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Ramazi S, Dadzadi M, Darvazi M, Seddigh N, Allahverdi A. Protein modification in neurodegenerative diseases. MedComm (Beijing) 2024; 5:e674. [PMID: 39105197 PMCID: PMC11298556 DOI: 10.1002/mco2.674] [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: 12/05/2023] [Revised: 07/02/2024] [Accepted: 07/08/2024] [Indexed: 08/07/2024] Open
Abstract
Posttranslational modifications play a crucial role in governing cellular functions and protein behavior. Researchers have implicated dysregulated posttranslational modifications in protein misfolding, which results in cytotoxicity, particularly in neurodegenerative diseases such as Alzheimer disease, Parkinson disease, and Huntington disease. These aberrant posttranslational modifications cause proteins to gather in certain parts of the brain that are linked to the development of the diseases. This leads to neuronal dysfunction and the start of neurodegenerative disease symptoms. Cognitive decline and neurological impairments commonly manifest in neurodegenerative disease patients, underscoring the urgency of comprehending the posttranslational modifications' impact on protein function for targeted therapeutic interventions. This review elucidates the critical link between neurodegenerative diseases and specific posttranslational modifications, focusing on Tau, APP, α-synuclein, Huntingtin protein, Parkin, DJ-1, and Drp1. By delineating the prominent aberrant posttranslational modifications within Alzheimer disease, Parkinson disease, and Huntington disease, the review underscores the significance of understanding the interplay among these modifications. Emphasizing 10 key abnormal posttranslational modifications, this study aims to provide a comprehensive framework for investigating neurodegenerative diseases holistically. The insights presented herein shed light on potential therapeutic avenues aimed at modulating posttranslational modifications to mitigate protein aggregation and retard neurodegenerative disease progression.
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Affiliation(s)
- Shahin Ramazi
- Department of BiophysicsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Maedeh Dadzadi
- Department of BiotechnologyFaculty of Advanced Science and TechnologyTehran Medical SciencesIslamic Azad UniversityTehranIran
| | - Mona Darvazi
- Department of BiophysicsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Nasrin Seddigh
- Department of BiochemistryFaculty of Advanced Science and TechnologyTehran Medical SciencesIslamic Azad UniversityTehranIran
| | - Abdollah Allahverdi
- Department of BiophysicsFaculty of Biological SciencesTarbiat Modares UniversityTehranIran
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2
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Temgire P, Arthur R, Kumar P. Neuroinflammation and the role of epigenetic-based therapies for Huntington's disease management: the new paradigm. Inflammopharmacology 2024; 32:1791-1804. [PMID: 38653938 DOI: 10.1007/s10787-024-01477-0] [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: 06/20/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
Huntington's disease (HD) is an inherited, autosomal, neurodegenerative ailment that affects the striatum of the brain. Despite its debilitating effect on its patients, there is no proven cure for HD management as of yet. Neuroinflammation, excitotoxicity, and environmental factors have been reported to influence the regulation of gene expression by modifying epigenetic mechanisms. Aside focusing on the etiology, changes in epigenetic mechanisms have become a crucial factor influencing the interaction between HTT protein and epigenetically transcribed genes involved in neuroinflammation and HD. This review presents relevant literature on epigenetics with special emphasis on neuroinflammation and HD. It summarizes pertinent research on the role of neuroinflammation and post-translational modifications of chromatin, including DNA methylation, histone modification, and miRNAs. To achieve this about 1500 articles were reviewed via databases like PubMed, ScienceDirect, Google Scholar, and Web of Science. They were reduced to 534 using MeSH words like 'epigenetics, neuroinflammation, and HD' coupled with Boolean operators. Results indicated that major contributing factors to the development of HD such as mitochondrial dysfunction, excitotoxicity, neuroinflammation, and apoptosis are affected by epigenetic alterations. However, the association between neuroinflammation-altered epigenetics and the reported transcriptional changes in HD is unknown. Also, the link between epigenetically dysregulated genomic regions and specific DNA sequences suggests the likelihood that transcription factors, chromatin-remodeling proteins, and enzymes that affect gene expression are all disrupted simultaneously. Hence, therapies that target pathogenic pathways in HD, including neuroinflammation, transcriptional dysregulation, triplet instability, vesicle trafficking dysfunction, and protein degradation, need to be developed.
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Affiliation(s)
- Pooja Temgire
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India
| | - Richmond Arthur
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India
| | - Puneet Kumar
- Department of Pharmacology, Central University of Punjab, Ghudda, Bathinda, 151401, Punjab, India.
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Achenbach J, Stodt B, Saft C. Factors Influencing the Total Functional Capacity Score as a Critical Endpoint in Huntington's Disease Research. Biomedicines 2023; 11:3336. [PMID: 38137557 PMCID: PMC10741795 DOI: 10.3390/biomedicines11123336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Background: The Total Functional Capacity (TFC) score is commonly used in Huntington's disease (HD) research. The classification separates each disease stage (1-5), e.g., as an inclusion criterion or endpoint in clinical trials accepted by the Food and Drug Administration (FDA). In addition to the quantification of age- and CAG-repeat-dependent effects as well as interacting effects of both on the TFC, we aimed to investigate factors influencing the TFC, such as neuropsychiatric, educational, and cognitive disease burden using data from the largest HD observational study to date. In addition, we analyzed data from pre-manifest stages to investigate the influence of the above-mentioned factors on the TFC in that stage. Methods: A moderated regression analysis was conducted to analyze the interaction effects of age and CAG-repeat length on the TFC in HD patients. A simple slope analysis was calculated to illustrate the effects. Depending on TFC results, motor-manifest patients were grouped into five stages. Data from pre-manifest participants were analyzed with regard to years to onset and CAP scores. Results: We identified N = 10,314 participants as manifest HD. A significant part of variance on the TFC was explained by age (R2 = 0.029, F (1;10,281) = 308.02, p < 0.001), CAG-repeat length (∆R2 = 0.132, ∆F (1;10,280) = 1611.22, p < 0.001), and their interaction (∆R2 = 0.049, ∆F (1;10,279) = 634.12, p < 0.001). The model explained altogether 20.9% of the TFC score's variance (F = 907.60, p < 0.001). Variance of psychiatric and cognitive symptoms significantly differed between stages. Exploratory analysis of median data in pre-manifest participants revealed the highest scores for neuropsychiatric changes between 5 to <20 years from the disease onset. Conclusions: TFC is mainly explained by the neurobiological factors, CAG-repeat length, and age, with subjects having more CAG-repeats showing a faster decline in function. Our study confirms TFC as a robust measure of progression in manifest HD.
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Affiliation(s)
- Jannis Achenbach
- Department of Neurology, Huntington Center North Rhine-Westphalia, St. Josef-Hospital Bochum, Ruhr-University Bochum, Gudrunstraße 56, 44791 Bochum, Germany;
| | - Benjamin Stodt
- Leibniz Research Center for Working Environment and Human Factors at the Technical University of Dortmund (IfADo), Ardeystraße 67, 44139 Dortmund, Germany;
| | - Carsten Saft
- Department of Neurology, Huntington Center North Rhine-Westphalia, St. Josef-Hospital Bochum, Ruhr-University Bochum, Gudrunstraße 56, 44791 Bochum, Germany;
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Steinberg N, Galleguillos D, Zaidi A, Horkey M, Sipione S. Naïve Huntington's disease microglia mount a normal response to inflammatory stimuli but display a partially impaired development of innate immune tolerance that can be counteracted by ganglioside GM1. J Neuroinflammation 2023; 20:276. [PMID: 37996924 PMCID: PMC10668379 DOI: 10.1186/s12974-023-02963-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 11/18/2023] [Indexed: 11/25/2023] Open
Abstract
Chronic activation and dysfunction of microglia have been implicated in the pathogenesis and progression of many neurodegenerative disorders, including Huntington's disease (HD). HD is a genetic condition caused by a mutation that affects the folding and function of huntingtin (HTT). Signs of microglia activation have been observed in HD patients even before the onset of symptoms. It is unclear, however, whether pro-inflammatory microglia activation in HD results from cell-autonomous expression of mutant HTT, is the response of microglia to a diseased brain environment, or both. In this study, we used primary microglia isolated from HD knock-in (Q140) and wild-type (Q7) mice to investigate their response to inflammatory conditions in vitro in the absence of confounding effects arising from brain pathology. We show that naïve Q140 microglia do not undergo spontaneous pro-inflammatory activation and respond to inflammatory triggers, including stimulation of TLR4 and TLR2 and exposure to necrotic cells, with similar kinetics of pro-inflammatory gene expression as wild-type microglia. Upon termination of the inflammatory insult, the transcription of pro-inflammatory cytokines is tapered off in Q140 and wild-type microglia with similar kinetics. However, the ability of Q140 microglia to develop tolerance in response to repeated inflammatory stimulations is partially impaired in vitro and in vivo, potentially contributing to the establishment of chronic neuroinflammation in HD. We further show that ganglioside GM1, a glycosphingolipid with anti-inflammatory effects on wild-type microglia, not only decreases the production of pro-inflammatory cytokines and nitric oxide in activated Q140 microglia, but also dramatically dampen microglia response to re-stimulation with LPS in an experimental model of tolerance. These effects are independent from the expression of interleukin 1 receptor associated kinase 3 (Irak-3), a strong modulator of LPS signaling involved in the development of innate immune tolerance and previously shown to be upregulated by immune cell treatment with gangliosides. Altogether, our data suggest that external triggers are required for HD microglia activation, but a cell-autonomous dysfunction that affects the ability of HD microglia to acquire tolerance might contribute to the establishment of neuroinflammation in HD. Administration of GM1 might be beneficial to attenuate chronic microglia activation and neuroinflammation.
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Affiliation(s)
- Noam Steinberg
- Department of Pharmacology, Neuroscience and Mental Health Institute and Glycomics Institute of Alberta, University of Alberta, Edmonton, AB, Canada
| | - Danny Galleguillos
- Department of Pharmacology, Neuroscience and Mental Health Institute and Glycomics Institute of Alberta, University of Alberta, Edmonton, AB, Canada
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Asifa Zaidi
- Department of Pharmacology, Neuroscience and Mental Health Institute and Glycomics Institute of Alberta, University of Alberta, Edmonton, AB, Canada
| | | | - Simonetta Sipione
- Department of Pharmacology, Neuroscience and Mental Health Institute and Glycomics Institute of Alberta, University of Alberta, Edmonton, AB, Canada.
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Saha G, Ghosh S, Dubey VK, Saudagar P. Gene Alterations Induced by Glutamine (Q) Encoding CAG Repeats Associated with Neurodegeneration. Methods Mol Biol 2023; 2575:3-23. [PMID: 36301468 DOI: 10.1007/978-1-0716-2716-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Several studies have been reported linking the role of polyglutamine (polyQ) disease-associated proteins with altered gene regulation induced by an unstable trinucleotide (CAG) repeat. Owing to their dynamic nature of expansion, these DNA repeats form secondary structures interfering with the normal cellular mechanisms like replication and transcription and, thereby, have become the underlying cause of numerous neurodegenerative disorders involving mental retardation and/or muscular or neuronal degeneration. Despite the widespread expression of the disease-causing protein, specific subsets of neurons are susceptible to specific patterns of inheritance and clinical symptoms. Although this cell-type selectivity is still elusive and less understood, it has been found that aberrant transcriptional regulation is one of the primary causes of polyQ diseases where the functions of histone-modifying complexes are disrupted. Besides, epigenetic modifications play a critical role in the pathogenesis of these diseases. In this chapter, we will be delving into how these polyQ repeats induce the self-assembly and aggregation of altered carrier proteins based on gene alterations, causing neuronal toxicity and cellular deaths. Besides, genomic instability in CAG repeats due to altered chromatin-related enzymes will be highlighted, along with epigenetic changes present in many polyQ disorders. Understanding the underlying molecular mechanisms in the root cause of these disorders will culminate in identifying therapeutic approaches for the treatment of these neurodegenerative disorders.
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Affiliation(s)
- Gundappa Saha
- Department of Basic & Translational Sciences, Penn Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sukanya Ghosh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Vikash Kumar Dubey
- School of Biochemical Engineering, Indian Institute of Technology BHU, Varanasi, Uttar Pradesh, India
| | - Prakash Saudagar
- Department of Biotechnology, National Institute of Technology, Warangal, Telangana, India.
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Ghafouri-Fard S, Khoshbakht T, Hussen BM, Taheri M, Ebrahimzadeh K, Noroozi R. The emerging role of long non-coding RNAs, microRNAs, and an accelerated epigenetic age in Huntington’s disease. Front Aging Neurosci 2022; 14:987174. [PMID: 36185471 PMCID: PMC9520620 DOI: 10.3389/fnagi.2022.987174] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Huntington’s disease (HD) is a dominantly inherited neurodegenerative disease with variable clinical manifestations. Recent studies highlighted the contribution of epigenetic alterations to HD progress and onset. The potential crosstalk between different epigenetic layers and players such as aberrant expression of non-coding RNAs and methylation alterations has been found to affect the pathogenesis of HD or mediate the effects of trinucleotide expansion in its pathophysiology. Also, microRNAs have been assessed for their roles in the modulation of HD manifestations, among them are miR-124, miR-128a, hsa-miR-323b-3p, miR-432, miR-146a, miR-19a, miR-27a, miR-101, miR-9*, miR-22, miR-132, and miR-214. Moreover, long non-coding RNAs such as DNM3OS, NEAT1, Meg3, and Abhd11os are suggested to be involved in the pathogenesis of HD. An accelerated DNA methylation age is another epigenetic signature reported recently for HD. The current literature search collected recent findings of dysregulation of miRNAs or lncRNAs as well as methylation changes and epigenetic age in HD.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq
- Center of Research and Strategic Studies, Lebanese French University, Erbil, Iraq
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kaveh Ebrahimzadeh
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Kaveh Ebrahimzadeh,
| | - Rezvan Noroozi
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Rezvan Noroozi,
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Kaye J, Reisine T, Finkbeiner S. Huntington's disease iPSC models-using human patient cells to understand the pathology caused by expanded CAG repeats. Fac Rev 2022; 11:16. [PMID: 35865413 PMCID: PMC9264339 DOI: 10.12703/r/11-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
A major advance in the study of Huntington's disease (HD) has been the development of human disease models employing induced pluripotent stem cells (iPSCs) derived from patients with HD. Because iPSCs provide an unlimited source of cells and can be obtained from large numbers of HD patients, they are a uniquely valuable tool for investigating disease mechanisms and for discovering potential disease-modifying therapeutics. Here, we summarize some of the important findings in HD pathophysiology that have emerged from studies of patient-derived iPSC lines. Because they retain the genome and actual disease mutations of the patient, they provide a cell source to investigate genetic contributions to the disease. iPSCs provide advantages over other disease models. While iPSC-based technology erases some epigenetic marks, newly developed transdifferentiation methods now let us investigate epigenetic factors that control expression of mutant huntingtin (mHTT). Human HD iPSC lines allow us to investigate how endogenous levels of mHTT affect cell health, in contrast to other models that often rely on overexpressing the protein. iPSCs can be differentiated into neurons and other disease-related cells such as astrocytes from different brain regions to study brain regional differences in the disease process, as well as the cell-cell dependencies involved in HD-associated neurodegeneration. They also serve as a tissue source to investigate factors that impact CAG repeat instability, which is involved in regional differences in neurodegeneration in the HD brain. Human iPSC models can serve as a powerful model system to identify genetic modifiers that may impact disease onset, progression, and symptomatology, providing novel molecular targets for drug discovery.
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Affiliation(s)
- Julia Kaye
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
| | - Terry Reisine
- Independent Scientific Consultant, Santa Cruz, CA, USA
| | - Steven Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, USA
- Taube/Koret Center for Neurodegenerative Disease Research, Gladstone Institutes, San Francisco, CA, USA
- Department of Neurology and Physiology, University of California, San Francisco, CA, USA
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8
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Posttranslational Modifications in Thyroid Cancer: Implications for Pathogenesis, Diagnosis, Classification, and Treatment. Cancers (Basel) 2022; 14:cancers14071610. [PMID: 35406382 PMCID: PMC8996999 DOI: 10.3390/cancers14071610] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 11/17/2022] Open
Abstract
There is evidence that posttranslational modifications, including phosphorylation, acetylation, methylation, ubiquitination, sumoylation, glycosylation, and succinylation, may be involved in thyroid cancer. We review recent reports supporting a role of posttranslational modifications in the tumorigenesis of thyroid cancer, sensitivity to radioiodine and other types of treatment, the identification of molecular treatment targets, and the development of molecular markers that may become useful as diagnostic tools. An increased understanding of posttranslational modifications may be an important supplement to the determination of alterations in gene expression that has gained increasing prominence in recent years.
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Sharma R, Sharma S, Thakur A, Singh A, Singh J, Nepali K, Liou JP. The Role of Epigenetic Mechanisms in Autoimmune, Neurodegenerative, Cardiovascular, and Imprinting Disorders. Mini Rev Med Chem 2022; 22:1977-2011. [PMID: 35176978 DOI: 10.2174/1389557522666220217103441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/01/2021] [Accepted: 11/11/2021] [Indexed: 11/22/2022]
Abstract
Epigenetic mutations like aberrant DNA methylation, histone modifications, or RNA silencing are found in a number of human diseases. This review article discusses the epigenetic mechanisms involved in neurodegenerative disorders, cardiovascular disorders, auto-immune disorder, and genomic imprinting disorders. In addition, emerging epigenetic therapeutic strategies for the treatment of such disorders are presented. Medicinal chemistry campaigns highlighting the efforts of the chemists invested towards the rational design of small molecule inhibitors have also been included. Pleasingly, several classes of epigenetic inhibitors, DNMT, HDAC, BET, HAT, and HMT inhibitors along with RNA based therapies have exhibited the potential to emerge as therapeutics in the longer run. It is quite hopeful that epigenetic modulator-based therapies will advance to clinical stage investigations by leaps and bounds.
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Affiliation(s)
- Ram Sharma
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Sachin Sharma
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Amandeep Thakur
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Arshdeep Singh
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Jagjeet Singh
- School of Pharmacy, University of Queensland, Brisbane, QLD, Australia.,Department of Pharmacy, Rayat-Bahara Group of Institutes, Hoshiarpur, India
| | - Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Jing Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
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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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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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12
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Hwang YJ, Hyeon SJ, Kim Y, Lim S, Lee MY, Kim J, Londhe AM, Gotina L, Kim Y, Pae AN, Cho YS, Seong J, Seo H, Kim YK, Choo H, Ryu H, Min SJ. Modulation of SETDB1 activity by APQ ameliorates heterochromatin condensation, motor function, and neuropathology in a Huntington's disease mouse model. J Enzyme Inhib Med Chem 2021; 36:856-868. [PMID: 33771089 PMCID: PMC8008885 DOI: 10.1080/14756366.2021.1900160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/18/2021] [Accepted: 03/01/2021] [Indexed: 12/03/2022] Open
Abstract
The present study describes evaluation of epigenetic regulation by a small molecule as the therapeutic potential for treatment of Huntington's disease (HD). We identified 5-allyloxy-2-(pyrrolidin-1-yl)quinoline (APQ) as a novel SETDB1/ESET inhibitor using a combined in silico and in vitro cell based screening system. APQ reduced SETDB1 activity and H3K9me3 levels in a HD cell line model. In particular, not only APQ reduced H3K9me3 levels in the striatum but it also improved motor function and neuropathological symptoms such as neuronal size and activity in HD transgenic (YAC128) mice with minimal toxicity. Using H3K9me3-ChIP and genome-wide sequencing, we also confirmed that APQ modulates H3K9me3-landscaped epigenomes in YAC128 mice. These data provide that APQ, a novel small molecule SETDB1 inhibitor, coordinates H3K9me-dependent heterochromatin remodelling and can be an epigenetic drug for treating HD, leading with hope in clinical trials of HD.
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Affiliation(s)
- Yu Jin Hwang
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Seung Jae Hyeon
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Younghee Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Sungsu Lim
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, KIST, Seoul, Republic of Korea
| | | | - Jieun Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Ashwini M. Londhe
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, KIST, Seoul, Republic of Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul, Republic of Korea
| | - Lizaveta Gotina
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, KIST, Seoul, Republic of Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul, Republic of Korea
| | - Yunha Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Ae Nim Pae
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, KIST, Seoul, Republic of Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul, Republic of Korea
| | - Yong Seo Cho
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul, Republic of Korea
| | - Jihye Seong
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, KIST, Seoul, Republic of Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul, Republic of Korea
| | - Hyemyung Seo
- Department of Molecular & Life Sciences, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, Republic of Korea
| | - Yun Kyung Kim
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, KIST, Seoul, Republic of Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul, Republic of Korea
| | - Hyunah Choo
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul, Republic of Korea
| | - Hoon Ryu
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
- Department of Neurology and Boston University Alzheimer’s Disease Center, Boston University School of Medicine, Boston, MA, USA
| | - Sun-Joon Min
- Department of Chemical & Molecular Engineering/Applied Chemistry, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, Republic of Korea
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13
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Kim C, Yousefian-Jazi A, Choi SH, Chang I, Lee J, Ryu H. Non-Cell Autonomous and Epigenetic Mechanisms of Huntington's Disease. Int J Mol Sci 2021; 22:12499. [PMID: 34830381 PMCID: PMC8617801 DOI: 10.3390/ijms222212499] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 02/06/2023] Open
Abstract
Huntington's disease (HD) is a rare neurodegenerative disorder caused by an expansion of CAG trinucleotide repeat located in the exon 1 of Huntingtin (HTT) gene in human chromosome 4. The HTT protein is ubiquitously expressed in the brain. Specifically, mutant HTT (mHTT) protein-mediated toxicity leads to a dramatic degeneration of the striatum among many regions of the brain. HD symptoms exhibit a major involuntary movement followed by cognitive and psychiatric dysfunctions. In this review, we address the conventional role of wild type HTT (wtHTT) and how mHTT protein disrupts the function of medium spiny neurons (MSNs). We also discuss how mHTT modulates epigenetic modifications and transcriptional pathways in MSNs. In addition, we define how non-cell autonomous pathways lead to damage and death of MSNs under HD pathological conditions. Lastly, we overview therapeutic approaches for HD. Together, understanding of precise neuropathological mechanisms of HD may improve therapeutic approaches to treat the onset and progression of HD.
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Affiliation(s)
- Chaebin Kim
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (C.K.); (A.Y.-J.); (S.-H.C.)
| | - Ali Yousefian-Jazi
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (C.K.); (A.Y.-J.); (S.-H.C.)
| | - Seung-Hye Choi
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (C.K.); (A.Y.-J.); (S.-H.C.)
| | - Inyoung Chang
- Department of Biology, Boston University, Boston, MA 02215, USA;
| | - Junghee Lee
- Boston University Alzheimer’s Disease Research Center, Boston University, Boston, MA 02118, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
- VA Boston Healthcare System, Boston, MA 02130, USA
| | - Hoon Ryu
- Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea; (C.K.); (A.Y.-J.); (S.-H.C.)
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14
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Hyeon SJ, Park J, Yoo J, Kim SH, Hwang YJ, Kim SC, Liu T, Shim HS, Kim Y, Cho Y, Woo J, Kim KS, Myers RH, Ryu HL, Kowall NW, Song EJ, Hwang EM, Seo H, Lee J, Ryu H. Dysfunction of X-linked inhibitor of apoptosis protein (XIAP) triggers neuropathological processes via altered p53 activity in Huntington's disease. Prog Neurobiol 2021; 204:102110. [PMID: 34166773 PMCID: PMC8364511 DOI: 10.1016/j.pneurobio.2021.102110] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 05/24/2021] [Accepted: 06/18/2021] [Indexed: 12/27/2022]
Abstract
Mitochondrial dysfunction is associated with neuronal damage in Huntington's disease (HD), but the precise mechanism of mitochondria-dependent pathogenesis is not understood yet. Herein, we found that colocalization of XIAP and p53 was prominent in the cytosolic compartments of normal subjects but reduced in HD patients and HD transgenic animal models. Overexpression of mutant Huntingtin (mHTT) reduced XIAP levels and elevated mitochondrial localization of p53 in striatal cells in vitro and in vivo. Interestingly, XIAP interacted directly with the C-terminal domain of p53 and decreased its stability via autophagy. Overexpression of XIAP prevented mitochondrially targeted-p53 (Mito-p53)-induced mitochondrial oxidative stress and striatal cell death, whereas, knockdown of XIAP exacerbated Mito-p53-induced neuronal damage in vitro. In vivo transduction of AAV-shRNA XIAP in the dorsal striatum induced rapid onset of disease and reduced the lifespan of HD transgenic (N171-82Q) mice compared to WT littermate mice. XIAP dysfunction led to ultrastructural changes of the mitochondrial cristae and nucleus morphology in striatal cells. Knockdown of XIAP exacerbated neuropathology and motor dysfunctions in N171-82Q mice. In contrast, XIAP overexpression improved neuropathology and motor behaviors in both AAV-mHTT-transduced mice and N171-82Q mice. Our data provides a molecular and pathological mechanism that deregulation of XIAP triggers mitochondria dysfunction and other neuropathological processes via the neurotoxic effect of p53 in HD. Together, the XIAP-p53 pathway is a novel pathological marker and can be a therapeutic target for improving the symptoms in HD.
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Affiliation(s)
- Seung Jae Hyeon
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, South Korea; Department of Molecular & Life Sciences, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 15588, South Korea
| | - Jinyoung Park
- Molecular Recognition Research Center, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Junsang Yoo
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Su-Hyun Kim
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Yu Jin Hwang
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Seung-Chan Kim
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Tian Liu
- USF Health Byrd Alzheimer's Institute and Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL 33613, USA
| | - Hyun Soo Shim
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Yunha Kim
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Yakdol Cho
- KIST Research Animal Resource Center, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Jiwan Woo
- KIST Research Animal Resource Center, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Key-Sun Kim
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, South Korea; KIST Research Animal Resource Center, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Richard H Myers
- Boston University Genome Science Institute and Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Hannah L Ryu
- Boston University Alzheimer's Disease Center and Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Neil W Kowall
- Boston University Alzheimer's Disease Center and Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA; VA Boston Healthcare System, Boston, MA 02130, USA
| | - Eun Joo Song
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul 03760, South Korea
| | - Eun Mi Hwang
- Center for Functional Connectomics, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Hyemyung Seo
- Department of Molecular & Life Sciences, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan 15588, South Korea.
| | - Junghee Lee
- Boston University Alzheimer's Disease Center and Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA; VA Boston Healthcare System, Boston, MA 02130, USA.
| | - Hoon Ryu
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, South Korea; Boston University Alzheimer's Disease Center and Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA.
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15
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Kumar R, Jain V, Kushwah N, Dheer A, Mishra KP, Prasad D, Singh SB. HDAC inhibition prevents hypobaric hypoxia-induced spatial memory impairment through PΙ3K/GSK3β/CREB pathway. J Cell Physiol 2021; 236:6754-6771. [PMID: 33788269 DOI: 10.1002/jcp.30337] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 12/14/2022]
Abstract
Hypobaric hypoxia at higher altitudes usually impairs cognitive function. Previous studies suggested that epigenetic modifications are the culprits for this condition. Here, we set out to determine how hypobaric hypoxia mediates epigenetic modifications and how this condition worsens neurodegeneration and memory loss in rats. In the current study, different duration of hypobaric hypoxia exposure showed a discrete pattern of histone acetyltransferases and histone deacetylases (HDACs) gene expression in the hippocampus when compared with control rat brains. The level of acetylation sites in histone H2A, H3 and H4 was significantly decreased under hypobaric hypoxia exposure compared to the control rat's hippocampus. Additionally, inhibiting the HDAC family with sodium butyrate administration (1.2 g/kg body weight) attenuated neurodegeneration and memory loss in hypobaric hypoxia-exposed rats. Moreover, histone acetylation increased at the promoter regions of brain-derived neurotrophic factor (BDNF); thereby its protein expression was enhanced significantly in hypobaric hypoxia exposed rats treated with HDAC inhibitor compared with hypoxic rats. Thus, BDNF expression upregulated cAMP-response element binding protein (CREB) phosphorylation by stimulation of PI3K/GSK3β/CREB axis, which counteracts hypobaric hypoxia-induced spatial memory impairment. In conclusion, these results suggested that sodium butyrate is a novel therapeutic agent for the treatment of spatial memory loss associated with hypobaric hypoxia, and also further studies are warranted to explore specific HDAC inhibitors in this condition.
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Affiliation(s)
- Rahul Kumar
- Neurobiology Division, Defence Institute of Physiology and Allied Science (DIPAS), DRDO, Timarpur, New Delhi, India
| | - Vishal Jain
- Neurophysiology Division, Defence Institute of Physiology and Allied Science (DIPAS), DRDO, Timarpur, New Delhi, India
| | - Neetu Kushwah
- Neurobiology Division, Defence Institute of Physiology and Allied Science (DIPAS), DRDO, Timarpur, New Delhi, India
| | - Aastha Dheer
- Neurobiology Division, Defence Institute of Physiology and Allied Science (DIPAS), DRDO, Timarpur, New Delhi, India
| | | | - Dipti Prasad
- Neurobiology Division, Defence Institute of Physiology and Allied Science (DIPAS), DRDO, Timarpur, New Delhi, India
| | - Shashi Bala Singh
- National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
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16
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Khorkova O, Hsiao J, Wahlestedt C. Nucleic Acid-Based Therapeutics in Orphan Neurological Disorders: Recent Developments. Front Mol Biosci 2021; 8:643681. [PMID: 33996898 PMCID: PMC8115123 DOI: 10.3389/fmolb.2021.643681] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/17/2021] [Indexed: 12/18/2022] Open
Abstract
The possibility of rational design and the resulting faster and more cost-efficient development cycles of nucleic acid–based therapeutics (NBTs), such as antisense oligonucleotides, siRNAs, and gene therapy vectors, have fueled increased activity in developing therapies for orphan diseases. Despite the difficulty of delivering NBTs beyond the blood–brain barrier, neurological diseases are significantly represented among the first targets for NBTs. As orphan disease NBTs are now entering the clinical stage, substantial efforts are required to develop the scientific background and infrastructure for NBT design and mechanistic studies, genetic testing, understanding natural history of orphan disorders, data sharing, NBT manufacturing, and regulatory support. The outcomes of these efforts will also benefit patients with “common” diseases by improving diagnostics, developing the widely applicable NBT technology platforms, and promoting deeper understanding of biological mechanisms that underlie disease pathogenesis. Furthermore, with successes in genetic research, a growing proportion of “common” disease cases can now be attributed to mutations in particular genes, essentially extending the orphan disease field. Together, the developments occurring in orphan diseases are building the foundation for the future of personalized medicine. In this review, we will focus on recent achievements in developing therapies for orphan neurological disorders.
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Affiliation(s)
| | | | - Claes Wahlestedt
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, United States
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17
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Singh M, Singh SP, Yadav D, Agarwal M, Agarwal S, Agarwal V, Swargiary G, Srivastava S, Tyagi S, Kaur R, Mani S. Targeted Delivery for Neurodegenerative Disorders Using Gene Therapy Vectors: Gene Next Therapeutic Goals. Curr Gene Ther 2021; 21:23-42. [PMID: 32811395 DOI: 10.2174/1566523220999200817164907] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 11/22/2022]
Abstract
The technique of gene therapy, ever since its advent nearly fifty years ago, has been utilized by scientists as a potential treatment option for various disorders. This review discusses some of the major neurodegenerative diseases (NDDs) like Alzheimer's disease (AD), Parkinson's Disease (PD), Motor neuron diseases (MND), Spinal Muscular Atrophy (SMA), Huntington's Disease (HD), Multiple Sclerosis (MS), etc. and their underlying genetic mechanisms along with the role that gene therapy can play in combating them. The pathogenesis and the molecular mechanisms specifying the altered gene expression of each of these NDDs have also been discussed in elaboration. The use of gene therapy vectors can prove to be an effective tool in the field of curative modern medicine for the generations to come. Therefore, consistent efforts and progressive research towards its implementation can provide us with powerful treatment options for disease conditions that have so far been considered as incurable.
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Affiliation(s)
- Manisha Singh
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT) Noida, U.P, India
| | - Surinder P Singh
- Bhartiya Nirdeshak Dravya Division, CSIR-National Physical Laboratory, New Delhi, India
| | - Deepshikha Yadav
- Bhartiya Nirdeshak Dravya Division, CSIR-National Physical Laboratory, New Delhi, India
| | - Mugdha Agarwal
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT) Noida, U.P., India
| | - Shriya Agarwal
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT) Noida, U.P., India
| | - Vinayak Agarwal
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT) Noida, U.P., India
| | - Geeta Swargiary
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT) Noida, U.P., India
| | - Sahil Srivastava
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT) Noida, U.P., India
| | - Sakshi Tyagi
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT) Noida, U.P., India
| | - Ramneek Kaur
- School of Medicine, Western Sydney University, Campbelltown, New South Wales, Australia
| | - Shalini Mani
- Department of Biotechnology, Jaypee Institute of Information Technology (JIIT) Noida, U.P., India
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Pathogenic Genome Signatures That Damage Motor Neurons in Amyotrophic Lateral Sclerosis. Cells 2020; 9:cells9122687. [PMID: 33333804 PMCID: PMC7765192 DOI: 10.3390/cells9122687] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is the most frequent motor neuron disease and a neurodegenerative disorder, affecting the upper and/or lower motor neurons. Notably, it invariably leads to death within a few years of onset. Although most ALS cases are sporadic, familial amyotrophic lateral sclerosis (fALS) forms 10% of the cases. In 1993, the first causative gene (SOD1) of fALS was identified. With rapid advances in genetics, over fifty potentially causative or disease-modifying genes have been found in ALS so far. Accordingly, routine diagnostic tests should encompass the oldest and most frequently mutated ALS genes as well as several new important genetic variants in ALS. Herein, we discuss current literatures on the four newly identified ALS-associated genes (CYLD, S1R, GLT8D1, and KIF5A) and the previously well-known ALS genes including SOD1, TARDBP, FUS, and C9orf72. Moreover, we review the pathogenic implications and disease mechanisms of these genes. Elucidation of the cellular and molecular functions of the mutated genes will bring substantial insights for the development of therapeutic approaches to treat ALS.
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19
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Ramazi S, Allahverdi A, Zahiri J. Evaluation of post-translational modifications in histone proteins: A review on histone modification defects in developmental and neurological disorders. J Biosci 2020. [DOI: 10.1007/s12038-020-00099-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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20
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Mohd Murshid N, Aminullah Lubis F, Makpol S. Epigenetic Changes and Its Intervention in Age-Related Neurodegenerative Diseases. Cell Mol Neurobiol 2020; 42:577-595. [DOI: 10.1007/s10571-020-00979-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023]
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21
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Epigenomic Remodeling in Huntington's Disease-Master or Servant? EPIGENOMES 2020; 4:epigenomes4030015. [PMID: 34968288 PMCID: PMC8594700 DOI: 10.3390/epigenomes4030015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 12/03/2022] Open
Abstract
In light of our aging population, neurodegenerative disorders are becoming a tremendous challenge, that modern societies have to face. They represent incurable, progressive conditions with diverse and complex pathological features, followed by catastrophic occurrences of massive neuronal loss at the later stages of the diseases. Some of these disorders, like Huntington’s disease (HD), rely on defined genetic factors. HD, as an incurable, fatal hereditary neurodegenerative disorder characterized by its mid-life onset, is caused by the expansion of CAG trinucleotide repeats coding for glutamine (Q) in exon 1 of the huntingtin gene. Apart from the genetic defect, environmental factors are thought to influence the risk, onset and progression of HD. As epigenetic mechanisms are known to readily respond to environmental stimuli, they are proposed to play a key role in HD pathogenesis. Indeed, dynamic epigenomic remodeling is observed in HD patients and in brains of HD animal models. Epigenetic signatures, such as DNA methylation, histone variants and modifications, are known to influence gene expression and to orchestrate various aspects of neuronal physiology. Hence, deciphering their implication in HD pathogenesis might open up new paths for novel therapeutic concepts, which are discussed in this review.
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22
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Bayer C, Pitschelatow G, Hannemann N, Linde J, Reichard J, Pensold D, Zimmer-Bensch G. DNA Methyltransferase 1 (DNMT1) Acts on Neurodegeneration by Modulating Proteostasis-Relevant Intracellular Processes. Int J Mol Sci 2020; 21:E5420. [PMID: 32751461 PMCID: PMC7432412 DOI: 10.3390/ijms21155420] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023] Open
Abstract
The limited regenerative capacity of neurons requires a tightly orchestrated cell death and survival regulation in the context of longevity, as well as age-associated and neurodegenerative diseases. Subordinate to genetic networks, epigenetic mechanisms, such as DNA methylation and histone modifications, are involved in the regulation of neuronal functionality and emerge as key contributors to the pathophysiology of neurodegenerative diseases. DNA methylation, a dynamic and reversible process, is executed by DNA methyltransferases (DNMTs). DNMT1 was previously shown to act on neuronal survival in the aged brain, whereby a DNMT1-dependent modulation of processes relevant for protein degradation was proposed as an underlying mechanism. Properly operating proteostasis networks are a mandatory prerequisite for the functionality and long-term survival of neurons. Malfunctioning proteostasis is found, inter alia, in neurodegenerative contexts. Here, we investigated whether DNMT1 affects critical aspects of the proteostasis network by a combination of expression studies, live cell imaging, and protein biochemical analyses. We found that DNMT1 negatively impacts retrograde trafficking and autophagy, with both being involved in the clearance of aggregation-prone proteins by the aggresome-autophagy pathway. In line with this, we found that the transport of GFP-labeled mutant huntingtin (HTT) to perinuclear regions, proposed to be cytoprotective, also depends on DNMT1. Depletion of Dnmt1 accelerated perinuclear HTT aggregation and improved the survival of cells transfected with mutant HTT. This suggests that mutant HTT-induced cytotoxicity is at least in part mediated by DNMT1-dependent modulation of degradative pathways.
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Affiliation(s)
| | | | | | | | | | | | - Geraldine Zimmer-Bensch
- Division of Functional Epigenetics in the Animal Model, Institute for Biology II, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany; (C.B.); (G.P.); (N.H.); (J.L.); (J.R.); (D.P.)
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23
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Meng Q, Yang G, Yang Y, Ding F, Hu F. Protective effects of histone deacetylase inhibition by Scriptaid on brain injury in neonatal rat models of cerebral ischemia and hypoxia. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2020; 13:179-191. [PMID: 32211098 PMCID: PMC7061803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 01/30/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Neonatal hypoxia-ischemia brain damage (HBID) can cause a series of neurological sequelae, such as movement and cognitive impairment, and there is currently no clinically effective treatment. Changes in epigenetic processes had been shown to be involved in the development of a series of neurodegenerative diseases, and HDAC inhibition by Scriptaid had been shown to reduce severe traumatic brain injury by suppressing inflammatory responses. This study investigated the protective effect of HDAC inhibition by Scriptaid after HBID. METHODS We established the neonatal rat HBID model, and used intraperitoneal injection of HDAC inhibitor scriptaid as a treatment. 7 days after HBID, nuclear magnetic resonance imaging (MRI) was used to detect infarct volume. The otarod test, wire hang test and Morris water maze were used to evaluate the HBID model of neurobehavioral dysfunction. Immunoblotting, immunofluorescence, and quantitative real-time PCR (RT-qPCR) were used to detect gene expression. RESULTS HDAC inhibition by Scriptaid treatment could not only reduce the infarct volume and neuronal degeneration in HBID rats, but also helped to improve their neurobehavioral dysfunction. 7 days after HBID, the expression of HDAC-1, HDAC-2 and HDAC-3 in the infarct volume of HBID + Veh group rats were much more than that in sham group (P<0.05), but Scriptaid could significantly inhibit those expression (P<0.05), and significantly increased the acetylation of H3 and H4 in HBID rats. In vivo and vitro results demonstrated that Scriptaid had no significant effect on oligodendrocyte MBP protein expression after OGD, but Scriptaid -treated microglia cultures had protective effects on OGD-treated OLG, M1 microglia suppressed OLG activity after OGD, and M2 enhanced its activity. In vivo experiments at 7 days after HBIDI injury showed that Scriptaid could promote the polarization of microglia into M2 microglia, reduced the expression of pro-inflammatory factors, and enhance the expression of anti-inflammatory cytokines. CONCLUSION After HBID, HDAC inhibitor Scriptaid inhibits inflammatory responses and protects the brain by promoting the polarization of microglia in brain tissue to M2 microglia.
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Affiliation(s)
- Qingmei Meng
- Department of Radiology, The Third People's Hospital of Qingdao Qingdao 266041, China
| | - Guifeng Yang
- Department of Radiology, The Third People's Hospital of Qingdao Qingdao 266041, China
| | - Yu Yang
- Department of Radiology, The Third People's Hospital of Qingdao Qingdao 266041, China
| | - Fucheng Ding
- Department of Radiology, The Third People's Hospital of Qingdao Qingdao 266041, China
| | - Fengxian Hu
- Department of Radiology, The Third People's Hospital of Qingdao Qingdao 266041, China
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24
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Kumar A, Kumar V, Singh K, Kumar S, Kim YS, Lee YM, Kim JJ. Therapeutic Advances for Huntington's Disease. Brain Sci 2020; 10:brainsci10010043. [PMID: 31940909 PMCID: PMC7016861 DOI: 10.3390/brainsci10010043] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 02/07/2023] Open
Abstract
Huntington’s disease (HD) is a progressive neurological disease that is inherited in an autosomal fashion. The cause of disease pathology is an expansion of cytosine-adenine-guanine (CAG) repeats within the huntingtin gene (HTT) on chromosome 4 (4p16.3), which codes the huntingtin protein (mHTT). The common symptoms of HD include motor and cognitive impairment of psychiatric functions. Patients exhibit a representative phenotype of involuntary movement (chorea) of limbs, impaired cognition, and severe psychiatric disturbances (mood swings, depression, and personality changes). A variety of symptomatic treatments (which target glutamate and dopamine pathways, caspases, inhibition of aggregation, mitochondrial dysfunction, transcriptional dysregulation, and fetal neural transplants, etc.) are available and some are in the pipeline. Advancement in novel therapeutic approaches include targeting the mutant huntingtin (mHTT) protein and the HTT gene. New gene editing techniques will reduce the CAG repeats. More appropriate and readily tractable treatment goals, coupled with advances in analytical tools will help to assess the clinical outcomes of HD treatments. This will not only improve the quality of life and life span of HD patients, but it will also provide a beneficial role in other inherited and neurological disorders. In this review, we aim to discuss current therapeutic research approaches and their possible uses for HD.
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Affiliation(s)
- Ashok Kumar
- Department of Genetics, Sanjay Gandhi Post-Graduate Institute of Medical Sciences, Lucknow 226014, UP, India;
| | - Vijay Kumar
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea; (Y.-S.K.); (Y.-M.L.)
- Correspondence: (V.K.); (J.-J.K.)
| | - Kritanjali Singh
- Central Research Station, Subharti Medical College, Swami Vivekanand Subharti University, Meerut 250002, India;
| | - Sukesh Kumar
- PG Department of Botany, Nalanda College, Bihar Sharif, Magadh University, Bihar 824234, India;
| | - You-Sam Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea; (Y.-S.K.); (Y.-M.L.)
| | - Yun-Mi Lee
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea; (Y.-S.K.); (Y.-M.L.)
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea; (Y.-S.K.); (Y.-M.L.)
- Correspondence: (V.K.); (J.-J.K.)
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25
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Goodnight AV, Kremsky I, Khampang S, Jung YH, Billingsley JM, Bosinger SE, Corces VG, Chan AWS. Chromatin accessibility and transcription dynamics during in vitro astrocyte differentiation of Huntington's Disease Monkey pluripotent stem cells. Epigenetics Chromatin 2019; 12:67. [PMID: 31722751 PMCID: PMC6852955 DOI: 10.1186/s13072-019-0313-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/25/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Huntington's Disease (HD) is a fatal neurodegenerative disorder caused by a CAG repeat expansion, resulting in a mutant huntingtin protein. While it is now clear that astrocytes are affected by HD and significantly contribute to neuronal dysfunction and pathogenesis, the alterations in the transcriptional and epigenetic profiles in HD astrocytes have yet to be characterized. Here, we examine global transcription and chromatin accessibility dynamics during in vitro astrocyte differentiation in a transgenic non-human primate model of HD. RESULTS We found global changes in accessibility and transcription across different stages of HD pluripotent stem cell differentiation, with distinct trends first observed in neural progenitor cells (NPCs), once cells have committed to a neural lineage. Transcription of p53 signaling and cell cycle pathway genes was highly impacted during differentiation, with depletion in HD NPCs and upregulation in HD astrocytes. E2F target genes also displayed this inverse expression pattern, and strong associations between E2F target gene expression and accessibility at nearby putative enhancers were observed. CONCLUSIONS The results suggest that chromatin accessibility and transcription are altered throughout in vitro HD astrocyte differentiation and provide evidence that E2F dysregulation contributes to aberrant cell-cycle re-entry and apoptosis throughout the progression from NPCs to astrocytes.
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Affiliation(s)
- Alexandra V Goodnight
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
- Genetics and Molecular Biology Program, Graduate Division of Biological and Biomedical Sciences, 1462 Clifton Rd, Atlanta, GA, 30322, USA
| | - Isaac Kremsky
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Sujittra Khampang
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
- Embryonic Stem Cell Research Center, School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Yoon Hee Jung
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - James M Billingsley
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Steven E Bosinger
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Victor G Corces
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA.
- Genetics and Molecular Biology Program, Graduate Division of Biological and Biomedical Sciences, 1462 Clifton Rd, Atlanta, GA, 30322, USA.
| | - Anthony W S Chan
- Division of Neuropharmacology and Neurologic Diseases, Yerkes National Primate Research Center, Atlanta, GA, 30322, USA.
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA.
- Genetics and Molecular Biology Program, Graduate Division of Biological and Biomedical Sciences, 1462 Clifton Rd, Atlanta, GA, 30322, USA.
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27
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Rustad SR, Papale LA, Alisch RS. DNA Methylation and Hydroxymethylation and Behavior. Curr Top Behav Neurosci 2019; 42:51-82. [PMID: 31392630 DOI: 10.1007/7854_2019_104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Environmentally sensitive molecular mechanisms in the brain, such as DNA methylation, have become a significant focus of neuroscience research because of mounting evidence indicating that they are critical in response to social situations, stress, threats, and behavior. The recent identification of 5-hydroxymethylcytosine (5hmC), which is enriched in the brain (tenfold over peripheral tissues), raises new questions as to the role of this base in mediating epigenetic effects in the brain. The development of genome-wide methods capable of distinguishing 5-methylcytosine (5mC) from 5hmC has revealed that a growing number of behaviors are linked to independent disruptions of 5mC and 5hmC levels, further emphasizing the unique importance of both of these modifications in the brain. Here, we review the recent links that indicate DNA methylation (both 5mC and 5hmC) is highly dynamic and that perturbations in this modification may contribute to behaviors related to psychiatric disorders and hold clinical relevance.
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Affiliation(s)
| | - Ligia A Papale
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA. .,Department of Neurological Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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Integrated Chemoinformatics Approaches Toward Epigenetic Drug Discovery. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2019. [DOI: 10.1007/978-3-030-05282-9_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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29
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Askeland G, Rodinova M, Štufková H, Dosoudilova Z, Baxa M, Smatlikova P, Bohuslavova B, Klempir J, Nguyen TD, Kuśnierczyk A, Bjørås M, Klungland A, Hansikova H, Ellederova Z, Eide L. A transgenic minipig model of Huntington's disease shows early signs of behavioral and molecular pathologies. Dis Model Mech 2018; 11:dmm.035949. [PMID: 30254085 PMCID: PMC6215428 DOI: 10.1242/dmm.035949] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/12/2018] [Indexed: 12/11/2022] Open
Abstract
Huntington's disease (HD) is a monogenic, progressive, neurodegenerative disorder with currently no available treatment. The Libechov transgenic minipig model for HD (TgHD) displays neuroanatomical similarities to humans and exhibits slow disease progression, and is therefore more powerful than available mouse models for the development of therapy. The phenotypic characterization of this model is still ongoing, and it is essential to validate biomarkers to monitor disease progression and intervention. In this study, the behavioral phenotype (cognitive, motor and behavior) of the TgHD model was assessed, along with biomarkers for mitochondrial capacity, oxidative stress, DNA integrity and DNA repair at different ages (24, 36 and 48 months), and compared with age-matched controls. The TgHD minipigs showed progressive accumulation of the mutant huntingtin (mHTT) fragment in brain tissue and exhibited locomotor functional decline at 48 months. Interestingly, this neuropathology progressed without any significant age-dependent changes in any of the other biomarkers assessed. Rather, we observed genotype-specific effects on mitochondrial DNA (mtDNA) damage, mtDNA copy number, 8-oxoguanine DNA glycosylase activity and global level of the epigenetic marker 5-methylcytosine that we believe is indicative of a metabolic alteration that manifests in progressive neuropathology. Peripheral blood mononuclear cells (PBMCs) were relatively spared in the TgHD minipig, probably due to the lack of detectable mHTT. Our data demonstrate that neuropathology in the TgHD model has an age of onset of 48 months, and that oxidative damage and electron transport chain impairment represent later states of the disease that are not optimal for assessing interventions. This article has an associated First Person interview with the first author of the paper. Summary: Here, we show that a minipig model of Huntington's disease mimics human neurodegeneration and holds promise for future intervention studies. However, minipig peripheral blood mononuclear cells express no detectable mutant huntingtin, eliminating their use as monitoring tools.
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Affiliation(s)
- Georgina Askeland
- Department of Medical Biochemistry, Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway.,Department of Microbiology, Oslo University Hospital, 0372 Oslo, Norway
| | - Marie Rodinova
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague 12808, Czech Republic
| | - Hana Štufková
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague 12808, Czech Republic
| | - Zaneta Dosoudilova
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague 12808, Czech Republic
| | - Monika Baxa
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague 12808, Czech Republic
| | - Petra Smatlikova
- Laboratory of Cell Regeneration and Plasticity, Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov 27721, Czech Republic
| | - Bozena Bohuslavova
- Laboratory of Cell Regeneration and Plasticity, Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov 27721, Czech Republic.,Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague 12843, Czech Republic
| | - Jiri Klempir
- Department of Neurology and Centre of Clinical Neuroscience, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague 12821, Czech Republic
| | - The Duong Nguyen
- Laboratory of Cell Regeneration and Plasticity, Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov 27721, Czech Republic.,Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague 12843, Czech Republic
| | - Anna Kuśnierczyk
- Proteomics and Metabolomics Core Facility, PROMEC, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital, 0372 Oslo, Norway.,Proteomics and Metabolomics Core Facility, PROMEC, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, 0372 Oslo, Norway
| | - Hana Hansikova
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague 12808, Czech Republic
| | - Zdenka Ellederova
- Laboratory of Cell Regeneration and Plasticity, Institute of Animal Physiology and Genetics, Czech Academy of Science, Libechov 27721, Czech Republic
| | - Lars Eide
- Department of Medical Biochemistry, Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
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30
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Zadel M, Maver A, Kovanda A, Peterlin B. DNA Methylation Profiles in Whole Blood of Huntington's Disease Patients. Front Neurol 2018; 9:655. [PMID: 30158895 PMCID: PMC6104454 DOI: 10.3389/fneur.2018.00655] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 07/23/2018] [Indexed: 12/14/2022] Open
Abstract
Epigenetic mechanisms, especially DNA methylation, are suggested to play a role in the age-of-onset in Huntington's disease (HD) based on studies on patient brains, and cellular and animal models. Methylation is tissue-specific and it is not clear how HD specific methylation in the brain correlates with the blood compartment, which represents a much more clinically accessible sample. Therefore, we explored the presence of HD specific DNA methylation patterns in whole blood on a cohort of HDM and healthy controls from Slovenia. We compared CpG site-specific DNA methylation in whole blood of 11 symptomatic and 9 pre-symptomatic HDM (HDM), and 15 healthy controls, by using bisulfite converted DNA on the Infinium® Human Methylation27 BeadChip microarray (Illumina) covering 27,578 CpG sites and 14,495 genes. Of the examined 14,495 genes, 437 were differentially methylated (p < 0.01) in pre-symptomatic HDM compared to controls, with three genes (CLDN16, DDC, NXT2) retaining statistical significance after the correction for multiple testing (false discovery rate, FDR < 0.05). Comparisons between symptomatic HDM and controls, and the comparison of symptomatic and pre-symptomatic HDM further identified 260 and 198 differentially methylated genes (p < 0.01), respectively, whereas the comparison of all HDM (symptomatic and pre-symptomatic) and healthy controls identified 326 differentially methylated genes (p < 0.01), however, none of these changes retained significance (FDR < 0.05) after the correction for multiple testing. The results of our study suggest that methylation signatures in the blood compartment are not robust enough to prove as valuable biomarkers for predicting HD progression, but recognizable changes in methylation deserve further research.
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Affiliation(s)
- Maja Zadel
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Community Health Centre Ljubljana, Ljubljana, Slovenia
| | - Aleš Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Anja Kovanda
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
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31
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Rosas-Arellano A, Estrada-Mondragón A, Piña R, Mantellero CA, Castro MA. The Tiny Drosophila Melanogaster for the Biggest Answers in Huntington's Disease. Int J Mol Sci 2018; 19:E2398. [PMID: 30110961 PMCID: PMC6121572 DOI: 10.3390/ijms19082398] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/08/2018] [Accepted: 08/09/2018] [Indexed: 12/18/2022] Open
Abstract
The average life expectancy for humans has increased over the last years. However, the quality of the later stages of life is low and is considered a public health issue of global importance. Late adulthood and the transition into the later stage of life occasionally leads to neurodegenerative diseases that selectively affect different types of neurons and brain regions, producing motor dysfunctions, cognitive impairment, and psychiatric disorders that are progressive, irreversible, without remission periods, and incurable. Huntington's disease (HD) is a common neurodegenerative disorder. In the 25 years since the mutation of the huntingtin (HTT) gene was identified as the molecule responsible for this neural disorder, a variety of animal models, including the fruit fly, have been used to study the disease. Here, we review recent research that used Drosophila as an experimental tool for improving knowledge about the molecular and cellular mechanisms underpinning HD.
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Affiliation(s)
- Abraham Rosas-Arellano
- Unidad de Imagenología, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico.
| | - Argel Estrada-Mondragón
- Department of Clinical and Experimental Medicine, Linköping University, 581 83 Linköping, Sweden.
| | - Ricardo Piña
- Laboratorio de Neurociencias, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9160000, Chile.
- Departamento de Ciencias Químicas y Biológicas, Universidad Bernardo O'Higgins, Santiago 8370993, Chile.
| | - Carola A Mantellero
- Facultad de Ciencias de la Salud, Universidad de Las Américas, Santiago 7500972, Chile.
| | - Maite A Castro
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia 5090000, Chile.
- Center for Interdisciplinary Studies on the Nervous System (CISNe), Universidad Austral de Chile, Valdivia 5090000, Chile.
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32
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Mollica PA, Zamponi M, Reid JA, Sharma DK, White AE, Ogle RC, Bruno RD, Sachs PC. Epigenetic alterations mediate iPSC-induced normalization of DNA repair gene expression and TNR stability in Huntington's disease cells. J Cell Sci 2018; 131:jcs.215343. [PMID: 29898922 DOI: 10.1242/jcs.215343] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/05/2018] [Indexed: 12/22/2022] Open
Abstract
Huntington's disease (HD) is a rare autosomal dominant neurodegenerative disorder caused by a cytosine-adenine-guanine (CAG) trinucleotide repeat (TNR) expansion within the HTT gene. The mechanisms underlying HD-associated cellular dysfunction in pluripotency and neurodevelopment are poorly understood. We had previously identified downregulation of selected DNA repair genes in HD fibroblasts relative to wild-type fibroblasts, as a result of promoter hypermethylation. Here, we tested the hypothesis that hypomethylation during cellular reprogramming to the induced pluripotent stem cell (iPSC) state leads to upregulation of DNA repair genes and stabilization of TNRs in HD cells. We sought to determine how the HD TNR region is affected by global epigenetic changes through cellular reprogramming and early neurodifferentiation. We find that early stage HD-affected neural stem cells (HD-NSCs) contain increased levels of global 5-hydroxymethylation (5-hmC) and normalized DNA repair gene expression. We confirm TNR stability is induced in iPSCs, and maintained in HD-NSCs. We also identify that upregulation of 5-hmC increases ten-eleven translocation 1 and 2 (TET1/2) protein levels, and show their knockdown leads to a corresponding decrease in the expression of select DNA repair genes. We further confirm decreased expression of TET1/2-regulating miR-29 family members in HD-NSCs. Our findings demonstrate that mechanisms associated with pluripotency induction lead to a recovery in the expression of select DNA repair gene and stabilize pathogenic TNRs in HD.
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Affiliation(s)
- Peter A Mollica
- Department of Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA 23529, USA.,Molecular Diagnostics Laboratory, Sentara Norfolk General Hospital, Norfolk, VA 23507, USA
| | - Martina Zamponi
- Department of Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA 23529, USA.,Biomedical Engineering Institute, Old Dominion University, Norfolk, VA 23529, USA
| | - John A Reid
- Department of Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA 23529, USA.,Biomedical Engineering Institute, Old Dominion University, Norfolk, VA 23529, USA
| | - Deepak K Sharma
- Department of Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA 23529, USA
| | - Alyson E White
- Department of Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA 23529, USA
| | - Roy C Ogle
- Department of Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA 23529, USA
| | - Robert D Bruno
- Department of Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA 23529, USA
| | - Patrick C Sachs
- Department of Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, VA 23529, USA
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33
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Zhao Y, Zurawel AA, Jenkins NP, Duennwald ML, Cheng C, Kettenbach AN, Supattapone S. Comparative Analysis of Mutant Huntingtin Binding Partners in Yeast Species. Sci Rep 2018; 8:9554. [PMID: 29934597 PMCID: PMC6015068 DOI: 10.1038/s41598-018-27900-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/12/2018] [Indexed: 12/21/2022] Open
Abstract
Huntington's disease is caused by the pathological expansion of a polyglutamine (polyQ) stretch in Huntingtin (Htt), but the molecular mechanisms by which polyQ expansion in Htt causes toxicity in selective neuronal populations remain poorly understood. Interestingly, heterologous expression of expanded polyQ Htt is toxic in Saccharomyces cerevisiae cells, but has no effect in Schizosaccharomyces pombe, a related yeast species possessing very few endogenous polyQ or Q/N-rich proteins. Here, we used a comprehensive and unbiased mass spectrometric approach to identify proteins that bind Htt in a length-dependent manner in both species. Analysis of the expanded polyQ-associated proteins reveals marked enrichment of proteins that are localized to and play functional roles in nucleoli and mitochondria in S. cerevisiae, but not in S. pombe. Moreover, expanded polyQ Htt appears to interact preferentially with endogenous polyQ and Q/N-rich proteins, which are rare in S. pombe, as well as proteins containing coiled-coil motifs in S. cerevisiae. Taken together, these results suggest that polyQ expansion of Htt may cause cellular toxicity in S. cerevisiae by sequestering endogenous polyQ and Q/N-rich proteins, particularly within nucleoli and mitochondria.
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Affiliation(s)
- Yanding Zhao
- Departments of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, 03755, United States
| | - Ashley A Zurawel
- Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, 03755, United States
| | - Nicole P Jenkins
- Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, 03755, United States
| | - Martin L Duennwald
- Department of Pathology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Chao Cheng
- Departments of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, 03755, United States
- Biomedical Data Sciences, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, 03755, United States
| | - Arminja N Kettenbach
- Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, 03755, United States
| | - Surachai Supattapone
- Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, 03755, United States.
- Medicine, Geisel School of Medicine at Dartmouth College, Hanover, New Hampshire, 03755, United States.
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Ciarochi JA, Liu J, Calhoun V, Johnson H, Misiura M, Bockholt HJ, Espinoza FA, Caprihan A, Plis S, Turner JA, Paulsen JS. High and Low Levels of an NTRK2-Driven Genetic Profile Affect Motor- and Cognition-Associated Frontal Gray Matter in Prodromal Huntington's Disease. Brain Sci 2018; 8:E116. [PMID: 29932126 PMCID: PMC6071032 DOI: 10.3390/brainsci8070116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/12/2018] [Accepted: 06/20/2018] [Indexed: 12/16/2022] Open
Abstract
This study assessed how BDNF (brain-derived neurotrophic factor) and other genes involved in its signaling influence brain structure and clinical functioning in pre-diagnosis Huntington's disease (HD). Parallel independent component analysis (pICA), a multivariate method for identifying correlated patterns in multimodal datasets, was applied to gray matter concentration (GMC) and genomic data from a sizeable PREDICT-HD prodromal cohort (N = 715). pICA identified a genetic component highlighting NTRK2, which encodes BDNF's TrkB receptor, that correlated with a GMC component including supplementary motor, precentral/premotor cortex, and other frontal areas (p < 0.001); this association appeared to be driven by participants with high or low levels of the genetic profile. The frontal GMC profile correlated with cognitive and motor variables (Trail Making Test A (p = 0.03); Stroop Color (p = 0.017); Stroop Interference (p = 0.04); Symbol Digit Modalities Test (p = 0.031); Total Motor Score (p = 0.01)). A top-weighted NTRK2 variant (rs2277193) was protectively associated with Trail Making Test B (p = 0.007); greater minor allele numbers were linked to a better performance. These results support the idea of a protective role of NTRK2 in prodromal HD, particularly in individuals with certain genotypes, and suggest that this gene may influence the preservation of frontal gray matter that is important for clinical functioning.
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Affiliation(s)
| | - Jingyu Liu
- The Mind Research Network, Albuquerque, NM 87106, USA.
| | - Vince Calhoun
- The Mind Research Network, Albuquerque, NM 87106, USA.
- Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM 87131, USA.
| | - Hans Johnson
- Iowa Mental Health Clinical Research Center, Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA.
| | - Maria Misiura
- Department of Psychology, Georgia State University, Atlanta, GA 30302, USA.
| | | | | | | | - Sergey Plis
- The Mind Research Network, Albuquerque, NM 87106, USA.
| | - Jessica A Turner
- Neuroscience Institute, Georgia State University, Atlanta, GA 30302, USA.
- Department of Psychology, Georgia State University, Atlanta, GA 30302, USA.
| | - Jane S Paulsen
- Iowa Mental Health Clinical Research Center, Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA.
- Department of Neurology, University of Iowa, Iowa City, IA 52242, USA.
- Department of Psychology, University of Iowa, Iowa City, IA 52242, USA.
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35
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Epigenetic Regulation in Neurodegenerative Diseases. Trends Neurosci 2018; 41:587-598. [PMID: 29885742 DOI: 10.1016/j.tins.2018.05.005] [Citation(s) in RCA: 214] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/01/2018] [Accepted: 05/08/2018] [Indexed: 12/13/2022]
Abstract
Mechanisms of epigenetic regulation, including DNA methylation, chromatin remodeling, and histone post-translational modifications, are involved in multiple aspects of neuronal function and development. Recent discoveries have shed light on critical functions of chromatin in the aging brain, with an emerging realization that the maintenance of a healthy brain relies heavily on epigenetic mechanisms. Here, we present recent advances, with a focus on histone modifications and the implications for several neurodegenerative diseases including Alzheimer's disease (AD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS). We highlight common and unique epigenetic mechanisms among these situations and point to emerging therapeutic approaches.
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36
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Lardenoije R, Pishva E, Lunnon K, van den Hove DL. Neuroepigenetics of Aging and Age-Related Neurodegenerative Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 158:49-82. [PMID: 30072060 DOI: 10.1016/bs.pmbts.2018.04.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Neurodegenerative diseases are complex, progressive disorders and affect millions of people worldwide, contributing significantly to the global burden of disease. In recent years, research has begun to investigate epigenetic mechanisms for a potential role in disease etiology. In this chapter, we describe the current state of play for epigenetic research into neurodegenerative disorders including Alzheimer's disease, Parkinson's disease and Huntington's disease. We focus on the recent evidence for a potential role of DNA modifications, histone modifications and non-coding RNA in the etiology of these disorders. Finally, we discuss how new technological and bioinformatics advances in the field of epigenetics could further progress our understanding about the underlying mechanisms of neurodegenerative diseases.
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Affiliation(s)
- Roy Lardenoije
- Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Ehsan Pishva
- Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands; University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Katie Lunnon
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Daniel L van den Hove
- Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands.
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37
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Hamzeiy H, Savaş D, Tunca C, Şen NE, Gündoğdu Eken A, Şahbaz I, Calini D, Tiloca C, Ticozzi N, Ratti A, Silani V, Başak AN. Elevated Global DNA Methylation Is Not Exclusive to Amyotrophic Lateral Sclerosis and Is Also Observed in Spinocerebellar Ataxia Types 1 and 2. NEURODEGENER DIS 2018; 18:38-48. [PMID: 29428949 DOI: 10.1159/000486201] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 12/08/2017] [Indexed: 12/12/2022] Open
Abstract
Adult-onset neurological disorders are caused and influenced by a multitude of different factors, including epigenetic modifications. Here, using an ELISA kit selected upon careful testing, we investigated global 5-methylcytosine (5-mC) levels in sporadic and familial amyotrophic lateral sclerosis (sALS and fALS), spinocerebellar ataxia types 1 and 2 (SCA1 and SCA2), Huntington's disease, Friedreich's ataxia, and myotonic dystrophy type 1. We report a significant elevation in global 5-mC levels of about 2-7% on average for sALS (p < 0.01 [F(1, 243) = 9.159, p = 0.0027]) and various forms of fALS along with SCA1 (p < 0.01 [F(1, 83) = 11.285], p = 0.0012) and SCA2 (p < 0.001 [F(1, 122) = 29.996, p = 0.0001]) when compared to age- and sex-matched healthy controls. C9orf72 expansion carrier ALS patients exhibit the highest global 5-mC levels along with C9orf72 promoter hypermethylation. We failed to measure global 5-hydroxymethylcytosine (5-hmC) levels in blood, probably due to the very low levels of 5-hmC and the limitations of the commercially available ELISA kits. Our results point towards a role for epigenetics modification in ALS, SCA1, and SCA2, and help conclude a dispute on the global 5-mC levels in sALS blood.
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Affiliation(s)
- Hamid Hamzeiy
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Doruk Savaş
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Ceren Tunca
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Nesli Ece Şen
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Aslı Gündoğdu Eken
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Irmak Şahbaz
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Daniela Calini
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Cinzia Tiloca
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Nicola Ticozzi
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Milan, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Milan, Italy
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Milan, Italy
| | - A Nazlı Başak
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
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38
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Lee J, Hwang YJ, Kim Y, Lee MY, Hyeon SJ, Lee S, Kim DH, Jang SJ, Im H, Min SJ, Choo H, Pae AN, Kim DJ, Cho KS, Kowall NW, Ryu H. Remodeling of heterochromatin structure slows neuropathological progression and prolongs survival in an animal model of Huntington's disease. Acta Neuropathol 2017; 134:729-748. [PMID: 28593442 DOI: 10.1007/s00401-017-1732-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 05/25/2017] [Accepted: 05/25/2017] [Indexed: 01/01/2023]
Abstract
Huntington's disease (HD) is an autosomal-dominant inherited neurological disorder caused by expanded CAG repeats in exon 1 of the Huntingtin (HTT) gene. Altered histone modifications and epigenetic mechanisms are closely associated with HD suggesting that transcriptional repression may play a pathogenic role. Epigenetic compounds have significant therapeutic effects in cellular and animal models of HD, but they have not been successful in clinical trials. Herein, we report that dSETDB1/ESET, a histone methyltransferase (HMT), is a mediator of mutant HTT-induced degeneration in a fly HD model. We found that nogalamycin, an anthracycline antibiotic and a chromatin remodeling drug, reduces trimethylated histone H3K9 (H3K9me3) levels and pericentromeric heterochromatin condensation by reducing the expression of Setdb1/Eset. H3K9me3-specific ChIP-on-ChIP analysis identified that the H3K9me3-enriched epigenome signatures of multiple neuronal pathways including Egr1, Fos, Ezh1, and Arc are deregulated in HD transgenic (R6/2) mice. Nogalamycin modulated the expression of the H3K9me3-landscaped epigenome in medium spiny neurons and reduced mutant HTT nuclear inclusion formation. Moreover, nogalamycin slowed neuropathological progression, preserved motor function, and extended the life span of R6/2 mice. Together, our results indicate that modulation of SETDB1/ESET and H3K9me3-dependent heterochromatin plasticity is responsible for the neuroprotective effects of nogalamycin in HD and that small compounds targeting dysfunctional histone modification and epigenetic modification by SETDB1/ESET may be a rational therapeutic strategy in HD.
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39
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Malankhanova TB, Malakhova AA, Medvedev SP, Zakian SM. Modern Genome Editing Technologies in Huntington's Disease Research. J Huntingtons Dis 2017; 6:19-31. [PMID: 28128770 PMCID: PMC5389024 DOI: 10.3233/jhd-160222] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The development of new revolutionary technologies for directed gene editing has made it possible to thoroughly model and study NgAgo human diseases at the cellular and molecular levels. Gene editing tools like ZFN, TALEN, CRISPR-based systems, NgAgo and SGN can introduce different modifications. In gene sequences and regulate gene expression in different types of cells including induced pluripotent stem cells (iPSCs). These tools can be successfully used for Huntington's disease (HD) modeling, for example, to generate isogenic cell lines bearing different numbers of CAG repeats or to correct the mutation causing the disease. This review presents common genome editing technologies and summarizes the progress made in using them in HD and other hereditary diseases. Furthermore, we will discuss prospects and limitations of genome editing in understanding HD pathology.
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Affiliation(s)
- Tuyana B Malankhanova
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia.,State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia.,Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasia A Malakhova
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia.,Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey P Medvedev
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia.,State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia.,Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Suren M Zakian
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia.,State Research Institute of Circulation Pathology, Ministry of Healthcare of the Russian Federation, Novosibirsk, Russia.,Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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40
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Baronchelli S, La Spada A, Ntai A, Barbieri A, Conforti P, Jotti GS, Redaelli S, Bentivegna A, De Blasio P, Biunno I. Epigenetic and transcriptional modulation of WDR5, a chromatin remodeling protein, in Huntington's disease human induced pluripotent stem cell (hiPSC) model. Mol Cell Neurosci 2017; 82:46-57. [PMID: 28476540 DOI: 10.1016/j.mcn.2017.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 04/04/2017] [Accepted: 04/13/2017] [Indexed: 11/24/2022] Open
Abstract
DNA methylation (DNAm) changes are of increasing relevance to neurodegenerative disorders, including Huntington's disease (HD). We performed genome-wide screening of possible DNAm changes occurring during striatal differentiation in human induced pluripotent stem cells derived from a HD patient (HD-hiPSCs) as cellular model. We identified 240 differentially methylated regions (DMRs) at promoters in fully differentiated HD-hiPSCs. Subsequently, we focused on the methylation differences in a subcluster of genes related to Jumonji Domain Containing 3 (JMJD3), a demethylase that epigenetically regulates neuronal differentiation and activates neuronal progenitor associated genes, which are indispensable for neuronal fate acquisition. Noticeably among these genes, WD repeat-containing protein 5 (WDR5) promoter was found hypermethylated in HD-hiPSCs, resulting in a significant down-modulation in its expression and of the encoded protein. A similar WDR5 expression decrease was seen in a small series of HD-hiPSC lines characterized by different CAG length. The decrease in WDR5 expression was particularly evident in HD-hiPSCs compared to hESCs and control-hiPSCs from healthy subjects. WDR5 is a core component of the MLL/SET1 chromatin remodeling complexes essential for H3K4me3, previously reported to play an important role in stem cells self-renewal and differentiation. These results suggest the existence of epigenetic mechanisms in HD and the identification of genes, which are able to modulate HD phenotype, is important both for biomarker discovery and therapeutic interventions.
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Affiliation(s)
- Simona Baronchelli
- Institute of Genetic and Biomedical Research, National Research Council (IRGB-CNR), via Fantoli 16/15, 20138 Milan, Italy
| | - Alberto La Spada
- Institute of Genetic and Biomedical Research, National Research Council (IRGB-CNR), via Fantoli 16/15, 20138 Milan, Italy
| | - Aikaterini Ntai
- Integrated Systems Engineering Srl, Via Fantoli 16/15, 20138 Milano, Italy
| | - Andrea Barbieri
- Institute of Genetic and Biomedical Research, National Research Council (IRGB-CNR), via Fantoli 16/15, 20138 Milan, Italy
| | - Paola Conforti
- Department of Biosciences, University of Milan and Istituto Nazionale di Genetica Molecolare Padiglione Invernizzi, Via Francesco Sforza 35, 20122 Milan, Italy
| | - Gloria Saccani Jotti
- Department of Biological Science, Biotechnology and Translational - S.Bi.Bi.T., University of Parma, Via Gramsci 14, 43121 Parma, Italy
| | - Serena Redaelli
- Department of Surgery and Translational Medicine, University of Milano-Bicocca, via Cadore 48, 20900 Monza, Milan, Italy
| | - Angela Bentivegna
- Department of Surgery and Translational Medicine, University of Milano-Bicocca, via Cadore 48, 20900 Monza, Milan, Italy; NeuroMI, Milan Center of Neuroscience, via Pergolesi 33, 20900 Monza, Italy
| | - Pasquale De Blasio
- Integrated Systems Engineering Srl, Via Fantoli 16/15, 20138 Milano, Italy
| | - Ida Biunno
- Institute of Genetic and Biomedical Research, National Research Council (IRGB-CNR), via Fantoli 16/15, 20138 Milan, Italy; IRCCS Multimedica, via Fantoli 16/15, 20138 Milano, Italy.
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41
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Fu I, Cai Y, Geacintov NE, Zhang Y, Broyde S. Nucleosome Histone Tail Conformation and Dynamics: Impacts of Lysine Acetylation and a Nearby Minor Groove Benzo[a]pyrene-Derived Lesion. Biochemistry 2017; 56:1963-1973. [PMID: 28304160 DOI: 10.1021/acs.biochem.6b01208] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Histone tails in nucleosomes play critical roles in regulation of many biological processes, including chromatin compaction, transcription, and DNA repair. Moreover, post-translational modifications, notably lysine acetylation, are crucial to these functions. While the tails have been intensively studied, how the structures and dynamics of tails are impacted by the presence of a nearby bulky DNA lesion is a frontier research area, and how these properties are impacted by tail lysine acetylation remains unexplored. To obtain molecular insight, we have utilized all atom 3 μs molecular dynamics simulations of nucleosome core particles (NCPs) to determine the impact of a nearby DNA lesion, 10S (+)-trans-anti-B[a]P-N2-dG-the major adduct derived from the procarcinogen benzo[a]pyrene-on H2B tail behavior in unacetylated and acetylated states. We similarly studied lesion-free NCPs to investigate the normal properties of the H2B tail in both states. In the lesion-free NCPs, charge neutralization upon lysine acetylation causes release of the tail from the DNA. When the lesion is present, it stably engulfs part of the nearby tail, impairing the interactions between DNA and tail. With the tail in an acetylated state, the lesion still interacts with part of it, although unstably. The lesion's partial entrapment of the tail should hinder the tail from interacting with other nucleosomes, and other proteins such as acetylases, deacetylases, and acetyl-lysine binding proteins, and thus disrupt critical tail-governed processes. Hence, the lesion would impede tail functions modulated by acetylation or deacetylation, causing aberrant chromatin structures and impaired biological transactions such as transcription and DNA repair.
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Affiliation(s)
| | | | | | - Yingkai Zhang
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China
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42
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Francelle L, Lotz C, Outeiro T, Brouillet E, Merienne K. Contribution of Neuroepigenetics to Huntington's Disease. Front Hum Neurosci 2017; 11:17. [PMID: 28194101 PMCID: PMC5276857 DOI: 10.3389/fnhum.2017.00017] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 01/10/2017] [Indexed: 12/29/2022] Open
Abstract
Unbalanced epigenetic regulation is thought to contribute to the progression of several neurodegenerative diseases, including Huntington’s disease (HD), a genetic disorder considered as a paradigm of epigenetic dysregulation. In this review, we attempt to address open questions regarding the role of epigenetic changes in HD, in the light of recent advances in neuroepigenetics. We particularly discuss studies using genome-wide scale approaches that provide insights into the relationship between epigenetic regulations, gene expression and neuronal activity in normal and diseased neurons, including HD neurons. We propose that cell-type specific techniques and 3D-based methods will advance knowledge of epigenome in the context of brain region vulnerability in neurodegenerative diseases. A better understanding of the mechanisms underlying epigenetic changes and of their consequences in neurodegenerative diseases is required to design therapeutic strategies more effective than current strategies based on histone deacetylase (HDAC) inhibitors. Researches in HD may play a driving role in this process.
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Affiliation(s)
- Laetitia Francelle
- Department of NeuroDegeneration and Restorative Research, University Medical Center Goettingen Goettingen, Germany
| | - Caroline Lotz
- CNRS UMR 7364, Laboratory of Cognitive and Adaptive Neurosciences, University of Strasbourg Strasbourg, France
| | - Tiago Outeiro
- Department of NeuroDegeneration and Restorative Research, University Medical Center Goettingen Goettingen, Germany
| | - Emmanuel Brouillet
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Département de Recherche Fondamentale, Institut d'Imagerie Biomédicale, Molecular Imaging Center, Neurodegenerative diseases Laboratory, UMR 9199, CNRS Université Paris-Sud, Université Paris-Saclay Fontenay-aux-Roses, France
| | - Karine Merienne
- CNRS UMR 7364, Laboratory of Cognitive and Adaptive Neurosciences, University of Strasbourg Strasbourg, France
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43
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Abstract
Huntington's disease (HD) is a genetic, fatal autosomal dominant neurodegenerative disorder typically occurring in midlife with symptoms ranging from chorea, to dementia, to personality disturbances (Philos Trans R Soc Lond Ser B Biol Sci 354:957-961, 1999). HD is inherited in a dominant fashion, and the underlying mutation in all cases is a CAG trinucleotide repeat expansion within exon 1 of the HD gene (Cell 72:971-983, 1993). The expanded CAG repeat, translated into a lengthened glutamine tract at the amino terminus of the huntingtin protein, affects its structural properties and functional activities. The effects are pleiotropic, as huntingtin is broadly expressed in different cellular compartments (i.e., cytosol, nucleus, mitochondria) as well as in all cell types of the body at all developmental stages, such that HD pathogenesis likely starts at conception and is a lifelong process (Front Neurosci 9:509, 2015). The rate-limiting mechanism(s) of neurodegeneration in HD still remains elusive: many different processes are commonly disrupted in HD cell lines and animal models, as well as in HD patient cells (Eur J Neurosci 27:2803-2820, 2008); however, epigenetic-chromatin deregulation, as determined by the analysis of DNA methylation, histone modifications, and noncoding RNAs, has now become a prevailing feature. Thus, the overarching goal of this chapter is to discuss the current status of the literature, reviewing how an aberrant epigenetic landscape can contribute to altered gene expression and neuronal dysfunction in HD.
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44
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Madrid A, Papale LA, Alisch RS. New hope: the emerging role of 5-hydroxymethylcytosine in mental health and disease. Epigenomics 2016; 8:981-91. [DOI: 10.2217/epi-2016-0020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Historically biomedical research has examined genetic influences on mental health but these approaches have been limited, likely due to the broad heritability of brain-related disorders (e.g., 30–90%). Epigenetic modifications, such as DNA methylation, are environmentally sensitive mechanisms that may play a role in the origins and progression of mental illness. Recently, genome-wide disruptions of 5-hydroxymethylcytosine (5hmC) were associated with the development of early and late onset mental illnesses such as autism and Alzheimer’s disease, bringing new hope to the field of psychiatry. Here, we review the recent links of 5hmC to mental illness and discuss several putative functions of 5hmC in the context of its promising clinical relevance.
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Affiliation(s)
- Andy Madrid
- Department of Psychiatry, University of Wisconsin, Madison, WI 53719, USA
- Neuroscience training program, University of Wisconsin, Madison, WI 53719, USA
| | - Ligia A Papale
- Department of Psychiatry, University of Wisconsin, Madison, WI 53719, USA
| | - Reid S Alisch
- Department of Psychiatry, University of Wisconsin, Madison, WI 53719, USA
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45
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Thomas EA. DNA methylation in Huntington's disease: Implications for transgenerational effects. Neurosci Lett 2016; 625:34-9. [PMID: 26522374 PMCID: PMC4864163 DOI: 10.1016/j.neulet.2015.10.060] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 10/08/2015] [Accepted: 10/23/2015] [Indexed: 12/29/2022]
Abstract
Huntington's disease (HD) is a devastating, neurodegenerative disorder caused by a CAG repeat mutation in the HTT gene. A growing body of evidence suggests that epigenetic modifications play a key role in HD pathogenesis. Expression of the disease protein, huntingtin, leads to extensive transcriptional dysregulation due to disruption of histone-modifying complexes and altered interactions with chromatin-related factors. Such epigenetic mechanisms also readily respond to environmental factors, which are now thought to influence the risk, onset and progression of neurodegenerative disorders, including HD. DNA methylation is an epigenetic modification that has been studied intensively, however, its role in HD is just emerging. In this review, DNA methylation differences associated with HD will be summarized, as well as the role of environmental factors to alter DNA methylation in a manner that could alter disease phenotypes. Further, transgenerational epigenetic inheritance will be discussed in the context of relevant environmental factors and their potential links to HD. The study of epigenetic states in HD presents an opportunity to gain new insights into risk factors and pathogenic mechanisms associated with HD, as well as to inform about treatment options.
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Affiliation(s)
- Elizabeth A Thomas
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, CA, United States.
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46
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Elhamamsy AR. DNA methylation dynamics in plants and mammals: overview of regulation and dysregulation. Cell Biochem Funct 2016; 34:289-98. [PMID: 27003927 DOI: 10.1002/cbf.3183] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 02/18/2016] [Accepted: 02/29/2016] [Indexed: 12/22/2022]
Abstract
DNA methylation is a major epigenetic marking mechanism regulating various biological functions in mammals and plant. The crucial role of DNA methylation has been observed in cellular differentiation, embryogenesis, genomic imprinting and X-chromosome inactivation. Furthermore, DNA methylation takes part in disease susceptibility, responses to environmental stimuli and the biodiversity of natural populations. In plant, different types of environmental stress have demonstrated the ability to alter the archetype of DNA methylation through the genome, change gene expression and confer a mechanism of adaptation. DNA methylation dynamics are regulated by three processes de novo DNA methylation, methylation maintenance and DNA demethylation. These processes have their similarities and differences between mammals and plants. Furthermore, the dysregulation of DNA methylation dynamics represents one of the primary molecular mechanisms of developing diseases in mammals. This review discusses the regulation and dysregulation of DNA methylation in plants and mammals. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Amr Rafat Elhamamsy
- Clinical Pharmacy Department, Faculty of Pharmacy, Tanta University, Tanta, Egypt
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47
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De Souza RAG, Islam SA, McEwen LM, Mathelier A, Hill A, Mah SM, Wasserman WW, Kobor MS, Leavitt BR. DNA methylation profiling in human Huntington's disease brain. Hum Mol Genet 2016; 25:2013-2030. [PMID: 26953320 DOI: 10.1093/hmg/ddw076] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/29/2016] [Indexed: 12/29/2022] Open
Abstract
Despite extensive progress in Huntington's disease (HD) research, very little is known about the association of epigenetic variation and HD pathogenesis in human brain tissues. Moreover, its contribution to the tissue-specific transcriptional regulation of the huntingtin gene (HTT), in which HTT expression levels are highest in brain and testes, is currently unknown. To investigate the role of DNA methylation in HD pathogenesis and tissue-specific expression of HTT, we utilized the Illumina HumanMethylation450K BeadChip array to measure DNA methylation in a cohort of age-matched HD and control human cortex and liver tissues. In cortex samples, we found minimal evidence of HD-associated DNA methylation at probed sites after correction for cell heterogeneity but did observe an association with the age of disease onset. In contrast, comparison of matched cortex and liver samples revealed tissue-specific DNA methylation of the HTT gene region at 38 sites (FDR < 0.05). Importantly, we identified a novel differentially methylated binding site in the HTT proximal promoter for the transcription factor CTCF. This CTCF site displayed increased occupancy in cortex, where HTT expression is higher, compared with the liver. Additionally, CTCF silencing reduced the activity of an HTT promoter-reporter construct, suggesting that CTCF plays a role in regulating HTT promoter function. Overall, although we were unable to detect HD-associated DNA methylation alterations at queried sites, we found that DNA methylation may be correlated to the age of disease onset in cortex tissues. Moreover, our data suggest that DNA methylation may, in part, contribute to tissue-specific HTT transcription through differential CTCF occupancy.
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Affiliation(s)
- Rebecca A G De Souza
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Sumaiya A Islam
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Lisa M McEwen
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Anthony Mathelier
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Austin Hill
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Sarah M Mah
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Wyeth W Wasserman
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
| | - Blair R Leavitt
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada V5Z 4H4
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48
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Ratovitski T, Arbez N, Stewart JC, Chighladze E, Ross CA. PRMT5- mediated symmetric arginine dimethylation is attenuated by mutant huntingtin and is impaired in Huntington's disease (HD). Cell Cycle 2016; 14:1716-29. [PMID: 25927346 DOI: 10.1080/15384101.2015.1033595] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Abnormal protein interactions of mutant huntingtin (Htt) triggered by polyglutamine expansion are thought to mediate Huntington's disease (HD) pathogenesis. Here, we explored a functional interaction of Htt with protein arginine methyltransferase 5 (PRMT5), an enzyme mediating symmetrical dimethylation of arginine (sDMA) of key cellular proteins, including histones, and spliceosomal Sm proteins. Gene transcription and RNA splicing are impaired in HD. We demonstrated PRMT5 and Htt interaction and their co-localization in transfected neurons and in HD brain. As a result of this interaction, normal (but to a lesser extend mutant) Htt stimulated PRMT5 activity in vitro. SDMA of histones H2A and H4 was reduced in the presence of mutant Htt in primary cultured neurons and in HD brain, consistent with a demonstrated reduction in R3Me2s occupancy at the transcriptionally repressed promoters in HD brain. SDMA of another PRMT5 substrate, Cajal body marker coilin, was also reduced in the HD mouse model and in human HD brain. Finally, compensation of PRMT5 deficiency by ectopic expression of PRMT5/MEP50 complexes, or by the knock-down of H4R3Me2 demethylase JMJD6, reversed the toxic effects of mutant Htt in primary cortical neurons, suggesting that PRMT5 deficiency may mediate, at least in part, HD pathogenesis. These studies revealed a potential new mechanism for disruption of gene expression and RNA processing in HD, involving a loss of normal function of Htt in facilitation of PRMT5, supporting the idea that epigenetic regulation of gene transcription may be involved in HD and highlighting symmetric dimethylation of arginine as potential new therapeutic target.
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Key Words
- BDNF, brain-derived neurotrophic factor
- CB, Cajal body
- ChIP, the chromatin immunoprecipitation
- DMEM, Dulbecco's modified Eagle's medium
- FBS, fetal bovine serum
- HD, Huntington's disease
- HEK, human embryonic kidney
- Htt, huntingtin
- Huntington's disease mechanism
- IP, immunoprecipitation
- IgG, immunoglobulin
- PIC, protease inhibitors cocktail
- PRMT5, protein arginine methyltransferase
- RNA processing
- SMN, survival of motor neurons
- Sm proteins, spleceosomal small nuclear ribonucleoproteins
- gene transcription
- huntingtin
- neurodegeneration
- polyQ, polyglutamine
- protein interactions
- protein methylation
- sDMA, symmetrical arginine dimethylation
- snRNPs, small nuclear ribonucleoprotein particles
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Affiliation(s)
- Tamara Ratovitski
- a Division of Neurobiology; Department of Psychiatry; Johns Hopkins University School of Medicine ; CMSC 8-121; Baltimore , MD , USA
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49
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Fu I, Cai Y, Zhang Y, Geacintov NE, Broyde S. Entrapment of a Histone Tail by a DNA Lesion in a Nucleosome Suggests the Lesion Impacts Epigenetic Marking: A Molecular Dynamics Study. Biochemistry 2016; 55:239-42. [PMID: 26709619 PMCID: PMC4721520 DOI: 10.1021/acs.biochem.5b01166] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/21/2015] [Indexed: 11/30/2022]
Abstract
Errors in epigenetic markings are associated with human diseases, including cancer. We have used molecular dynamics simulations of a nucleosome containing the 10S (+)-trans-anti-B[a]P-N(2)-dG lesion, derived from the environmental pro-carcinogen benzo[a]pyrene, to elucidate the impact of the lesion on the structure and dynamics of a nearby histone N-terminal tail. Our results show that a lysine-containing part of this H2B tail that is subject to post-translational modification is engulfed by the enlarged DNA minor groove imposed by the lesion. The tail entrapment suggests that epigenetic markings could be hampered by this lesion, thereby impacting critical cellular functions, including transcription and repair.
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Affiliation(s)
- Iwen Fu
- Department of Biology and Department of
Chemistry, New York University, New York, New York 10003, United States
| | - Yuqin Cai
- Department of Biology and Department of
Chemistry, New York University, New York, New York 10003, United States
| | - Yingkai Zhang
- Department of Biology and Department of
Chemistry, New York University, New York, New York 10003, United States
- NYU-ECNU
Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Nicholas E. Geacintov
- Department of Biology and Department of
Chemistry, New York University, New York, New York 10003, United States
| | - Suse Broyde
- Department of Biology and Department of
Chemistry, New York University, New York, New York 10003, United States
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Kerschbamer E, Biagioli M. Huntington's Disease as Neurodevelopmental Disorder: Altered Chromatin Regulation, Coding, and Non-Coding RNA Transcription. Front Neurosci 2016; 9:509. [PMID: 26793052 PMCID: PMC4710752 DOI: 10.3389/fnins.2015.00509] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/21/2015] [Indexed: 01/05/2023] Open
Affiliation(s)
- Emanuela Kerschbamer
- NeuroEpigenetics Laboratory, Centre for Integrative Biology, University of Trento Trento, Italy
| | - Marta Biagioli
- NeuroEpigenetics Laboratory, Centre for Integrative Biology, University of Trento Trento, Italy
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