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Affiliation(s)
- Shuai Gao
- Department of Neurosurgery, Huashan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, 200040, China
| | - Yuqing Wang
- Department of Neurology, Zhongshan Hospital, Department of Laboratory Animal Science, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
- Department of Medical Science, Medical College of Jinzhou Medical University, Jinzhou, Liaoning, 121010, China
| | - Xiaoyu Li
- Department of Neurosurgery, Huashan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, 200040, China
| | - Yuqing Liang
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Zhihao Jin
- Department of Neurology, Zhongshan Hospital, Department of Laboratory Animal Science, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Baozhi Yang
- Department of Neurology, Zhongshan Hospital, Department of Laboratory Animal Science, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Ti-Fei Yuan
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 201108, China
| | - Hengli Tian
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Bo Peng
- Department of Neurosurgery, Huashan Hospital, Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Innovative Center for New Drug Development of Immune Inflammatory Diseases, Ministry of Education, Fudan University, Shanghai, 200040, China
- Department of Neurology, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Yanxia Rao
- Department of Neurology, Zhongshan Hospital, Department of Laboratory Animal Science, MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
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3
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Kraveishvili N, Kvaratskhelia E, Surmava S, Kvintradze M, Zarandia M, Gorgiladze T, Abzianidze E. DNA methylation status of interspersed repetitive sequences in patients with migraine. J Int Med Res 2023; 51:3000605231152109. [PMID: 36734246 PMCID: PMC9900668 DOI: 10.1177/03000605231152109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVE To analyse the methylation status of the Long Interspersed Nuclear Element-1 (LINE-1) and Short Interspersed Nuclear Element Alu (Alu) of peripheral blood mononuclear cells (PBMCs) from patients with migraine compared with healthy control subjects. METHODS This case-control study recruited patients with migraine without aura and age-matched healthy control subjects. PBMCs were purified from peripheral blood samples. Methylation levels and patterns of LINE-1 and Alu sequences were evaluated using combined bisulfite restriction analysis-interspersed repetitive sequences polymerase chain reaction. RESULTS A total of 84 patients with migraine and 82 age-matched healthy controls were enrolled in the study. High levels of unmethylated cytosines in both the LINE-1 and Alu repetitive elements were observed in the migraine group compared with the control subjects. In addition, a significant difference was detected in the methylation level of LINE-1 between TT and CC genotype groups of the methylenetetrahydrofolate reductase gene. CONCLUSIONS These results suggest that analysis of epigenetic biomarkers in PBMCs may help to identify patients at a higher risk of migraine development.
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Affiliation(s)
- Nino Kraveishvili
- Department of Molecular and Medical Genetics, Tbilisi State
Medical University, Tbilisi, Georgia,Department of Neurology, Tbilisi Institute of Medicine, Tbilisi,
Georgia
| | - Eka Kvaratskhelia
- Department of Molecular and Medical Genetics, Tbilisi State
Medical University, Tbilisi, Georgia,Eka Kvaratskhelia, Department of Molecular
and Medical Genetics, Tbilisi State Medical University, 5 Khvichia str., 0160
Tbilisi, Georgia.
| | - Sandro Surmava
- Department of Molecular and Medical Genetics, Tbilisi State
Medical University, Tbilisi, Georgia
| | - Merab Kvintradze
- Department of Molecular and Medical Genetics, Tbilisi State
Medical University, Tbilisi, Georgia
| | - Maia Zarandia
- Department of Molecular and Medical Genetics, Tbilisi State
Medical University, Tbilisi, Georgia
| | - Tinatin Gorgiladze
- Department of Dentistry, Batumi Shota Rustaveli State
University, Batumi, Georgia
| | - Elene Abzianidze
- Department of Molecular and Medical Genetics, Tbilisi State
Medical University, Tbilisi, Georgia
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4
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Dynamic Regulation of DNA Methylation and Brain Functions. BIOLOGY 2023; 12:biology12020152. [PMID: 36829430 PMCID: PMC9952911 DOI: 10.3390/biology12020152] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
DNA cytosine methylation is a principal epigenetic mechanism underlying transcription during development and aging. Growing evidence suggests that DNA methylation plays a critical role in brain function, including neurogenesis, neuronal differentiation, synaptogenesis, learning, and memory. However, the mechanisms underlying aberrant DNA methylation in neurodegenerative diseases remain unclear. In this review, we provide an overview of the contribution of 5-methycytosine (5mC) and 5-hydroxylcytosine (5hmC) to brain development and aging, with a focus on the roles of dynamic 5mC and 5hmC changes in the pathogenesis of neurodegenerative diseases, particularly Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD). Identification of aberrant DNA methylation sites could provide potential candidates for epigenetic-based diagnostic and therapeutic strategies for neurodegenerative diseases.
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5
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Morel C, Schroeder H, Emond C, Turner JD, Lichtfouse E, Grova N. Brominated flame retardants, a cornelian dilemma. ENVIRONMENTAL CHEMISTRY LETTERS 2023; 21:9-14. [PMID: 35095379 PMCID: PMC8783781 DOI: 10.1007/s10311-022-01392-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Affiliation(s)
- Chloé Morel
- Calbinotox, Faculty of Science and Technology, University of Lorraine, Campus Aiguillettes, B.P. 70239, 54506 Vandoeuvre-lès-Nancy, France
| | - Henri Schroeder
- Calbinotox, Faculty of Science and Technology, University of Lorraine, Campus Aiguillettes, B.P. 70239, 54506 Vandoeuvre-lès-Nancy, France
- UMR Inserm 1256 nGERE, Nutrition-Génétique et Exposition aux risques environnementaux, Institute of Medical Research (Pôle BMS, University of Lorraine, B.P. 184, 54511 Vandoeuvre-lès-Nancy, France
| | - Claude Emond
- Calbinotox, Faculty of Science and Technology, University of Lorraine, Campus Aiguillettes, B.P. 70239, 54506 Vandoeuvre-lès-Nancy, France
- PKSH Inc, Mascouche, QC Canada
- School of Public Health, DSEST, University of Montreal, Montreal, QC Canada
| | - Jonathan D. Turner
- Immune Endocrine Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354 Esch-Sur-Alzette, Grand Duchy of Luxembourg
| | - Eric Lichtfouse
- Aix-Marseille Univ, CNRS, IRD, INRAE, CEREGE, 13100 Aix en Provence, France
| | - Nathalie Grova
- Calbinotox, Faculty of Science and Technology, University of Lorraine, Campus Aiguillettes, B.P. 70239, 54506 Vandoeuvre-lès-Nancy, France
- UMR Inserm 1256 nGERE, Nutrition-Génétique et Exposition aux risques environnementaux, Institute of Medical Research (Pôle BMS, University of Lorraine, B.P. 184, 54511 Vandoeuvre-lès-Nancy, France
- Immune Endocrine Epigenetics Research Group, Department of Infection and Immunity, Luxembourg Institute of Health, 29, rue Henri Koch, L-4354 Esch-Sur-Alzette, Grand Duchy of Luxembourg
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6
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Zeng W, Gautam A, Huson DH. MuLan-Methyl-multiple transformer-based language models for accurate DNA methylation prediction. Gigascience 2022; 12:giad054. [PMID: 37489753 PMCID: PMC10367125 DOI: 10.1093/gigascience/giad054] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 05/09/2023] [Accepted: 07/18/2023] [Indexed: 07/26/2023] Open
Abstract
Transformer-based language models are successfully used to address massive text-related tasks. DNA methylation is an important epigenetic mechanism, and its analysis provides valuable insights into gene regulation and biomarker identification. Several deep learning-based methods have been proposed to identify DNA methylation, and each seeks to strike a balance between computational effort and accuracy. Here, we introduce MuLan-Methyl, a deep learning framework for predicting DNA methylation sites, which is based on 5 popular transformer-based language models. The framework identifies methylation sites for 3 different types of DNA methylation: N6-adenine, N4-cytosine, and 5-hydroxymethylcytosine. Each of the employed language models is adapted to the task using the "pretrain and fine-tune" paradigm. Pretraining is performed on a custom corpus of DNA fragments and taxonomy lineages using self-supervised learning. Fine-tuning aims at predicting the DNA methylation status of each type. The 5 models are used to collectively predict the DNA methylation status. We report excellent performance of MuLan-Methyl on a benchmark dataset. Moreover, we argue that the model captures characteristic differences between different species that are relevant for methylation. This work demonstrates that language models can be successfully adapted to applications in biological sequence analysis and that joint utilization of different language models improves model performance. Mulan-Methyl is open source, and we provide a web server that implements the approach.
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Affiliation(s)
- Wenhuan Zeng
- Algorithms in Bioinformatics, Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Germany
| | - Anupam Gautam
- Algorithms in Bioinformatics, Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Germany
- International Max Planck Research School “From Molecules to Organisms”, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen, 72076 Tübingen, Germany
| | - Daniel H Huson
- Algorithms in Bioinformatics, Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Germany
- International Max Planck Research School “From Molecules to Organisms”, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen, 72076 Tübingen, Germany
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7
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Zima L, West R, Smolen P, Kobori N, Hergenroeder G, Choi HA, Moore AN, Redell JB, Dash PK. Epigenetic Modifications and Their Potential Contribution to Traumatic Brain Injury Pathobiology and Outcome. J Neurotrauma 2022; 39:1279-1288. [PMID: 35481812 PMCID: PMC9529317 DOI: 10.1089/neu.2022.0128] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Epigenetic information is not permanently encoded in the DNA sequence, but rather consists of reversible, heritable modifications that regulate the gene expression profile of a cell. Epigenetic modifications can result in cellular changes that can be long lasting and include DNA methylation, histone methylation, histone acetylation, and RNA methylation. As epigenetic modifications are reversible, the enzymes that add (epigenetic writers), the proteins that decode (epigenetic readers), and the enzymes that remove (epigenetic erasers) these modifications can be targeted to alter cellular function and disease biology. While epigenetic modifications and their contributions are intense topics of current research in the context of a number of diseases, including cancer, inflammatory diseases, and Alzheimer disease, the study of epigenetics in the context of traumatic brain injury (TBI) is in its infancy. In this review, we will summarize the experimental and clinical findings demonstrating that TBI triggers epigenetic modifications, with a focus on changes in DNA methylation, histone methylation, and the translational utility of the universal methyl donor S-adenosylmethionine (SAM). Finally, we will review the evidence for using methyl donors as possible treatments for TBI-associated pathology and outcome.
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Affiliation(s)
- Laura Zima
- Department of Neurological Surgery, University of Texas Health Science Center McGovern Medical School, Houston, Texas, USA
| | - Rebecca West
- Department of Neurobiology and Anatomy, University of Texas Health Science Center McGovern Medical School, Houston, Texas, USA
| | - Paul Smolen
- Department of Neurobiology and Anatomy, University of Texas Health Science Center McGovern Medical School, Houston, Texas, USA
| | - Nobuhide Kobori
- Department of Neurobiology and Anatomy, University of Texas Health Science Center McGovern Medical School, Houston, Texas, USA
| | - Georgene Hergenroeder
- Department of Neurological Surgery, University of Texas Health Science Center McGovern Medical School, Houston, Texas, USA
| | - HuiMahn A. Choi
- Department of Neurological Surgery, University of Texas Health Science Center McGovern Medical School, Houston, Texas, USA
| | - Anthony N. Moore
- Department of Neurobiology and Anatomy, University of Texas Health Science Center McGovern Medical School, Houston, Texas, USA
| | - John B. Redell
- Department of Neurobiology and Anatomy, University of Texas Health Science Center McGovern Medical School, Houston, Texas, USA
| | - Pramod K. Dash
- Department of Neurobiology and Anatomy, University of Texas Health Science Center McGovern Medical School, Houston, Texas, USA
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8
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Zhang N, Ding C, Zuo Y, Peng Y, Zuo L. N6-methyladenosine and Neurological Diseases. Mol Neurobiol 2022; 59:1925-1937. [PMID: 35032318 DOI: 10.1007/s12035-022-02739-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/08/2022] [Indexed: 12/14/2022]
Abstract
N6-methyladenosine (m6A) is a dynamic reversible methylation modification of the adenosine N6 position and is the most common chemical epigenetic modification among mRNA post-transcriptional modifications, including methylation, demethylation, and recognition. Post-transcriptional modification involves multiple protein molecules, including METTL3, METTL14, WTAP, KIAA1429, ALKBH5, YTHDF1/2/3, and YTHDC1/2. m6A-related proteins are expressed in almost all cells. However, the abnormal expression of m6A-related proteins may occur in the nervous system, thereby affecting neuritogenesis, brain volume, learning and memory, memory formation and consolidation, etc., and is implicated in the development of diseases, such as Parkinson's disease, Alzheimer's disease, multiple sclerosis, depression, epilepsy, and brain tumors. This review focuses on the functions of m6A in the development of central nervous system diseases, thus contributing to a deeper understanding of disease pathogenesis and providing potential clinical therapeutic targets for neurological diseases.
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Affiliation(s)
- Nan Zhang
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical College, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, China
| | - Chunhong Ding
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical College, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, China
| | - Yuxin Zuo
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical College, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, China
| | - Yu Peng
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical College, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, China
| | - Lielian Zuo
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical College, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, China.
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Kaur G, Rathod SSS, Ghoneim MM, Alshehri S, Ahmad J, Mishra A, Alhakamy NA. DNA Methylation: A Promising Approach in Management of Alzheimer's Disease and Other Neurodegenerative Disorders. BIOLOGY 2022; 11:biology11010090. [PMID: 35053088 PMCID: PMC8773419 DOI: 10.3390/biology11010090] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/13/2022]
Abstract
Simple Summary DNA methylation is an epigenetic modification of genes which affects corresponding gene expression. During the developmental stage, embryonic stem cells undergo various epigenetic modifications to produce different specialized cells. DNA methylation appears as one of the important epigenetic modifications which not only potentiate neuronal development but also have been sought in various neurodegenerative diseases, such as Alzheimer’s disease. The present work focuses on the history of DNA methylation, its role in neurodevelopment functions, and how assessment of DNA hypermethylation and hypomethylation can be utilized for the prognosis of AD and other neurodegenerative diseases. This review also paves the way for the development of novel treatment strategies based on targeting DNA methylation in neurodegenerative diseases. Abstract DNA methylation, in the mammalian genome, is an epigenetic modification that involves the transfer of a methyl group on the C5 position of cytosine to derive 5-methylcytosine. The role of DNA methylation in the development of the nervous system and the progression of neurodegenerative diseases such as Alzheimer’s disease has been an interesting research area. Furthermore, mutations altering DNA methylation affect neurodevelopmental functions and may cause the progression of several neurodegenerative diseases. Epigenetic modifications in neurodegenerative diseases are widely studied in different populations to uncover the plausible mechanisms contributing to the development and progression of the disease and detect novel biomarkers for early prognosis and future pharmacotherapeutic targets. In this manuscript, we summarize the association of DNA methylation with the pathogenesis of the most common neurodegenerative diseases, such as, Alzheimer’s disease, Parkinson’s disease, Huntington diseases, and amyotrophic lateral sclerosis, and discuss the potential of DNA methylation as a potential biomarker and therapeutic tool for neurogenerative diseases.
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Affiliation(s)
- Gagandeep Kaur
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, Punjab, India; (G.K.); (S.S.S.R.)
| | - Suraj Singh S. Rathod
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, Punjab, India; (G.K.); (S.S.S.R.)
| | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia;
| | - Sultan Alshehri
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Javed Ahmad
- Department of Pharmaceutics, College of Pharmacy, Najran University, Najran 11001, Saudi Arabia;
| | - Awanish Mishra
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, Kamrup 781101, Assam, India
- Correspondence: or ; Tel.: +91-972-1554-158 or +91-829-976-4600
| | - Nabil A. Alhakamy
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
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10
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Tost J. Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:395-469. [DOI: 10.1007/978-3-031-11454-0_16] [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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11
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Heinsberg LW, Liu D, Shaffer JR, Weeks DE, Conley YP. Characterization of cerebrospinal fluid DNA methylation age during the acute recovery period following aneurysmal subarachnoid hemorrhage. EPIGENETICS COMMUNICATIONS 2021; 1. [PMID: 35083469 PMCID: PMC8787331 DOI: 10.1186/s43682-021-00002-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Abstract
Background
Biological aging may occur at different rates than chronological aging due to genetic, social, and environmental factors. DNA methylation (DNAm) age is thought to be a reliable measure of accelerated biological aging which has been linked to an array of poor health outcomes. Given the importance of chronological age in recovery following aneurysmal subarachnoid hemorrhage (aSAH), a type of stroke, DNAm age may also be an important biomarker of outcomes, further improving predictive models. Cerebrospinal fluid (CSF) is a unique tissue representing the local central nervous system environment post-aSAH. However, the validity of CSF DNAm age is unknown, and it is unclear which epigenetic clock is ideal to compute CSF DNAm age, particularly given changes in cell type heterogeneity (CTH) during the acute recovery period. Further, the stability of DNAm age post-aSAH, specifically, has not been examined and may improve our understanding of patient recovery post-aSAH. Therefore, the purpose of this study was to characterize CSF DNAm age over 14 days post-aSAH using four epigenetic clocks.
Results
Genome-wide DNAm data were available for two tissues: (1) CSF for N = 273 participants with serial sampling over 14 days post-aSAH (N = 850 samples) and (2) blood for a subset of n = 72 participants at one time point post-aSAH. DNAm age was calculated using the Horvath, Hannum, Levine, and “Improved Precision” (Zhang) epigenetic clocks. “Age acceleration” was computed as the residuals of DNAm age regressed on chronological age both with and without correcting for CTH. Using scatterplots, Pearson correlations, and group-based trajectory analysis, we examined the relationships between CSF DNAm age and chronological age, the concordance between DNAm ages calculated from CSF versus blood, and the stability (i.e., trajectories) of CSF DNAm age acceleration over time during recovery from aSAH. We observed moderate to strong correlations between CSF DNAm age and chronological age (R = 0.66 [Levine] to R = 0.97 [Zhang]), moderate to strong correlations between DNAm age in CSF versus blood (R = 0.69 [Levine] to R = 0.98 [Zhang]), and stable CSF age acceleration trajectories over 14 days post-aSAH in the Horvath and Zhang clocks (unadjusted for CTH), as well as the Hannum clock (adjusted for CTH).
Conclusions
CSF DNAm age was generally stable post-aSAH. Although correlated, CSF DNAm age differs from blood DNAm age in the Horvath, Hannum, and Levine clocks, but not in the Zhang clock. Taken together, our results suggest that, of the clocks examined here, the Zhang clock is the most robust to CTH and is recommended for use in complex tissues such as CSF.
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12
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Chao CC, Shen PW, Tzeng TY, Kung HJ, Tsai TF, Wong YH. Human iPSC-Derived Neurons as A Platform for Deciphering the Mechanisms behind Brain Aging. Biomedicines 2021; 9:1635. [PMID: 34829864 PMCID: PMC8615703 DOI: 10.3390/biomedicines9111635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 12/21/2022] Open
Abstract
With an increased life expectancy among humans, aging has recently emerged as a major focus in biomedical research. The lack of in vitro aging models-especially for neurological disorders, where access to human brain tissues is limited-has hampered the progress in studies on human brain aging and various age-associated neurodegenerative diseases at the cellular and molecular level. In this review, we provide an overview of age-related changes in the transcriptome, in signaling pathways, and in relation to epigenetic factors that occur in senescent neurons. Moreover, we explore the current cell models used to study neuronal aging in vitro, including immortalized cell lines, primary neuronal culture, neurons directly converted from fibroblasts (Fib-iNs), and iPSC-derived neurons (iPSC-iNs); we also discuss the advantages and limitations of these models. In addition, the key phenotypes associated with cellular senescence that have been observed by these models are compared. Finally, we focus on the potential of combining human iPSC-iNs with genome editing technology in order to further our understanding of brain aging and neurodegenerative diseases, and discuss the future directions and challenges in the field.
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Affiliation(s)
- Chuan-Chuan Chao
- Aging and Health Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (C.-C.C.); (T.-F.T.)
- Department of Neurology, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Po-Wen Shen
- Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 112, Taiwan;
- Ph.D. Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Tsai-Yu Tzeng
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan;
| | - Hsing-Jien Kung
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli 350, Taiwan;
- Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 110, Taiwan
- Department of Biochemistry and Molecular Medicine, Comprehensive Cancer Center, University of California at Davis, Sacramento, CA 95817, USA
| | - Ting-Fen Tsai
- Aging and Health Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (C.-C.C.); (T.-F.T.)
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli 350, Taiwan;
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Yu-Hui Wong
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
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13
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Qu W, Zhuang Y, Li X. The roles of epigenetic modifications in neurodegenerative diseases. Zhejiang Da Xue Xue Bao Yi Xue Ban 2021; 50:642-650. [PMID: 34986527 PMCID: PMC8732261 DOI: 10.3724/zdxbyxb-2021-0160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/30/2021] [Indexed: 06/14/2023]
Abstract
In neuronal system, epigenetic modifications are essential for neuronal development, the fate determination of neural stem cells and neuronal function. The dysfunction of epigenetic regulation is closely related to occurrence and development of neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Huntington's disease. Abnormally elevated DNA methylation inhibits the expression of some DNA repair-related genes and affects the progression of Huntington's disease. In the brain of Alzheimer's disease patients, the levels of H3K27ac and H3K9ac histone modifications increased. In addition, the alteration of RNA methylation in animal models of Alzheimer's disease and Parkinson's disease showed discrepancy trends. Therefore, epigenetic modifications may serve as potential therapeutic targets for neurodegenerative diseases. Here, we summarize the recent progress of the roles of epigenetic modifications in neurodegenerative diseases.
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Affiliation(s)
- Wenzheng Qu
- of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| | - Yingliang Zhuang
- of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| | - Xuekun Li
- of Translational Medicine, Zhejiang University, Hangzhou 310029, China
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14
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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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15
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Komilova NR, Angelova PR, Berezhnov AV, Stelmashchuk OA, Mirkhodjaev UZ, Houlden H, Gourine AV, Esteras N, Abramov AY. Metabolically induced intracellular pH changes activate mitophagy, autophagy, and cell protection in familial forms of Parkinson's disease. FEBS J 2021; 289:699-711. [PMID: 34528385 DOI: 10.1111/febs.16198] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/26/2021] [Accepted: 09/13/2021] [Indexed: 12/29/2022]
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder induced by the loss of dopaminergic neurons in midbrain. The mechanism of neurodegeneration is associated with aggregation of misfolded proteins, oxidative stress, and mitochondrial dysfunction. Considering this, the process of removal of unwanted organelles or proteins by autophagy is vitally important in neurons, and activation of these processes could be protective in PD. Short-time acidification of the cytosol can activate mitophagy and autophagy. Here, we used sodium pyruvate and sodium lactate to induce changes in intracellular pH in human fibroblasts with PD mutations (Pink1, Pink1/Park2, α-synuclein triplication, A53T). We have found that both lactate and pyruvate in millimolar concentrations can induce a short-time acidification of the cytosol in these cells. This induced activation of mitophagy and autophagy in control and PD fibroblasts and protected against cell death. Importantly, application of lactate to acute brain slices of WT and Pink1 KO mice also induced a reduction of pH in neurons and astrocytes that increased the level of mitophagy. Thus, acidification of the cytosol by compounds, which play an important role in cell metabolism, can also activate mitophagy and autophagy and protect cells in the familial form of PD.
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Affiliation(s)
- Nafisa R Komilova
- Department of Biophysics, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Plamena R Angelova
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Alexey V Berezhnov
- Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino, Russia.,Cell Physiology and Pathology Laboratory, Orel State University, Russia
| | | | | | - Henry Houlden
- Department of Neurodegenerative diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Alexander V Gourine
- Department of Neuroscience, Physiology, Pharmacology, University College London, UK
| | - Noemi Esteras
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Andrey Y Abramov
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.,Cell Physiology and Pathology Laboratory, Orel State University, Russia
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16
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Urban JM, Foulk MS, Bliss JE, Coleman CM, Lu N, Mazloom R, Brown SJ, Spradling AC, Gerbi SA. High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing. BMC Genomics 2021; 22:643. [PMID: 34488624 PMCID: PMC8419958 DOI: 10.1186/s12864-021-07926-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 08/08/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisjunction during spermatogenesis, paternal X elimination during embryogenesis, intrachromosomal DNA amplification of DNA puff loci during larval development, and germline-limited chromosome elimination from all somatic cells. Paternal chromosome elimination in Sciara was the first observation of imprinting, though the mechanism remains a mystery. Here, we present the first draft genome sequence for Sciara coprophila to take a large step forward in addressing these features. RESULTS We assembled the Sciara genome using PacBio, Nanopore, and Illumina sequencing. To find an optimal assembly using these datasets, we generated 44 short-read and 50 long-read assemblies. We ranked assemblies using 27 metrics assessing contiguity, gene content, and dataset concordance. The highest-ranking assemblies were scaffolded using BioNano optical maps. RNA-seq datasets from multiple life stages and both sexes facilitated genome annotation. A set of 66 metrics was used to select the first draft assembly for Sciara. Nearly half of the Sciara genome sequence was anchored into chromosomes, and all scaffolds were classified as X-linked or autosomal by coverage. CONCLUSIONS We determined that X-linked genes in Sciara males undergo dosage compensation. An entire bacterial genome from the Rickettsia genus, a group known to be endosymbionts in insects, was co-assembled with the Sciara genome, opening the possibility that Rickettsia may function in sex determination in Sciara. Finally, the signal level of the PacBio and Nanopore data support the presence of cytosine and adenine modifications in the Sciara genome, consistent with a possible role in imprinting.
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Affiliation(s)
- John M Urban
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life Sciences, 185 Meeting Street, Providence, RI, 02912, USA.
- Department of Embryology, Carnegie Institution for Science, Howard Hughes Medical Institute Research Laboratories, 3520 San Martin Drive, Baltimore, MD, 21218, USA.
| | - Michael S Foulk
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life Sciences, 185 Meeting Street, Providence, RI, 02912, USA
- Present Address: Department of Biology, Mercyhurst University, Erie, PA, 16546, USA
| | - Jacob E Bliss
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life Sciences, 185 Meeting Street, Providence, RI, 02912, USA
| | - C Michelle Coleman
- KSU Bioinformatics Center, Kansas State University Division of Biology, Ackert Hall, Manhattan, Kansas, 66502, USA
| | - Nanyan Lu
- KSU Bioinformatics Center, Kansas State University Division of Biology, Ackert Hall, Manhattan, Kansas, 66502, USA
| | - Reza Mazloom
- KSU Bioinformatics Center, Kansas State University Division of Biology, Ackert Hall, Manhattan, Kansas, 66502, USA
| | - Susan J Brown
- KSU Bioinformatics Center, Kansas State University Division of Biology, Ackert Hall, Manhattan, Kansas, 66502, USA
| | - Allan C Spradling
- Department of Embryology, Carnegie Institution for Science, Howard Hughes Medical Institute Research Laboratories, 3520 San Martin Drive, Baltimore, MD, 21218, USA
| | - Susan A Gerbi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life Sciences, 185 Meeting Street, Providence, RI, 02912, USA.
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17
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Bara A, Ferland JMN, Rompala G, Szutorisz H, Hurd YL. Cannabis and synaptic reprogramming of the developing brain. Nat Rev Neurosci 2021; 22:423-438. [PMID: 34021274 DOI: 10.1038/s41583-021-00465-5] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2021] [Indexed: 02/08/2023]
Abstract
Recent years have been transformational in regard to the perception of the health risks and benefits of cannabis with increased acceptance of use. This has unintended neurodevelopmental implications given the increased use of cannabis and the potent levels of Δ9-tetrahydrocannabinol today being consumed by pregnant women, young mothers and teens. In this Review, we provide an overview of the neurobiological effects of cannabinoid exposure during prenatal/perinatal and adolescent periods, in which the endogenous cannabinoid system plays a fundamental role in neurodevelopmental processes. We highlight impaired synaptic plasticity as characteristic of developmental exposure and the important contribution of epigenetic reprogramming that maintains the long-term impact into adulthood and across generations. Such epigenetic influence by its very nature being highly responsive to the environment also provides the potential to diminish neural perturbations associated with developmental cannabis exposure.
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Affiliation(s)
- Anissa Bara
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY, USA.,Addiction Institute of Mount Sinai, Mount Sinai, NY, USA.,Friedman Brain Institute, Mount Sinai, NY, USA
| | - Jacqueline-Marie N Ferland
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY, USA.,Addiction Institute of Mount Sinai, Mount Sinai, NY, USA.,Friedman Brain Institute, Mount Sinai, NY, USA
| | - Gregory Rompala
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY, USA.,Addiction Institute of Mount Sinai, Mount Sinai, NY, USA.,Friedman Brain Institute, Mount Sinai, NY, USA
| | - Henrietta Szutorisz
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY, USA.,Addiction Institute of Mount Sinai, Mount Sinai, NY, USA.,Friedman Brain Institute, Mount Sinai, NY, USA
| | - Yasmin L Hurd
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY, USA. .,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY, USA. .,Addiction Institute of Mount Sinai, Mount Sinai, NY, USA. .,Friedman Brain Institute, Mount Sinai, NY, USA.
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18
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Tao Y, Zhou X, Zheng X, Li S, Mou C. Deciphering the Forebrain Disorder in a Chicken Model of Cerebral Hernia. Genes (Basel) 2020; 11:E1008. [PMID: 32867218 PMCID: PMC7564858 DOI: 10.3390/genes11091008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/02/2020] [Accepted: 08/20/2020] [Indexed: 12/16/2022] Open
Abstract
Cerebral hernia in crested chicken has been characterized as the protrusion of cerebral hemispheres into the unsealed skull for hundreds of years, since Charles Darwin. The development of deformed forebrain (telencephalon) of cerebral hernia remains largely unknown. Here, the unsealed frontal skull combined with misplaced sphenoid bone was observed and potentially associated with brain protuberance. The shifted pallidum, elongated hippocampus, expanded mesopallium and nidopallium, and reduced hyperpallium were observed in seven regions of the malformed telencephalon. The neurons were detected with nuclear pyknosis and decreased density. Astrocytes showed uneven distribution and disordered protuberances in hyperpallium and hippocampus. Transcriptome analyses of chicken telencephalon (cerebral hernia vs. control) revealed 547 differentially expressed genes (DEGs), mainly related to nervous system development, and immune system processes, including astrocyte marker gene GFAP, and neuron and astrocyte developmental gene S100A6. The upregulation of GFAP and S100A6 genes in abnormal telencephalon was correlated with reduced DNA methylation levels in the promoter regions. The morphological, cellular, and molecular variations in the shape, regional specification, and cellular states of malformed telencephalon potentially participate in brain plasticity and previously reported behavior changes. Chickens with cerebral hernia might be an interesting and valuable disease model to further explore the recognition, diagnosis, and therapy of cerebral hernia development of crested chickens and other species.
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Affiliation(s)
| | | | | | | | - Chunyan Mou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, HuaZhong Agricultural University, Wuhan 430070, China; (Y.T.); (X.Z.); (X.Z.); (S.L.)
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19
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De Coster W, Stovner EB, Strazisar M. Methplotlib: analysis of modified nucleotides from nanopore sequencing. Bioinformatics 2020; 36:3236-3238. [PMID: 32053166 PMCID: PMC7214038 DOI: 10.1093/bioinformatics/btaa093] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/03/2020] [Accepted: 02/05/2020] [Indexed: 02/06/2023] Open
Abstract
SUMMARY Modified nucleotides play a crucial role in gene expression regulation. Here, we describe methplotlib, a tool developed for the visualization of modified nucleotides detected from Oxford Nanopore Technologies sequencing platforms, together with additional scripts for statistical analysis of allele-specific modification within-subjects and differential modification frequency across subjects. AVAILABILITY AND IMPLEMENTATION The methplotlib command-line tool is written in Python3, is compatible with Linux, Mac OS and the MS Windows 10 Subsystem for Linux and released under the MIT license. The source code can be found at https://github.com/wdecoster/methplotlib and can be installed from PyPI and bioconda. Our repository includes test data, and the tool is continuously tested at travis-ci.com. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Endre Bakken Stovner
- Department of Computer Science, Norwegian University of Science and Technology, Trondheim 7013, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7013, Norway
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20
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Martínez-Cué C, Rueda N. Cellular Senescence in Neurodegenerative Diseases. Front Cell Neurosci 2020; 14:16. [PMID: 32116562 PMCID: PMC7026683 DOI: 10.3389/fncel.2020.00016] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/21/2020] [Indexed: 01/10/2023] Open
Abstract
Cellular senescence is a homeostatic biological process characterized by a permanent state of cell cycle arrest that can contribute to the decline of the regenerative potential and function of tissues. The increased presence of senescent cells in different neurodegenerative diseases suggests the contribution of senescence in the pathophysiology of these disorders. Although several factors can induce senescence, DNA damage, oxidative stress, neuroinflammation, and altered proteostasis have been shown to play a role in its onset. Oxidative stress contributes to accelerated aging and cognitive dysfunction stages affecting neurogenesis, neuronal differentiation, connectivity, and survival. During later life stages, it is implicated in the progression of cognitive decline, synapse loss, and neuronal degeneration. Also, neuroinflammation exacerbates oxidative stress, synaptic dysfunction, and neuronal death through the harmful effects of pro-inflammatory cytokines on cell proliferation and maturation. Both oxidative stress and neuroinflammation can induce DNA damage and alterations in DNA repair that, in turn, can exacerbate them. Another important feature associated with senescence is altered proteostasis. Because of the disruption in the function and balance of the proteome, senescence can modify the proper synthesis, folding, quality control, and degradation rate of proteins producing, in some diseases, misfolded proteins or aggregation of abnormal proteins. There is an extensive body of literature that associates cellular senescence with several neurodegenerative disorders including Alzheimer’s disease (AD), Down syndrome (DS), and Parkinson’s disease (PD). This review summarizes the evidence of the shared neuropathological events in these neurodegenerative diseases and the implication of cellular senescence in their onset or aggravation. Understanding the role that cellular senescence plays in them could help to develop new therapeutic strategies.
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Affiliation(s)
- Carmen Martínez-Cué
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, Santander, Spain
| | - Noemí Rueda
- Department of Physiology and Pharmacology, Faculty of Medicine, University of Cantabria, Santander, Spain
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21
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Fila M, Chojnacki C, Chojnacki J, Blasiak J. Is an "Epigenetic Diet" for Migraines Justified? The Case of Folate and DNA Methylation. Nutrients 2019; 11:E2763. [PMID: 31739474 PMCID: PMC6893742 DOI: 10.3390/nu11112763] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/05/2019] [Accepted: 11/12/2019] [Indexed: 12/15/2022] Open
Abstract
Migraines are a common disease with limited treatment options and some dietary factors are recognized to trigger headaches. Although migraine pathogenesis is not completely known, aberrant DNA methylation has been reported to be associated with its occurrence. Folate, an essential micronutrient involved in one-carbon metabolism and DNA methylation, was shown to have beneficial effects on migraines. Moreover, the variability of the methylenetetrahydrofolate reductase gene, important in both folate metabolism and migraine pathogenesis, modulates the beneficial effects of folate for migraines. Therefore, migraine could be targeted by a folate-rich, DNA methylation-directed diet, but there are no data showing that beneficial effects of folate consumption result from its epigenetic action. Furthermore, contrary to epigenetic drugs, epigenetic diets contain many compounds, some yet unidentified, with poorly known or completely unknown potential to interfere with the epigenetic action of the main dietary components. The application of epigenetic diets for migraines and other diseases requires its personalization to the epigenetic profile of a patient, which is largely unknown. Results obtained so far do not warrant the recommendation of any epigenetic diet as effective in migraine prevention and therapy. Further studies including a folate-rich diet fortified with valproic acid, another modifier of epigenetic profile effective in migraine prophylaxis, may help to clarify this issue.
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Affiliation(s)
- Michal Fila
- Department of Neurology, Polish Mother Memorial Hospital, Research Institute, 93-338 Lodz, Poland;
| | - Cezary Chojnacki
- Department of Clinical Nutrition and Gastroenterological Diagnostics, Medical University of Lodz, 90-647 Lodz, Poland; (C.C.); (J.C.)
| | - Jan Chojnacki
- Department of Clinical Nutrition and Gastroenterological Diagnostics, Medical University of Lodz, 90-647 Lodz, Poland; (C.C.); (J.C.)
| | - Janusz Blasiak
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland
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