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Cacabelos R, Torrellas C. Epigenetics of Aging and Alzheimer's Disease: Implications for Pharmacogenomics and Drug Response. Int J Mol Sci 2015; 16:30483-543. [PMID: 26703582 PMCID: PMC4691177 DOI: 10.3390/ijms161226236] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/16/2015] [Accepted: 12/08/2015] [Indexed: 02/07/2023] Open
Abstract
Epigenetic variability (DNA methylation/demethylation, histone modifications, microRNA regulation) is common in physiological and pathological conditions. Epigenetic alterations are present in different tissues along the aging process and in neurodegenerative disorders, such as Alzheimer’s disease (AD). Epigenetics affect life span and longevity. AD-related genes exhibit epigenetic changes, indicating that epigenetics might exert a pathogenic role in dementia. Epigenetic modifications are reversible and can potentially be targeted by pharmacological intervention. Epigenetic drugs may be useful for the treatment of major problems of health (e.g., cancer, cardiovascular disorders, brain disorders). The efficacy and safety of these and other medications depend upon the efficiency of the pharmacogenetic process in which different clusters of genes (pathogenic, mechanistic, metabolic, transporter, pleiotropic) are involved. Most of these genes are also under the influence of the epigenetic machinery. The information available on the pharmacoepigenomics of most drugs is very limited; however, growing evidence indicates that epigenetic changes are determinant in the pathogenesis of many medical conditions and in drug response and drug resistance. Consequently, pharmacoepigenetic studies should be incorporated in drug development and personalized treatments.
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Affiliation(s)
- Ramón Cacabelos
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165-Bergondo, Corunna, Spain.
- Chair of Genomic Medicine, Camilo José Cela University, 28692-Madrid, Spain.
| | - Clara Torrellas
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165-Bergondo, Corunna, Spain.
- Chair of Genomic Medicine, Camilo José Cela University, 28692-Madrid, Spain.
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Dong X, Tsuji J, Labadorf A, Roussos P, Chen JF, Myers RH, Akbarian S, Weng Z. The Role of H3K4me3 in Transcriptional Regulation Is Altered in Huntington's Disease. PLoS One 2015; 10:e0144398. [PMID: 26636336 PMCID: PMC4670094 DOI: 10.1371/journal.pone.0144398] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/17/2015] [Indexed: 01/22/2023] Open
Abstract
Huntington's disease (HD) is an autosomal-dominant neurodegenerative disorder resulting from expansion of CAG repeats in the Huntingtin (HTT) gene. Previous studies have shown mutant HTT can alter expression of genes associated with dysregulated epigenetic modifications. One of the most widely studied chromatin modifications is trimethylated lysine 4 of histone 3 (H3K4me3). Here, we conducted the first comprehensive study of H3K4me3 ChIP-sequencing in neuronal chromatin from the prefrontal cortex of six HD cases and six non-neurologic controls, and its association with gene expression measured by RNA-sequencing. We detected 2,830 differentially enriched H3K4me3 peaks between HD and controls, with 55% of them down-regulated in HD. Although H3K4me3 signals are expected to be associated with mRNA levels, we found an unexpected discordance between altered H3K4me3 peaks and mRNA levels. Gene ontology (GO) term enrichment analysis of the genes with differential H3K4me3 peaks, revealed statistically significantly enriched GO terms only in the genes with down-regulated signals in HD. The most frequently implicated biological process terms are organ morphogenesis and positive regulation of gene expression. More than 9,000 H3K4me3 peaks were located not near any recognized transcription start sites and approximately 36% of these "distal" peaks co-localized to known enhancer sites. Six transcription factors and chromatin remodelers are differentially enriched in HD H3K4me3 distal peaks, including EZH2 and SUZ12, two core subunits of the polycomb repressive complex 2 (PRC2). Moreover, PRC2 repressive state was significantly depleted in HD-enriched peaks, suggesting the epigenetic role of PRC2 inhibition associated with up-regulated H3K4me3 in Huntington's disease. In summary, our study provides new insights into transcriptional dysregulation of Huntington's disease by analyzing the differentiation of H3K4me3 enrichment.
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Affiliation(s)
- Xianjun Dong
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Junko Tsuji
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Adam Labadorf
- Department of Neurology, Boston University School of Medicine, Boston, MA, United States of America
- Bioinformatics Program, Boston University, Boston, MA, United States of America
| | - Panos Roussos
- Friedman Brain Institute, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, United States of America
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY, United States of America
| | - Jiang-Fan Chen
- Department of Neurology, Boston University School of Medicine, Boston, MA, United States of America
| | - Richard H Myers
- Department of Neurology, Boston University School of Medicine, Boston, MA, United States of America
- Bioinformatics Program, Boston University, Boston, MA, United States of America
- Genome Science Institute, Boston University School of Medicine, Boston, MA, United States of America
| | - Schahram Akbarian
- Friedman Brain Institute, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, United States of America
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, United States of America
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53
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Mir AR, Moinuddin. Glycoxidation of histone proteins in autoimmune disorders. Clin Chim Acta 2015; 450:25-30. [DOI: 10.1016/j.cca.2015.07.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/26/2015] [Accepted: 07/28/2015] [Indexed: 01/08/2023]
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Lardenoije R, Iatrou A, Kenis G, Kompotis K, Steinbusch HWM, Mastroeni D, Coleman P, Lemere CA, Hof PR, van den Hove DLA, Rutten BPF. The epigenetics of aging and neurodegeneration. Prog Neurobiol 2015; 131:21-64. [PMID: 26072273 PMCID: PMC6477921 DOI: 10.1016/j.pneurobio.2015.05.002] [Citation(s) in RCA: 246] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 05/13/2015] [Accepted: 05/13/2015] [Indexed: 12/14/2022]
Abstract
Epigenetics is a quickly growing field encompassing mechanisms regulating gene expression that do not involve changes in the genotype. Epigenetics is of increasing relevance to neuroscience, with epigenetic mechanisms being implicated in brain development and neuronal differentiation, as well as in more dynamic processes related to cognition. Epigenetic regulation covers multiple levels of gene expression; from direct modifications of the DNA and histone tails, regulating the level of transcription, to interactions with messenger RNAs, regulating the level of translation. Importantly, epigenetic dysregulation currently garners much attention as a pivotal player in aging and age-related neurodegenerative disorders, such as Alzheimer's disease, Parkinson's disease, and Huntington's disease, where it may mediate interactions between genetic and environmental risk factors, or directly interact with disease-specific pathological factors. We review current knowledge about the major epigenetic mechanisms, including DNA methylation and DNA demethylation, chromatin remodeling and non-coding RNAs, as well as the involvement of these mechanisms in normal aging and in the pathophysiology of the most common neurodegenerative diseases. Additionally, we examine the current state of epigenetics-based therapeutic strategies for these diseases, which either aim to restore the epigenetic homeostasis or skew it to a favorable direction to counter disease pathology. Finally, methodological challenges of epigenetic investigations and future perspectives are discussed.
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Affiliation(s)
- Roy Lardenoije
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands
| | - Artemis Iatrou
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands
| | - Gunter Kenis
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands
| | - Konstantinos Kompotis
- Center for Integrative Genomics, University of Lausanne, Genopode Building, 1015 Lausanne-Dorigny, Switzerland
| | - Harry W M Steinbusch
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands
| | - Diego Mastroeni
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands; L.J. Roberts Alzheimer's Disease Center, Banner Sun Health Research Institute, 10515 W. Santa Fe Drive, Sun City, AZ 85351, USA
| | - Paul Coleman
- L.J. Roberts Alzheimer's Disease Center, Banner Sun Health Research Institute, 10515 W. Santa Fe Drive, Sun City, AZ 85351, USA
| | - Cynthia A Lemere
- Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Patrick R Hof
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Daniel L A van den Hove
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands; Laboratory of Translational Neuroscience, Department of Psychiatry, Psychosomatics and Psychotherapy, University of Wuerzburg, Fuechsleinstrasse 15, 97080 Wuerzburg, Germany
| | - Bart P F Rutten
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands.
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Insects as models to study the epigenetic basis of disease. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 118:69-78. [DOI: 10.1016/j.pbiomolbio.2015.02.009] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 01/06/2015] [Accepted: 02/23/2015] [Indexed: 12/17/2022]
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Rosser A, Svendsen CN. Stem cells for cell replacement therapy: a therapeutic strategy for HD? Mov Disord 2015; 29:1446-54. [PMID: 25216372 DOI: 10.1002/mds.26026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/20/2014] [Accepted: 08/20/2014] [Indexed: 12/17/2022] Open
Abstract
Much interest has been expressed over the last couple of decades in the potential application of stem cells to medicine, both for research and diagnostic tools and as a source of donor cells for therapeutic purposes. Potential therapeutic applications include replacement of cells in many body organs where the capacity for intrinsic repair is limited, including the pancreas, heart, and brain. A key challenge is to generate the relevant donor cell types, and this is particularly challenging in the brain where the number of different neuronal subtypes is so great. Although dopamine neuron replacement in Parkinson's disease has been the focus of most clinical studies, great interest has been shown in this approach for other disorders, including Huntington's disease. Replacing complete neural circuits in the adult brain is clearly challenging, and there are many other complexities with regard to both donor cells and host. This article presents the pros and cons of taking a cell therapy approach in Huntington's disease. It considers the implantation both of cells that are already of the same neural subtype as those lost in the disease process (ie, primary fetal cells derived from the developing striatum) and those derived from stem cells, which require "directing" toward that phenotype.
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Affiliation(s)
- Anne Rosser
- Cardiff Brain Repair Group, Schools of Medicine and Biosciences, The Sir Martin Evans Building, Museum Avenue, Cardiff, United Kingdom
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Cacabelos R. Epigenomic networking in drug development: from pathogenic mechanisms to pharmacogenomics. Drug Dev Res 2015; 75:348-65. [PMID: 25195579 DOI: 10.1002/ddr.21219] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Different epigenetic alterations (DNA methylation, histone modifications, chromatin remodeling, noncoding RNA dysregulation) are associated with the phenotypic expression of complex disorders in which genomic, epigenomic, proteomic, and metabolomic changes, in conjunction with environmental factors, are involved. As epigenetic modifications are reversible and can be potentially targeted by pharmacological and dietary interventions, a series of epigenetic drugs have been developed, including DNA methyltransferase inhibitors (nucleoside analogs, small molecules, bioproducts, antisense oligonucleotides, miRNAs), histone deacetylase inhibitors (short-chain fatty acids, hydroxamic acids, cyclic peptides, benzamides, ketones, sirtuin inhibitors, sirtuin activators), histone acetyltransferase modulators, histone methyltransferase inhibitors, histone demethylase inhibitors, and noncoding RNAs (miRNAs), with potential effects against myelodysplastic syndromes, different types of cancer, and neurodegenerative disorders. Pharmacogenetic and pharmacoepigenetic studies are required for the proper evaluation of efficacy and safety issues in clinical trials with epigenetic drugs.
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Affiliation(s)
- Ramón Cacabelos
- Genomic Medicine, Camilo José Cela University, Madrid, 28692, Spain; EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, Corunna, 15165, Spain
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58
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Parlato R, Bierhoff H. Role of nucleolar dysfunction in neurodegenerative disorders: a game of genes? AIMS MOLECULAR SCIENCE 2015. [DOI: 10.3934/molsci.2015.3.211] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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Panegyres PK, Shu CC, Chen HY, Paulsen JS. Factors influencing the clinical expression of intermediate CAG repeat length mutations of the Huntington's disease gene. J Neurol 2014; 262:277-84. [PMID: 25380582 DOI: 10.1007/s00415-014-7559-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 02/07/2023]
Abstract
Our aim is to elucidate the clinical variables associated with the development of manifest HD in patients with intermediate CAG repeat lengths. 2,167 participants were seen throughout 44 research sites in the United States, Canada or Australia over a five-year natural history observational study (2006-2011) (Trial # NCT00313495). The Chi-square test and a generalised linear model were used to examine the differences in demographics and cognitive tests among three groups of CAG repeat length. The mixed model was then used to examine the time effect on cognitive assessments by CAG groups. No patient with CAG repeat length 27-35 developed manifest HD, whereas three patients with 36-39 did. Total motor score, maximal chorea score and maximal dystonia score were significantly different at baseline (p < 0.001) for each measure between those patients with a repeat length 27-35 versus those 36-39; as were total functional assessment, independence scale and total functional capacity (p < 0.001). Being aged 65 years or more (OR 5.81, 95 % CI 0.37-90.58, p = 0.02) and smoking (OR 13.99, 95 % CI 2.03-96.44, p = 0.007) were related to manifest HD in patients with CAG 36-39; those with an associated university degree or higher education were less frequently diagnosed as manifest HD (OR 0.10, 95 % CI 0.02-0.54, p = 0.007). Age, smoking and lower education achievement were found to be significantly associated with higher odds of manifest HD in patients with intermediate CAG repeat length mutations.
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Affiliation(s)
- Peter K Panegyres
- Neurodegenerative Disorders Research Pty Ltd, 4 Lawrence Avenue, 6005, West Perth, WA, Australia,
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60
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Zhan L, Huang C, Meng XM, Song Y, Wu XQ, Yang Y, Li J. Hypoxia-inducible factor-1alpha in hepatic fibrosis: A promising therapeutic target. Biochimie 2014; 108:1-7. [PMID: 25447141 DOI: 10.1016/j.biochi.2014.10.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 10/17/2014] [Indexed: 02/08/2023]
Abstract
Hypoxia-inducible factor-1alpha (HIF-1α) is a regulated subunit of the hypoxia-inducible factor 1 (HIF1), which functions as a key transcription factor in response to hypoxic stress by regulating genes involved in maintaining oxygen homeostasis. In recent years, a growing body of studies showed that HIF-1α was significantly increased in hepatic fibrotic tissues and activated hepatic stellate cells (HSCs). Furthermore, knockdown of HIF-1α expression inhibited the proliferation and activation of HSCs. In addition, HIF-1α-dependent genes and the extensive network of signaling cascades focus on HIF-1α have been reported to associate with the development of hepatic fibrosis, suggesting that HIF-1α might play a crucial role in hepatic fibrosis. However, the mechanisms by which HIF-1α regulates hepatic fibrosis are still undefined. In this review, we concentrate on multiple signaling pathways and genes related with HIF-1α which may be involved in the development of hepatic fibrosis, further discussing its potential as a novel therapeutic target for hepatic fibrosis.
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Affiliation(s)
- Lei Zhan
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China
| | - Cheng Huang
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China
| | - Xiao-Ming Meng
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China
| | - Yang Song
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China
| | - Xiao Qin Wu
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China
| | - Yang Yang
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China
| | - Jun Li
- School of Pharmacy, Anhui Medical University, Meishan Road, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (AMU), China.
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Basso M, Sleiman S, Ratan RR. Looking above but not beyond the genome for therapeutics in neurology and psychiatry: epigenetic proteins and RNAs find a new focus. Neurotherapeutics 2013; 10:551-5. [PMID: 24092616 PMCID: PMC3805863 DOI: 10.1007/s13311-013-0225-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Manuela Basso
- />Burke Medical Research Institute, Weill Medical College of Cornell University, 785 Mamaroneck Avenue, White Plains, New York, 10605 NY USA
- />Brain and Mind Research Institute, Weill Medical College of Cornell University, New York, NY USA
- />Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Sama Sleiman
- />Burke Medical Research Institute, Weill Medical College of Cornell University, 785 Mamaroneck Avenue, White Plains, New York, 10605 NY USA
- />Brain and Mind Research Institute, Weill Medical College of Cornell University, New York, NY USA
- />Molecular Neurobiology Program, Skirball Institute of Bimolecular Medicine, New York University School of Medicine, New York, NY USA
| | - Rajiv R. Ratan
- />Burke Medical Research Institute, Weill Medical College of Cornell University, 785 Mamaroneck Avenue, White Plains, New York, 10605 NY USA
- />Brain and Mind Research Institute, Weill Medical College of Cornell University, New York, NY USA
- />Department of Neurology, Weill Medical College of Cornell University, New York, NY USA
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