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Reis AHDEO, Figalo LB, Orsini M, Lemos B. The implications of DNA methylation for amyotrophic lateral sclerosis. AN ACAD BRAS CIENC 2023; 95:e20230277. [PMID: 37909610 DOI: 10.1590/0001-3765202320230277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/11/2023] [Indexed: 11/03/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a complex and serious neurodegenerative disorder that develops in consequence of the progressive loss of the upper and lower motor neurons. Cases of ALS are classified as sporadic (sALS), or familial (fALS). Over 90% of cases are sALS, while roughly 10% are related to inherited genetic mutations (fALS). Approximately 70% of the genetic mutations that contribute to fALS have been identified. On the other hand, the majority of the sALS cases have an undetermined genetic contributor and few mutations have been described, despite the advanced genetic analysis methods. Also, several factors contribute to the onset and progression of ALS. Numerous lines of evidence indicate that epigenetic changes are linked to aging, as well as neurodegenerative disorders, such as ALS. In most cases, they act as the heritable regulation of transcription by DNA methylation, histone modification and expression of noncoding RNAs. Mechanisms involving aberrant DNA methylation could be relevant to human ALS pathobiology and therapeutic targeting. Despite advances in research to find factors associated with ALS and more effective treatments, this disease remains complex and has low patient survival. Here, we provide a narrative review of the role of DNA methylation for this complex neurodegenerative disorder.
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Affiliation(s)
- Adriana Helena DE Oliveira Reis
- Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto Alcantara Gomes, Departamento de Genética, Pavilhão Haroldo Lisboa da Cunha, Rua São Francisco Xavier, 524, Sala 501F, 20550-900 Rio de Janeiro, RJ, Brazil
| | - Luna B Figalo
- Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto Alcantara Gomes, Departamento de Genética, Pavilhão Haroldo Lisboa da Cunha, Rua São Francisco Xavier, 524, Sala 501F, 20550-900 Rio de Janeiro, RJ, Brazil
| | - Marco Orsini
- Programa de Pós-Graduação em Vigilância em Saúde, Universidade Iguaçu, Av. Abílio Augusto Távora, 2134, 26260-045 Nova Iguaçu, RJ, Brazil
- Universidade Federal do Rio de Janeiro, Departamento de Psiquiatria, Av. Venceslau Brás, 71, Botafogo, 22290-140 Rio de Janeiro, RJ, Brazil
| | - Bernardo Lemos
- Coit Center for longevity and Neurotheraéutics, Departament of pharmacology and toxicology, R Ken Coit College of Pharmacy, University of Arizona, 1703 E. Mabel St. PO Box 210207 Tucson, Arizona, USA
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2
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Sucha M, Benediktova S, Tichanek F, Jedlicka J, Kapl S, Jelinkova D, Purkartova Z, Tuma J, Kuncova J, Cendelin J. Experimental Treatment with Edaravone in a Mouse Model of Spinocerebellar Ataxia 1. Int J Mol Sci 2023; 24:10689. [PMID: 37445867 DOI: 10.3390/ijms241310689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Edaravone is a mitochondrially targeted drug with a suggested capability to modify the course of diverse neurological diseases. Nevertheless, edaravone has not been tested yet in the context of spinocerebellar ataxia 1 (SCA1), an incurable neurodegenerative disease characterized mainly by cerebellar disorder, with a strong contribution of inflammation and mitochondrial dysfunction. This study aimed to address this gap, exploring the potential of edaravone to slow down SCA1 progression in a mouse knock-in SCA1 model. SCA1154Q/2Q and healthy SCA12Q/2Q mice were administered either edaravone or saline daily for more than 13 weeks. The functional impairments were assessed via a wide spectrum of behavioral assays reflecting motor and cognitive deficits and behavioral abnormalities. Moreover, we used high-resolution respirometry to explore mitochondrial function, and immunohistochemical and biochemical tools to assess the magnitude of neurodegeneration, inflammation, and neuroplasticity. Data were analyzed using (hierarchical) Bayesian regression models, combined with the methods of multivariate statistics. Our analysis pointed out various previously documented neurological and behavioral deficits of SCA1 mice. However, we did not detect any plausible therapeutic effect of edaravone on either behavioral dysfunctions or other disease hallmarks in SCA1 mice. Thus, our results did not provide support for the therapeutic potential of edaravone in SCA1.
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Affiliation(s)
- Martina Sucha
- Department of Pathological Physiology, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00 Pilsen, Czech Republic
- Laboratory of Neurodegenerative Disorders, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00 Pilsen, Czech Republic
| | - Simona Benediktova
- Department of Pathological Physiology, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00 Pilsen, Czech Republic
| | - Filip Tichanek
- Department of Pathological Physiology, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00 Pilsen, Czech Republic
- Laboratory of Neurodegenerative Disorders, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00 Pilsen, Czech Republic
| | - Jan Jedlicka
- Department of Physiology, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00 Pilsen, Czech Republic
- Mitochondrial Laboratory, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00 Pilsen, Czech Republic
| | - Stepan Kapl
- Department of Pathological Physiology, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00 Pilsen, Czech Republic
- Laboratory of Experimental Neurophysiology, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00 Pilsen, Czech Republic
| | - Dana Jelinkova
- Department of Pathological Physiology, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00 Pilsen, Czech Republic
- Laboratory of Neurodegenerative Disorders, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00 Pilsen, Czech Republic
| | - Zdenka Purkartova
- Department of Pathological Physiology, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00 Pilsen, Czech Republic
| | - Jan Tuma
- Department of Pathological Physiology, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00 Pilsen, Czech Republic
| | - Jitka Kuncova
- Department of Physiology, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00 Pilsen, Czech Republic
- Mitochondrial Laboratory, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00 Pilsen, Czech Republic
| | - Jan Cendelin
- Department of Pathological Physiology, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00 Pilsen, Czech Republic
- Laboratory of Neurodegenerative Disorders, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, alej Svobody 76, 323 00 Pilsen, Czech Republic
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Epigenetic Changes in Prion and Prion-like Neurodegenerative Diseases: Recent Advances, Potential as Biomarkers, and Future Perspectives. Int J Mol Sci 2022; 23:ijms232012609. [PMID: 36293477 PMCID: PMC9604074 DOI: 10.3390/ijms232012609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/09/2022] [Accepted: 10/18/2022] [Indexed: 12/01/2022] Open
Abstract
Prion diseases are transmissible spongiform encephalopathies (TSEs) caused by a conformational conversion of the native cellular prion protein (PrPC) to an abnormal, infectious isoform called PrPSc. Amyotrophic lateral sclerosis, Alzheimer’s, Parkinson’s, and Huntington’s diseases are also known as prion-like diseases because they share common features with prion diseases, including protein misfolding and aggregation, as well as the spread of these misfolded proteins into different brain regions. Increasing evidence proposes the involvement of epigenetic mechanisms, namely DNA methylation, post-translational modifications of histones, and microRNA-mediated post-transcriptional gene regulation in the pathogenesis of prion-like diseases. Little is known about the role of epigenetic modifications in prion diseases, but recent findings also point to a potential regulatory role of epigenetic mechanisms in the pathology of these diseases. This review highlights recent findings on epigenetic modifications in TSEs and prion-like diseases and discusses the potential role of such mechanisms in disease pathology and their use as potential biomarkers.
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Barbé L, Finkbeiner S. Genetic and Epigenetic Interplay Define Disease Onset and Severity in Repeat Diseases. Front Aging Neurosci 2022; 14:750629. [PMID: 35592702 PMCID: PMC9110800 DOI: 10.3389/fnagi.2022.750629] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Repeat diseases, such as fragile X syndrome, myotonic dystrophy, Friedreich ataxia, Huntington disease, spinocerebellar ataxias, and some forms of amyotrophic lateral sclerosis, are caused by repetitive DNA sequences that are expanded in affected individuals. The age at which an individual begins to experience symptoms, and the severity of disease, are partially determined by the size of the repeat. However, the epigenetic state of the area in and around the repeat also plays an important role in determining the age of disease onset and the rate of disease progression. Many repeat diseases share a common epigenetic pattern of increased methylation at CpG islands near the repeat region. CpG islands are CG-rich sequences that are tightly regulated by methylation and are often found at gene enhancer or insulator elements in the genome. Methylation of CpG islands can inhibit binding of the transcriptional regulator CTCF, resulting in a closed chromatin state and gene down regulation. The downregulation of these genes leads to some disease-specific symptoms. Additionally, a genetic and epigenetic interplay is suggested by an effect of methylation on repeat instability, a hallmark of large repeat expansions that leads to increasing disease severity in successive generations. In this review, we will discuss the common epigenetic patterns shared across repeat diseases, how the genetics and epigenetics interact, and how this could be involved in disease manifestation. We also discuss the currently available stem cell and mouse models, which frequently do not recapitulate epigenetic patterns observed in human disease, and propose alternative strategies to study the role of epigenetics in repeat diseases.
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Affiliation(s)
- Lise Barbé
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Physiology, University of California, San Francisco, San Francisco, CA, United States
| | - Steve Finkbeiner
- Center for Systems and Therapeutics, Gladstone Institutes, San Francisco, CA, United States
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States
- Department of Physiology, University of California, San Francisco, San Francisco, CA, United States
- *Correspondence: Steve Finkbeiner,
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Pacetti M, De Conti L, Marasco LE, Romano M, Rashid MM, Nubiè M, Baralle FE, Baralle M. Physiological tissue-specific and age-related reduction of mouse TDP-43 levels is regulated by epigenetic modifications. Dis Model Mech 2022; 15:274621. [PMID: 35243489 PMCID: PMC9066495 DOI: 10.1242/dmm.049032] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 02/04/2022] [Indexed: 12/26/2022] Open
Abstract
The cellular level of TDP-43 (also known as TARDBP) is tightly regulated; increases or decreases in TDP-43 have deleterious effects in cells. The predominant mechanism responsible for the regulation of the level of TDP-43 is an autoregulatory negative feedback loop. In this study, we identified an in vivo cause-effect relationship between Tardbp gene promoter methylation and specific histone modification and the TDP-43 level in tissues of mice at two different ages. Furthermore, epigenetic control was observed in mouse and human cultured cell lines. In amyotrophic lateral sclerosis, the formation of TDP-43-containing brain inclusions removes functional protein from the system. This phenomenon is continuous but compensated by newly synthesized protein. The balance between sequestration and new synthesis might become critical with ageing, if accompanied by an epigenetic modification-regulated decrease in newly synthesized TDP-43. Sequestration by aggregates would then decrease the amount of functional TDP-43 to a level lower than those needed by the cell and thereby trigger the onset of symptoms. Summary: Identification of a cause-effect relationship between epigenetic modifications that occur on the promoter and histones of mouse TARDBP and the level of TDP-43 both in tissues and in cell culture.
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Affiliation(s)
- Miriam Pacetti
- RNA Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Laura De Conti
- RNA Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Luciano E Marasco
- Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CP1428 Buenos Aires, Argentina
| | - Maurizio Romano
- Department of Life Sciences, Via Valerio 28, University of Trieste, 34127 Trieste, Italy
| | - Mohammad M Rashid
- RNA Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Martina Nubiè
- RNA Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Francisco E Baralle
- Fondazione Italiana Fegato-Onlus, Bldg. Q, AREA Science Park, ss14, Km 163.5, Basovizza, 34149 Trieste, Italy
| | - Marco Baralle
- RNA Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
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6
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Espinosa-Espinosa J, González-Barriga A, López-Castel A, Artero R. Deciphering the Complex Molecular Pathogenesis of Myotonic Dystrophy Type 1 through Omics Studies. Int J Mol Sci 2022; 23:ijms23031441. [PMID: 35163365 PMCID: PMC8836095 DOI: 10.3390/ijms23031441] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 12/15/2022] Open
Abstract
Omics studies are crucial to improve our understanding of myotonic dystrophy type 1 (DM1), the most common muscular dystrophy in adults. Employing tissue samples and cell lines derived from patients and animal models, omics approaches have revealed the myriad alterations in gene and microRNA expression, alternative splicing, 3′ polyadenylation, CpG methylation, and proteins levels, among others, that contribute to this complex multisystem disease. In addition, omics characterization of drug candidate treatment experiments provides crucial insight into the degree of therapeutic rescue and off-target effects that can be achieved. Finally, several innovative technologies such as single-cell sequencing and artificial intelligence will have a significant impact on future DM1 research.
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Affiliation(s)
- Jorge Espinosa-Espinosa
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, 46100 Valencia, Spain; (J.E.-E.); (R.A.)
- Translational Genomics Group, Incliva Biomedical Research Institute, 46010 Valencia, Spain
| | - Anchel González-Barriga
- Centre de Recherche en Myologie, Inserm, Institut de Myologie, Sorbonne Université, 75013 Paris, France;
| | - Arturo López-Castel
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, 46100 Valencia, Spain; (J.E.-E.); (R.A.)
- Translational Genomics Group, Incliva Biomedical Research Institute, 46010 Valencia, Spain
- Correspondence: ; Tel.: +34-963543028
| | - Rubén Artero
- University Research Institute for Biotechnology and Biomedicine (BIOTECMED), Universidad de Valencia, 46100 Valencia, Spain; (J.E.-E.); (R.A.)
- Translational Genomics Group, Incliva Biomedical Research Institute, 46010 Valencia, Spain
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7
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Jin Y, Allen EG, Jin P. Cell-free DNA methylation as a potential biomarker in brain disorders. Epigenomics 2022; 14:369-374. [PMID: 35034473 PMCID: PMC9066291 DOI: 10.2217/epi-2021-0416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Yulin Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Emily G Allen
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
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Coppedè F. One-carbon epigenetics and redox biology of neurodegeneration. Free Radic Biol Med 2021; 170:19-33. [PMID: 33307166 DOI: 10.1016/j.freeradbiomed.2020.12.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/12/2022]
Abstract
One-carbon metabolism provides the methyl groups for both DNA and histone tail methylation reactions, two of the main epigenetic processes that tightly regulate the chromatin structure and gene expression levels. Several enzymes involved in one-carbon metabolism, as well as several epigenetic enzymes, are regulated by intracellular metabolites and redox cofactors, but their expression levels are in turn regulated by epigenetic modifications, in such a way that metabolism and gene expression reciprocally regulate each other to maintain homeostasis and regulate cell growth, survival, differentiation and response to environmental stimuli. Increasing evidence highlights the contribution of impaired one-carbon metabolism and epigenetic modifications in neurodegeneration. This article provides an overview of DNA and histone tail methylation changes in major neurodegenerative disorders, namely Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis, discussing the contribution of oxidative stress and impaired one-carbon and redox metabolism to their onset and progression.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Via Roma 55, 56126, Pisa, Italy.
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9
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Robichaud PP, Arseneault M, O'Connell C, Ouellette RJ, Morin PJ. Circulating cell-free DNA as potential diagnostic tools for amyotrophic lateral sclerosis. Neurosci Lett 2021; 750:135813. [PMID: 33705931 DOI: 10.1016/j.neulet.2021.135813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/24/2021] [Accepted: 03/04/2021] [Indexed: 12/13/2022]
Abstract
DNA methylation has garnered much attention in recent years for its diagnostic potential in multiple conditions including cancer and neurodegenerative diseases. Conversely, advances regarding the potential diagnostic relevance of DNA methylation status have been sparse in the field of amyotrophic lateral sclerosis (ALS) even though patients diagnosed with this condition would significantly benefit from improved molecular assays aimed at furthering the current diagnostic and therapeutic options available. This review will provide an overview of the current diagnostic approaches available for ALS diagnosis and discuss the potential clinical usefulness of DNA methylation. We will also present examples of DNA methylation as a diagnostic tool in various types of cancer and neurodegenerative conditions and expand on how circulating cfDNA methylation may be leveraged for the early detection of ALS. In general, this article will reinforce the importance of cfDNA methylation as diagnostic tools and will further highlight its clinical relevance for persons diagnosed with ALS.
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Affiliation(s)
- Philippe-Pierre Robichaud
- Vitalité Health Network, Dr. Georges-L.-Dumont University Hospital Centre, Department of Genetic Services, 330 Université Ave, Moncton, New Brunswick, E1C 2Z3, Canada; Atlantic Cancer Research Institute, Pavillon Hôtel-Dieu, 35 Providence Street, Moncton, New Brunswick, E1C 8X3, Canada; Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada
| | - Michael Arseneault
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada
| | - Colleen O'Connell
- Stan Cassidy Centre for Rehabilitation, 800 Priestman Street, Fredericton, New Brunswick, E3B 0C7, Canada
| | - Rodney J Ouellette
- Atlantic Cancer Research Institute, Pavillon Hôtel-Dieu, 35 Providence Street, Moncton, New Brunswick, E1C 8X3, Canada
| | - Pier Jr Morin
- Department of Chemistry and Biochemistry, Université de Moncton, 18 Antonine-Maillet Avenue, Moncton, New Brunswick, E1A 3E9, Canada.
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Abstract
Neuromuscular disorders are a heterogeneous group of conditions affecting the neuromuscular system. The aim of this article is to review the major epigenetic findings in motor neuron diseases and major hereditary muscular dystrophies. DNA methylation changes are observed in both hereditary and sporadic forms, and combining DNA methylation analysis with mutational screening holds the potential for better diagnostic and prognostic accuracy. Novel, less toxic and more selective epigenetic drugs are designed and tested in animal and cell culture models of neuromuscular disorders, and non-coding RNAs are being investigated as either disease biomarkers or targets of therapeutic approaches to restore gene expression levels. Overall, neuromuscular disorder epigenetic biomarkers have a strong potential for clinical applications in the near future.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research & of New Surgical & Medical Technologies, University of Pisa, Via Roma 55, 56126 Pisa, Italy
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11
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Armstrong MJ, Jin Y, Allen EG, Jin P. Diverse and dynamic DNA modifications in brain and diseases. Hum Mol Genet 2020; 28:R241-R253. [PMID: 31348493 DOI: 10.1093/hmg/ddz179] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 12/17/2022] Open
Abstract
DNA methylation is a class of epigenetic modification essential for coordinating gene expression timing and magnitude throughout normal brain development and for proper brain function following development. Aberrant methylation changes are associated with changes in chromatin architecture, transcriptional alterations and a host of neurological disorders and diseases. This review highlights recent advances in our understanding of the methylome's functionality and covers potential new roles for DNA methylation, their readers, writers, and erasers. Additionally, we examine novel insights into the relationship between the methylome, DNA-protein interactions, and their contribution to neurodegenerative diseases. Lastly, we outline the gaps in our knowledge that will likely be filled through the widespread use of newer technologies that provide greater resolution into how individual cell types are affected by disease and the contribution of each individual modification site to disease pathogenicity.
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Affiliation(s)
- Matthew J Armstrong
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Yulin Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Emily G Allen
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
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Tunca C, Şeker T, Akçimen F, Coşkun C, Bayraktar E, Palvadeau R, Zor S, Koçoğlu C, Kartal E, Şen NE, Hamzeiy H, Özoğuz Erimiş A, Norman U, Karakahya O, Olgun G, Akgün T, Durmuş H, Şahin E, Çakar A, Başar Gürsoy E, Babacan Yıldız G, İşak B, Uluç K, Hanağası H, Bilgiç B, Turgut N, Aysal F, Ertaş M, Boz C, Kotan D, İdrisoğlu H, Soysal A, Uzun Adatepe N, Akalın MA, Koç F, Tan E, Oflazer P, Deymeer F, Taştan Ö, Çiçek AE, Kavak E, Parman Y, Başak AN. Revisiting the complex architecture of ALS in Turkey: Expanding genotypes, shared phenotypes, molecular networks, and a public variant database. Hum Mutat 2020; 41:e7-e45. [PMID: 32579787 DOI: 10.1002/humu.24055] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/05/2020] [Accepted: 05/18/2020] [Indexed: 12/11/2022]
Abstract
The last decade has proven that amyotrophic lateral sclerosis (ALS) is clinically and genetically heterogeneous, and that the genetic component in sporadic cases might be stronger than expected. This study investigates 1,200 patients to revisit ALS in the ethnically heterogeneous yet inbred Turkish population. Familial ALS (fALS) accounts for 20% of our cases. The rates of consanguinity are 30% in fALS and 23% in sporadic ALS (sALS). Major ALS genes explained the disease cause in only 35% of fALS, as compared with ~70% in Europe and North America. Whole exome sequencing resulted in a discovery rate of 42% (53/127). Whole genome analyses in 623 sALS cases and 142 population controls, sequenced within Project MinE, revealed well-established fALS gene variants, solidifying the concept of incomplete penetrance in ALS. Genome-wide association studies (GWAS) with whole genome sequencing data did not indicate a new risk locus. Coupling GWAS with a coexpression network of disease-associated candidates, points to a significant enrichment for cell cycle- and division-related genes. Within this network, literature text-mining highlights DECR1, ATL1, HDAC2, GEMIN4, and HNRNPA3 as important genes. Finally, information on ALS-related gene variants in the Turkish cohort sequenced within Project MinE was compiled in the GeNDAL variant browser (www.gendal.org).
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Affiliation(s)
- Ceren Tunca
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Research Center for Translational Medicine (KUTTAM), Koç University School of Medicine, Istanbul, Turkey.,Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Tuncay Şeker
- Genomize Inc., Boğaziçi University Technology Development Region, Istanbul, Turkey
| | - Fulya Akçimen
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Cemre Coşkun
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Elif Bayraktar
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Research Center for Translational Medicine (KUTTAM), Koç University School of Medicine, Istanbul, Turkey
| | - Robin Palvadeau
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Research Center for Translational Medicine (KUTTAM), Koç University School of Medicine, Istanbul, Turkey
| | - Seyit Zor
- Genomize Inc., Boğaziçi University Technology Development Region, Istanbul, Turkey
| | - Cemile Koçoğlu
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Ece Kartal
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Nesli Ece Şen
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Hamid Hamzeiy
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Aslıhan Özoğuz Erimiş
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Utku Norman
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Oğuzhan Karakahya
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Gülden Olgun
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Tahsin Akgün
- Department of Anesthesiology and Reanimation, American Hospital, Istanbul, Turkey
| | - Hacer Durmuş
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Erdi Şahin
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Arman Çakar
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Esra Başar Gürsoy
- Department of Neurology, Faculty of Medicine, Bezmialem Vakıf University, Istanbul, Turkey
| | - Gülsen Babacan Yıldız
- Department of Neurology, Faculty of Medicine, Bezmialem Vakıf University, Istanbul, Turkey
| | - Barış İşak
- Department of Neurology, Marmara University School of Medicine, Istanbul, Turkey
| | - Kayıhan Uluç
- Department of Neurology, Marmara University School of Medicine, Istanbul, Turkey
| | - Haşmet Hanağası
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Başar Bilgiç
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Nilda Turgut
- Department of Neurology, Namık Kemal University School of Medicine, Tekirdağ, Turkey
| | - Fikret Aysal
- Department of Neurology, Medipol University School of Medicine, Istanbul, Turkey
| | - Mustafa Ertaş
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Cavit Boz
- Department of Neurology, Karadeniz Technical University School of Medicine, Trabzon, Turkey
| | - Dilcan Kotan
- Department of Neurology, Faculty of Medicine, Sakarya University, Sakarya, Turkey
| | - Halil İdrisoğlu
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Aysun Soysal
- Department of Neurology, Bakırköy Research and Training Hospital for Neurologic and Psychiatric Diseases, Istanbul, Turkey
| | - Nurten Uzun Adatepe
- Department of Neurology, Cerrahpaşa Medical School, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Mehmet Ali Akalın
- Department of Neurology, Cerrahpaşa Medical School, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Filiz Koç
- Department of Neurology, Çukurova University Medical School, Adana, Turkey
| | - Ersin Tan
- Department of Neurology, Hacettepe University Medical School, Ankara, Turkey
| | - Piraye Oflazer
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Feza Deymeer
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - Öznur Taştan
- Department of Computer Science and Engineering, Sabancı University, Istanbul, Turkey
| | - A Ercüment Çiçek
- Department of Computer Engineering, Bilkent University, Ankara, Turkey.,Department of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Erşen Kavak
- Genomize Inc., Boğaziçi University Technology Development Region, Istanbul, Turkey
| | - Yeşim Parman
- Department of Neurology, Istanbul Medical School, Istanbul University, Istanbul, Turkey
| | - A Nazlı Başak
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Research Center for Translational Medicine (KUTTAM), Koç University School of Medicine, Istanbul, Turkey.,Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
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13
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Egorova PA, Bezprozvanny IB. Molecular Mechanisms and Therapeutics for Spinocerebellar Ataxia Type 2. Neurotherapeutics 2019; 16:1050-1073. [PMID: 31435879 PMCID: PMC6985344 DOI: 10.1007/s13311-019-00777-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The effective therapeutic treatment and the disease-modifying therapy for spinocerebellar ataxia type 2 (SCA2) (a progressive hereditary disease caused by an expansion of polyglutamine in the ataxin-2 protein) is not available yet. At present, only symptomatic treatment and methods of palliative care are prescribed to the patients. Many attempts were made to study the physiological, molecular, and biochemical changes in SCA2 patients and in a variety of the model systems to find new therapeutic targets for SCA2 treatment. A better understanding of the uncovered molecular mechanisms of the disease allowed the scientific community to develop strategies of potential therapy and helped to create some promising therapeutic approaches for SCA2 treatment. Recent progress in this field will be discussed in this review article.
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Affiliation(s)
- Polina A Egorova
- Laboratory of Molecular Neurodegeneration, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, 195251, Russia
| | - Ilya B Bezprozvanny
- Laboratory of Molecular Neurodegeneration, Peter the Great St.Petersburg Polytechnic University, St. Petersburg, 195251, Russia.
- Department of Physiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, ND12.200, Dallas, Texas, 75390, USA.
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14
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Cheon H, Paik JH, Choi M, Yang HJ, Son JH. Detection and manipulation of methylation in blood cancer DNA using terahertz radiation. Sci Rep 2019; 9:6413. [PMID: 31015556 PMCID: PMC6478716 DOI: 10.1038/s41598-019-42855-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 04/10/2019] [Indexed: 12/14/2022] Open
Abstract
DNA methylation is a pivotal epigenetic modification of DNA that regulates gene expression. Abnormal regulation of gene expression is closely related to carcinogenesis, which is why the assessment of DNA methylation is a key factor in cancer research. Terahertz radiation may play an important role in active demethylation for cancer therapy because the characteristic frequency of the methylated DNA exists in the terahertz region. Here, we present a novel technique for the detection and manipulation of DNA methylation using terahertz radiation in blood cancer cell lines. We observed the degree of DNA methylation in blood cancer at the characteristic resonance of approximately 1.7 THz using terahertz time-domain spectroscopy. The terahertz results were cross-checked with global DNA methylation quantification using an enzyme-linked immunosorbent assay. We also achieved the demethylation of cancer DNA using high-power terahertz radiation at the 1.7-THz resonance. The demethylation degrees ranged from 10% to 70%, depending on the type of cancer cell line. Our results show the detection of DNA methylation based on the terahertz molecular resonance and the manipulation of global DNA methylation using high-power terahertz radiation. Terahertz radiation may have potential applications as an epigenetic inhibitor in cancer treatment, by virtue of its ability to induce DNA demethylation, similarly to decitabine.
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Affiliation(s)
- Hwayeong Cheon
- Department of Physics, University of Seoul, Seoul, 02504, Republic of Korea
| | - Jin Ho Paik
- Department of Pathology, Seoul National University Bundang Hospital, Seong-Nam, 13620, Republic of Korea
| | - Moran Choi
- Department of Neurosurgery, SMG-SNU Boramae Medical Centre, Seoul, 07061, Republic of Korea
| | - Hee-Jin Yang
- Department of Neurosurgery, SMG-SNU Boramae Medical Centre, Seoul, 07061, Republic of Korea.
| | - Joo-Hiuk Son
- Department of Physics, University of Seoul, Seoul, 02504, Republic of Korea.
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15
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Pereira GC, Sanchez L, Schaughency PM, Rubio-Roldán A, Choi JA, Planet E, Batra R, Turelli P, Trono D, Ostrow LW, Ravits J, Kazazian HH, Wheelan SJ, Heras SR, Mayer J, García-Pérez JL, Goodier JL. Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis. Mob DNA 2018; 9:35. [PMID: 30564290 PMCID: PMC6295051 DOI: 10.1186/s13100-018-0138-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/15/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease involving loss of motor neurons and having no known cure and uncertain etiology. Several studies have drawn connections between altered retrotransposon expression and ALS. Certain features of the LINE-1 (L1) retrotransposon-encoded ORF1 protein (ORF1p) are analogous to those of neurodegeneration-associated RNA-binding proteins, including formation of cytoplasmic aggregates. In this study we explore these features and consider possible links between L1 expression and ALS. RESULTS We first considered factors that modulate aggregation and subcellular distribution of LINE-1 ORF1p, including nuclear localization. Changes to some ORF1p amino acid residues alter both retrotransposition efficiency and protein aggregation dynamics, and we found that one such polymorphism is present in endogenous L1s abundant in the human genome. We failed, however, to identify CRM1-mediated nuclear export signals in ORF1p nor strict involvement of cell cycle in endogenous ORF1p nuclear localization in human 2102Ep germline teratocarcinoma cells. Some proteins linked with ALS bind and colocalize with L1 ORF1p ribonucleoprotein particles in cytoplasmic RNA granules. Increased expression of several ALS-associated proteins, including TAR DNA Binding Protein (TDP-43), strongly limits cell culture retrotransposition, while some disease-related mutations modify these effects. Using quantitative reverse transcription PCR (RT-qPCR) of ALS tissues and reanalysis of publicly available RNA-Seq datasets, we asked if changes in expression of retrotransposons are associated with ALS. We found minimal altered expression in sporadic ALS tissues but confirmed a previous report of differential expression of many repeat subfamilies in C9orf72 gene-mutated ALS patients. CONCLUSIONS Here we extended understanding of the subcellular localization dynamics of the aggregation-prone LINE-1 ORF1p RNA-binding protein. However, we failed to find compelling evidence for misregulation of LINE-1 retrotransposons in sporadic ALS nor a clear effect of ALS-associated TDP-43 protein on L1 expression. In sum, our study reveals that the interplay of active retrotransposons and the molecular features of ALS are more complex than anticipated. Thus, the potential consequences of altered retrotransposon activity for ALS and other neurodegenerative disorders are worthy of continued investigation.
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Affiliation(s)
- Gavin C. Pereira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Laura Sanchez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Paul M. Schaughency
- Oncology Center-Cancer Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Alejandro Rubio-Roldán
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Jungbin A. Choi
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Evarist Planet
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ranjan Batra
- Department of Neurosciences, School of Medicine, University of California at San Diego, San Diego, California USA
| | - Priscilla Turelli
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Lyle W. Ostrow
- Neuromuscular Division, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - John Ravits
- Department of Neurosciences, School of Medicine, University of California at San Diego, San Diego, California USA
| | - Haig H. Kazazian
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Sarah J. Wheelan
- Oncology Center-Cancer Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Sara R. Heras
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Jens Mayer
- Department of Human Genetics, Medical Faculty, University of Saarland, Homburg/Saar, Germany
| | - Jose Luis García-Pérez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - John L. Goodier
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
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16
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Yau WY, O'Connor E, Sullivan R, Akijian L, Wood NW. DNA repair in trinucleotide repeat ataxias. FEBS J 2018; 285:3669-3682. [PMID: 30152109 DOI: 10.1111/febs.14644] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/15/2018] [Accepted: 08/23/2018] [Indexed: 12/21/2022]
Abstract
The inherited cerebellar ataxias comprise of a genetic heterogeneous group of disorders. Pathogenic expansions of cytosine-adenine-guanine (CAG) encoding polyglutamine tracts account for the largest proportion of autosomal dominant cerebellar ataxias, while GAA expansion in the first introns of frataxin gene is the commonest cause of autosomal recessive cerebellar ataxias. Currently, there is no available treatment to alter the disease trajectory, with devastating consequences for affected individuals. Inter- and Intrafamily phenotypic variability suggest the existence of genetic modifiers, which may become targets amendable to treatment. Recent studies have demonstrated the importance of DNA repair pathways in modifying spinocerebellar ataxia with CAG repeat expansions. In this review, we discuss the mechanisms in which DNA repair pathways, epigenetics and other genetic factors may act as modifiers in cerebellar ataxias due to trinucleotide repeat expansions.
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Affiliation(s)
- Wai Yan Yau
- Department of Molecular Neuroscience, Institute of Neurology, University College London, UK
| | - Emer O'Connor
- Department of Molecular Neuroscience, Institute of Neurology, University College London, UK
| | - Roisin Sullivan
- Department of Molecular Neuroscience, Institute of Neurology, University College London, UK
| | - Layan Akijian
- Department of Neurology, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Nicholas W Wood
- Department of Molecular Neuroscience, Institute of Neurology, University College London, UK.,Neurogenetics laboratory, The National Hospital for Neurology and Neurosurgery, London, UK
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17
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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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18
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Stoccoro A, Mosca L, Carnicelli V, Cavallari U, Lunetta C, Marocchi A, Migliore L, Coppedè F. Mitochondrial DNA copy number and D-loop region methylation in carriers of amyotrophic lateral sclerosis gene mutations. Epigenomics 2018; 10:1431-1443. [PMID: 30088417 DOI: 10.2217/epi-2018-0072] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AIM To investigate mitochondrial DNA (mtDNA) copy number and D-loop region methylation in carriers of SOD1, TARDBP, FUS and C9orf72 mutations. METHODS Investigations were performed in blood DNA from 114 individuals, including amyotrophic lateral sclerosis (ALS) patients, presymptomatic carriers and noncarrier family members. RESULTS Increased mtDNA copy number (p = 0.0001) was observed in ALS patients, and particularly in those with SOD1 or C9orf72 mutations. SOD1 mutation carriers showed also a significant decrease in D-loop methylation levels (p = 0.003). An inverse correlation between D-loop methylation levels and the mtDNA copy number (p = 0.0005) was observed. CONCLUSION Demethylation of the D-loop region could represent a compensatory mechanism for mtDNA upregulation in carriers of ALS-linked SOD1 mutations.
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Affiliation(s)
- Andrea Stoccoro
- Department of Translational Research & New Technologies in Medicine & Surgery, Medical Genetics Laboratory, University of Pisa, Pisa, Italy.,Doctoral School in Genetics Oncology & Clinical Medicine, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Lorena Mosca
- Medical Genetics Unit, Department of Laboratory Medicine, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Vittoria Carnicelli
- Department of Surgical, Medical & Molecular Pathology & Critical Care Medicine, University of Pisa, Pisa, Italy
| | - Ugo Cavallari
- Medical Genetics Unit, Department of Laboratory Medicine, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Christian Lunetta
- NEuroMuscular Omnicentre (NEMO), ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Alessandro Marocchi
- Medical Genetics Unit, Department of Laboratory Medicine, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Lucia Migliore
- Department of Translational Research & New Technologies in Medicine & Surgery, Medical Genetics Laboratory, University of Pisa, Pisa, Italy
| | - Fabio Coppedè
- Department of Translational Research & New Technologies in Medicine & Surgery, Medical Genetics Laboratory, University of Pisa, Pisa, Italy
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19
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Mayer J, Harz C, Sanchez L, Pereira GC, Maldener E, Heras SR, Ostrow LW, Ravits J, Batra R, Meese E, García-Pérez JL, Goodier JL. Transcriptional profiling of HERV-K(HML-2) in amyotrophic lateral sclerosis and potential implications for expression of HML-2 proteins. Mol Neurodegener 2018; 13:39. [PMID: 30068350 PMCID: PMC6091006 DOI: 10.1186/s13024-018-0275-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 07/23/2018] [Indexed: 12/12/2022] Open
Abstract
Background Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder. About 90% of ALS cases are without a known genetic cause. The human endogenous retrovirus multi-copy HERV-K(HML-2) group was recently reported to potentially contribute to neurodegeneration and disease pathogenesis in ALS because of transcriptional upregulation and toxic effects of HML-2 Envelope (Env) protein. Env and other proteins are encoded by some transcriptionally active HML-2 loci. However, more detailed information is required regarding which HML-2 loci are transcribed in ALS, which of their proteins are expressed, and differences between the disease and non-disease states. Methods For brain and spinal cord tissue samples from ALS patients and controls, we identified transcribed HML-2 loci by generating and mapping HML-2-specific cDNA sequences. We predicted expression of HML-2 env gene-derived proteins based on the observed cDNA sequences. Furthermore, we determined overall HML-2 transcript levels by RT-qPCR and investigated presence of HML-2 Env protein in ALS and control tissue samples by Western blotting. Results We identified 24 different transcribed HML-2 loci. Some of those loci are transcribed at relatively high levels. However, significant differences in HML-2 loci transcriptional activities were not seen when comparing ALS and controls. Likewise, overall HML-2 transcript levels, as determined by RT-qPCR, were not significantly different between ALS and controls. Indeed, we were unable to detect full-length HML-2 Env protein in ALS and control tissue samples despite reasonable sensitivity. Rather our analyses suggest that a number of HML-2 protein variants other than full-length Env may potentially be expressed in ALS patients. Conclusions Our results expand and refine recent publications on HERV-K(HML-2) and ALS. Some of our results are in conflict with recent findings and call for further specific analyses. Our profiling of HML-2 transcription in ALS opens up the possibility that HML-2 proteins other than canonical full-length Env may have to be considered when studying the role of HML-2 in ALS disease. Electronic supplementary material The online version of this article (10.1186/s13024-018-0275-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jens Mayer
- Department of Human Genetics, University of Saarland, Homburg, Germany.
| | - Christian Harz
- Department of Human Genetics, University of Saarland, Homburg, Germany
| | - Laura Sanchez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Gavin C Pereira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Esther Maldener
- Department of Human Genetics, University of Saarland, Homburg, Germany
| | - Sara R Heras
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain.,Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18071, Granada, Spain
| | - Lyle W Ostrow
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 28217, USA
| | - John Ravits
- Department of Neurosciences, School of Medicine, UCSD, San Diego, CA, USA
| | - Ranjan Batra
- Department of Neurosciences, School of Medicine, UCSD, San Diego, CA, USA
| | - Eckart Meese
- Department of Human Genetics, University of Saarland, Homburg, Germany
| | - Jose Luis García-Pérez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - John L Goodier
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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