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Kong W, Li X, Guo X, Sun Y, Chai W, Chang Y, Huang Q, Wang P, Wang X. Ultrasound-Assisted CRISPRi-Exosome for Epigenetic Modification of α-Synuclein Gene in a Mouse Model of Parkinson's Disease. ACS NANO 2024; 18:7837-7851. [PMID: 38437635 DOI: 10.1021/acsnano.3c05864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Currently, there is a lack of effective treatment for Parkinson's disease (PD). In PD patients, aberrant methylation of SNCA (α-synuclein gene) has been reported and may be a potential therapeutic target. In this study, we established an epigenetic regulation platform based on an exosomal CRISPR intervention system. With the assist of focused ultrasound (FUS) opening the blood-brain barrier, engineered exosomes carrying RVG (rabies viral glycoprotein) targeting peptide, sgRNA (single guide RNA), and dCas9-DNMT3A (named RVG-CRISPRi-Exo) were efficiently delivered into the brain lesions and induced specific methylation of SNCA. In vivo, FUS combined with RVG-CRISPRi-Exo significantly improved motor performance, balance coordination, and neurosensitivity in PD mice, greatly down-regulated the elevation of α-synuclein (α-syn) caused by modeling, rescued cell apoptosis, and alleviated the progression of PD in mice. [18F]-FP-DTBZ imaging suggested that the synaptic function of the nigrostriatal pathway could be restored, which was conducive to the control of motor behavior in PD mice. Pyrosequencing results showed that RVG-CRISPRi-Exo could methylate CpG at specific sites of SNCA, and this fine-tuned editing achieved good therapeutic effects in PD model mice. In vitro, RVG-CRISPRi-Exo down-regulated SNCA transcripts and α-syn expression and relieved neuronal cell damage. Collectively, our findings provide a proof-of-principle for the development of targeted brain nanodelivery based on engineered exosomes and provide insights into epigenetic regulation of brain diseases.
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Affiliation(s)
- Weirong Kong
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, #620 West Chang'an Road, Xi'an 710119, China
| | - Xin Li
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, #620 West Chang'an Road, Xi'an 710119, China
| | - Xiaoyu Guo
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, #620 West Chang'an Road, Xi'an 710119, China
| | - Yue Sun
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, #620 West Chang'an Road, Xi'an 710119, China
| | - Wenyu Chai
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, #620 West Chang'an Road, Xi'an 710119, China
| | - Yawei Chang
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, #620 West Chang'an Road, Xi'an 710119, China
| | - Qichao Huang
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, #620 West Chang'an Road, Xi'an 710119, China
| | - Pan Wang
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, #620 West Chang'an Road, Xi'an 710119, China
| | - Xiaobing Wang
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, College of Life Sciences, Shaanxi Normal University, #620 West Chang'an Road, Xi'an 710119, China
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Gionco JT, Bernstein AI. Emerging Role of Environmental Epitranscriptomics and RNA Modifications in Parkinson's Disease. JOURNAL OF PARKINSON'S DISEASE 2024; 14:643-656. [PMID: 38578904 PMCID: PMC11191529 DOI: 10.3233/jpd-230457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/10/2024] [Indexed: 04/07/2024]
Abstract
Environmental risk factors and gene-environment interactions play a critical role in Parkinson's disease (PD). However, the relatively large contribution of environmental risk factors in the overwhelming majority of PD cases has been widely neglected in the field. A "PD prevention agenda" proposed in this journal laid out a set of research priorities focused on preventing PD through modification of environmental risk factors. This agenda includes a call for preclinical studies to employ new high-throughput methods for analyzing transcriptomics and epigenomics to provide a deeper understanding of the effects of exposures linked to PD. Here, we focus on epitranscriptomics as a novel area of research with the potential to add to our understanding of the interplay between genes and environmental exposures in PD. Both epigenetics and epitranscriptomics have been recognized as potential mediators of the complex relationship between genes, environment, and disease. Multiple studies have identified epigenetic alterations, such as DNA methylation, associated with PD and PD-related exposures in human studies and preclinical models. In addition, recent technological advancements have made it possible to study epitranscriptomic RNA modifications, such as RNA N6-methyladenosine (m6A), and a handful of recent studies have begun to explore epitranscriptomics in PD-relevant exposure models. Continued exploration of epitranscriptomic mechanisms in environmentally relevant PD models offers the opportunity to identify biomarkers, pre-degenerative changes that precede symptom onset, and potential mitigation strategies for disease prevention and treatment.
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Affiliation(s)
- John T. Gionco
- Graduate Program in Cell and Developmental Biology, Rutgers University, Piscataway, NJ, USA
| | - Alison I. Bernstein
- Department of Pharmacology and Toxicology, Rutgers University, Piscataway, NJ, USA
- Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, NJ, USA
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3
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Salas-Leal AC, Salas-Pacheco SM, Hernández-Cosaín EI, Vélez-Vélez LM, Antuna-Salcido EI, Castellanos-Juárez FX, Méndez-Hernández EM, Llave-León OL, Quiñones-Canales G, Arias-Carrión O, Sandoval-Carrillo AA, Salas-Pacheco JM. Differential expression of PSMC4, SKP1, and HSPA8 in Parkinson's disease: insights from a Mexican mestizo population. Front Mol Neurosci 2023; 16:1298560. [PMID: 38115821 PMCID: PMC10728481 DOI: 10.3389/fnmol.2023.1298560] [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: 09/21/2023] [Accepted: 11/13/2023] [Indexed: 12/21/2023] Open
Abstract
Parkinson's disease (PD) is a complex neurodegenerative condition characterized by alpha-synuclein aggregation and dysfunctional protein degradation pathways. This study investigates the differential gene expression of pivotal components (UBE2K, PSMC4, SKP1, and HSPA8) within these pathways in a Mexican-Mestizo PD population compared to healthy controls. We enrolled 87 PD patients and 87 controls, assessing their gene expression levels via RT-qPCR. Our results reveal a significant downregulation of PSMC4, SKP1, and HSPA8 in the PD group (p = 0.033, p = 0.003, and p = 0.002, respectively). Logistic regression analyses establish a strong association between PD and reduced expression of PSMC4, SKP1, and HSPA8 (OR = 0.640, 95% CI = 0.415-0.987; OR = 0.000, 95% CI = 0.000-0.075; OR = 0.550, 95% CI = 0.368-0.823, respectively). Conversely, UBE2K exhibited no significant association or expression difference between the groups. Furthermore, we develop a gene expression model based on HSPA8, PSMC4, and SKP1, demonstrating robust discrimination between healthy controls and PD patients. Notably, the model's diagnostic efficacy is particularly pronounced in early-stage PD. In conclusion, our study provides compelling evidence linking decreased gene expression of PSMC4, SKP1, and HSPA8 to PD in the Mexican-Mestizo population. Additionally, our gene expression model exhibits promise as a diagnostic tool, particularly for early-stage PD diagnosis.
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Affiliation(s)
- Alma C. Salas-Leal
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, México
| | - Sergio M. Salas-Pacheco
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, México
| | - Erik I. Hernández-Cosaín
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, México
| | - Lilia M. Vélez-Vélez
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, México
| | | | | | - Edna M. Méndez-Hernández
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, México
| | - Osmel La Llave-León
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, México
| | | | - Oscar Arias-Carrión
- Unidad de Trastornos del Movimiento y Sueño, Hospital General Dr. Manuel Gea González, Ciudad de México, México
| | - Ada A. Sandoval-Carrillo
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, México
| | - José M. Salas-Pacheco
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, México
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Andersen MS, Leikfoss IS, Brorson IS, Cappelletti C, Bettencourt C, Toft M, Pihlstrøm L. Epigenome-wide association study of peripheral immune cell populations in Parkinson's disease. NPJ Parkinsons Dis 2023; 9:149. [PMID: 37903812 PMCID: PMC10616224 DOI: 10.1038/s41531-023-00594-x] [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: 06/13/2023] [Accepted: 10/19/2023] [Indexed: 11/01/2023] Open
Abstract
Understanding the contribution of immune mechanisms to Parkinson's disease pathogenesis is an important challenge, potentially of major therapeutic implications. To further elucidate the involvement of peripheral immune cells, we studied epigenome-wide DNA methylation in isolated populations of CD14+ monocytes, CD19+ B cells, CD4+ T cells, and CD8+ T cells from Parkinson's disease patients and healthy control participants. We included 25 patients with a maximum five years of disease duration and 25 controls, and isolated four immune cell populations from each fresh blood sample. Epigenome-wide DNA methylation profiles were generated from 186 samples using the Illumina MethylationEpic array and association with disease status was tested using linear regression models. We identified six differentially methylated CpGs in CD14+ monocytes and one in CD8 + T cells. Four differentially methylated regions were identified in monocytes, including a region upstream of RAB32, a gene that has been linked to LRRK2. Methylation upstream of RAB32 correlated negatively with mRNA expression, and RAB32 expression was upregulated in Parkinson's disease both in our samples and in summary statistics from a previous study. Our epigenome-wide association study of early Parkinson's disease provides evidence for methylation changes across different peripheral immune cell types, highlighting monocytes and the RAB32 locus. The findings were predominantly cell-type-specific, demonstrating the value of isolating purified cell populations for genomic studies.
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Affiliation(s)
- Maren Stolp Andersen
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | | | - Conceicao Bettencourt
- Department of Neurodegenerative Disease and Queen Square Brain Bank for Neurological Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway.
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5
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Tang D, Quan C, Huang S, Wei F. Integrating LC-MS and HS-GC-MS for the metabolite characterization of the Chinese medicinal plant Platostoma palustre under different processing methods. Front Nutr 2023; 10:1181942. [PMID: 37275652 PMCID: PMC10235517 DOI: 10.3389/fnut.2023.1181942] [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: 03/08/2023] [Accepted: 04/18/2023] [Indexed: 06/07/2023] Open
Abstract
Platostoma palustre (or Mesona chinensis Benth) is an important medicinal and edible plant in China and Southeast Asian countries. To study the effects of different processing methods on the quality, nutrition, and flavor of P. palustre, we adopted the LC-MS and HS-GC-MS to compare the influences of tedding (S), sweating (M), and drying (H) on the metabolites and volatile substances of P. palustre. Biochemical determinations revealed that the M treatment could promote the accumulation of the contents of total sugar, soluble sugar, and total pectin compared with the H and S treatments but decrease the total flavonoid contents. LC-MS and HS-GC-MS uncovered 98 differential metabolites and 27 differential volatile substances among the three treatments, respectively. Overall, the M treatment facilitated the stabilization and improvement of the quality of polysaccharides and volatile substances, while the H treatment could promote the level of amino acids in P. palustre. The current study provided a theoretical reference for establishing standardized processing methods and sustaining the quality stability of P. palustre in future.
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Affiliation(s)
- Danfeng Tang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Traditional Chinese Medicine Inheritance and Innovation Center, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Changqian Quan
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Traditional Chinese Medicine Inheritance and Innovation Center, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Suhua Huang
- College of Pharmacy, Guangxi Medical University, Nanning, China
| | - Fan Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Traditional Chinese Medicine Inheritance and Innovation Center, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
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6
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Zhang JN, Li Q, Yang F. Role of epigenetic modifications in Parkinson's disease. Epigenomics 2023; 15:573-576. [PMID: 37431571 DOI: 10.2217/epi-2023-0211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023] Open
Affiliation(s)
- Jian-Nan Zhang
- Department of Neurobiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Qian Li
- Beijing Key Laboratory of Neural Regeneration & Repair, Capital Medical University, Beijing, 100069, China
- Department of Biochemistry & Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
- Beijing Key Laboratory of Cancer Invasion & Metastasis Research, Capital Medical University, Beijing, 100069, China
| | - Fei Yang
- Department of Neurobiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
- Beijing Key Laboratory of Neural Regeneration & Repair, Capital Medical University, Beijing, 100069, China
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7
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la Torre A, Lo Vecchio F, Greco A. Epigenetic Mechanisms of Aging and Aging-Associated Diseases. Cells 2023; 12:cells12081163. [PMID: 37190071 DOI: 10.3390/cells12081163] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023] Open
Abstract
Aging is an inevitable outcome of life, characterized by a progressive decline in tissue and organ function. At a molecular level, it is marked by the gradual alterations of biomolecules. Indeed, important changes are observed on the DNA, as well as at a protein level, that are influenced by both genetic and environmental parameters. These molecular changes directly contribute to the development or progression of several human pathologies, including cancer, diabetes, osteoporosis, neurodegenerative disorders and others aging-related diseases. Additionally, they increase the risk of mortality. Therefore, deciphering the hallmarks of aging represents a possibility for identifying potential druggable targets to attenuate the aging process, and then the age-related comorbidities. Given the link between aging, genetic, and epigenetic alterations, and given the reversible nature of epigenetic mechanisms, the precisely understanding of these factors may provide a potential therapeutic approach for age-related decline and disease. In this review, we center on epigenetic regulatory mechanisms and their aging-associated changes, highlighting their inferences in age-associated diseases.
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Affiliation(s)
- Annamaria la Torre
- Laboratory of Gerontology and Geriatrics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| | - Filomena Lo Vecchio
- Laboratory of Gerontology and Geriatrics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
| | - Antonio Greco
- Complex Unit of Geriatrics, Department of Medical Sciences, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
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SNCA Gene Methylation in Parkinson's Disease and Multiple System Atrophy. EPIGENOMES 2023; 7:epigenomes7010005. [PMID: 36810559 PMCID: PMC9944792 DOI: 10.3390/epigenomes7010005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
In recent years, epigenetic mechanisms have been implicated in the development of multifactorial diseases including neurodegenerative disorders. In Parkinson's disease (PD), as a synucleinopathy, most studies focused on DNA methylation of SNCA gene coding alpha-synuclein but obtained results were rather contradictory. In another neurodegenerative synucleinopathy, multiple system atrophy (MSA), very few studies investigated the epigenetic regulation. This study included patients with PD (n = 82), patients with MSA (n = 24), and a control group (n = 50). In three groups, methylation levels of CpG and non-CpG sites in regulatory regions of the SNCA gene were analyzed. We revealed hypomethylation of CpG sites in the SNCA intron 1 in PD and hypermethylation of predominantly non-CpG sites in the SNCA promoter region in MSA. In PD patients, hypomethylation in the intron 1 was associated with earlier age at the disease onset. In MSA patients, hypermethylation in the promotor was associated with shorter disease duration (before examination). These results showed different patterns of the epigenetic regulation in two synucleinopathies-PD and MSA.
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Martínez-Iglesias O, Naidoo V, Carrera I, Corzo L, Cacabelos R. Natural Bioactive Products as Epigenetic Modulators for Treating Neurodegenerative Disorders. Pharmaceuticals (Basel) 2023; 16:216. [PMID: 37259364 PMCID: PMC9967112 DOI: 10.3390/ph16020216] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 08/27/2023] Open
Abstract
Neurodegenerative disorders (NDDs) are major health issues in Western countries. Despite significant efforts, no effective therapeutics for NDDs exist. Several drugs that target epigenetic mechanisms (epidrugs) have been recently developed for the treatment of NDDs, and several of these are currently being tested in clinical trials. Furthermore, various bioproducts have shown important biological effects for the potential prevention and treatment of these disorders. Here, we review the use of natural products as epidrugs to treat NDDs in order to explore the epigenetic effects and benefits of functional foods and natural bioproducts on neurodegeneration.
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Affiliation(s)
- Olaia Martínez-Iglesias
- EuroEspes Biomedical Research Center, International Center of Neuroscience and Genomic Medicine, 15165 Bergondo, Corunna, Spain
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10
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Dynamic Regulation of DNA Methylation and Brain Functions. BIOLOGY 2023; 12:biology12020152. [PMID: 36829430 PMCID: PMC9952911 DOI: 10.3390/biology12020152] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
DNA cytosine methylation is a principal epigenetic mechanism underlying transcription during development and aging. Growing evidence suggests that DNA methylation plays a critical role in brain function, including neurogenesis, neuronal differentiation, synaptogenesis, learning, and memory. However, the mechanisms underlying aberrant DNA methylation in neurodegenerative diseases remain unclear. In this review, we provide an overview of the contribution of 5-methycytosine (5mC) and 5-hydroxylcytosine (5hmC) to brain development and aging, with a focus on the roles of dynamic 5mC and 5hmC changes in the pathogenesis of neurodegenerative diseases, particularly Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD). Identification of aberrant DNA methylation sites could provide potential candidates for epigenetic-based diagnostic and therapeutic strategies for neurodegenerative diseases.
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Yazar V, Dawson VL, Dawson TM, Kang SU. DNA Methylation Signature of Aging: Potential Impact on the Pathogenesis of Parkinson's Disease. JOURNAL OF PARKINSON'S DISEASE 2023; 13:145-164. [PMID: 36710687 PMCID: PMC10041453 DOI: 10.3233/jpd-223517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Regulation of gene expression by epigenetic modifications means lasting and heritable changes in the function of genes without alterations in the DNA sequence. Of all epigenetic mechanisms identified thus far, DNA methylation has been of particular interest in both aging and age-related disease research over the last decade given the consistency of site-specific DNA methylation changes during aging that can predict future health and lifespan. An increasing line of evidence has implied the dynamic nature of DNA (de)methylation events that occur throughout the lifespan has a role in the pathophysiology of aging and age-associated neurodegenerative conditions, including Parkinson's disease (PD). In this regard, PD methylome shows, to some extent, similar genome-wide changes observed in the methylome of healthy individuals of matching age. In this review, we start by providing a brief overview of studies outlining global patterns of DNA methylation, then its mechanisms and regulation, within the context of aging and PD. Considering diverging lines of evidence from different experimental and animal models of neurodegeneration and how they combine to shape our current understanding of tissue-specific changes in DNA methylome in health and disease, we report a high-level comparison of the genomic methylation landscapes of brain, with an emphasis on dopaminergic neurons in PD and in natural aging. We believe this will be particularly useful for systematically dissecting overlapping genome-wide alterations in DNA methylation during PD and healthy aging, and for improving our knowledge of PD-specific changes in methylation patterns independent of aging process.
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Affiliation(s)
- Volkan Yazar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pharmacology and and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA
| | - Sung-Ung Kang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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12
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Younesian S, Yousefi AM, Momeny M, Ghaffari SH, Bashash D. The DNA Methylation in Neurological Diseases. Cells 2022; 11:3439. [PMID: 36359835 PMCID: PMC9657829 DOI: 10.3390/cells11213439] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 10/25/2022] [Indexed: 07/30/2023] Open
Abstract
DNA methylation is critical for the normal development and functioning of the human brain, such as the proliferation and differentiation of neural stem cells, synaptic plasticity, neuronal reparation, learning, and memory. Despite the physical stability of DNA and methylated DNA compared to other epigenetic modifications, some DNA methylation-based biomarkers have translated into clinical practice. Increasing reports indicate a strong association between DNA methylation profiles and various clinical outcomes in neurological diseases, making DNA methylation profiles valuable as novel clinical markers. In this review, we aim to discuss the latest evidence concerning DNA methylation alterations in the development of neurodegenerative, neurodevelopmental, and neuropsychiatric diseases. We also highlighted the relationship of DNA methylation alterations with the disease progression and outcome in many neurological diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, frontotemporal dementia, and autism.
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Affiliation(s)
- Samareh Younesian
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1971653313, Iran
| | - Amir-Mohammad Yousefi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1971653313, Iran
| | - Majid Momeny
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Seyed H. Ghaffari
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1971653313, Iran
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Parkinson's disease-associated, sex-specific changes in DNA methylation at PARK7 (DJ-1), SLC17A6 (VGLUT2), PTPRN2 (IA-2β), and NR4A2 (NURR1) in cortical neurons. NPJ Parkinsons Dis 2022; 8:120. [PMID: 36151217 PMCID: PMC9508164 DOI: 10.1038/s41531-022-00355-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 06/24/2022] [Indexed: 12/04/2022] Open
Abstract
Evidence for epigenetic regulation playing a role in Parkinson's disease (PD) is growing, particularly for DNA methylation. Approximately 90% of PD cases are due to a complex interaction between age, genes, and environmental factors, and epigenetic marks are thought to mediate the relationship between aging, genetics, the environment, and disease risk. To date, there are a small number of published genome-wide studies of DNA methylation in PD, but none accounted for cell type or sex in their analyses. Given the heterogeneity of bulk brain tissue samples and known sex differences in PD risk, progression, and severity, these are critical variables to account for. In this genome-wide analysis of DNA methylation in an enriched neuronal population from PD postmortem parietal cortex, we report sex-specific PD-associated methylation changes in PARK7 (DJ-1), SLC17A6 (VGLUT2), PTPRN2 (IA-2β), NR4A2 (NURR1), and other genes involved in developmental pathways, neurotransmitter packaging and release, and axon and neuron projection guidance.
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14
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Pihlstrøm L, Shireby G, Geut H, Henriksen SP, Rozemuller AJM, Tunold JA, Hannon E, Francis P, Thomas AJ, Love S, Mill J, van de Berg WDJ, Toft M. Epigenome-wide association study of human frontal cortex identifies differential methylation in Lewy body pathology. Nat Commun 2022; 13:4932. [PMID: 35995800 PMCID: PMC9395387 DOI: 10.1038/s41467-022-32619-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 08/09/2022] [Indexed: 11/09/2022] Open
Abstract
Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are closely related progressive disorders with no available disease-modifying therapy, neuropathologically characterized by intraneuronal aggregates of misfolded α-synuclein. To explore the role of DNA methylation changes in PD and DLB pathogenesis, we performed an epigenome-wide association study (EWAS) of 322 postmortem frontal cortex samples and replicated results in an independent set of 200 donors. We report novel differentially methylated replicating loci associated with Braak Lewy body stage near TMCC2, SFMBT2, AKAP6 and PHYHIP. Differentially methylated probes were independent of known PD genetic risk alleles. Meta-analysis provided suggestive evidence for a differentially methylated locus within the chromosomal region affected by the PD-associated 22q11.2 deletion. Our findings elucidate novel disease pathways in PD and DLB and generate hypotheses for future molecular studies of Lewy body pathology.
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Affiliation(s)
- Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway.
| | - Gemma Shireby
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Hanneke Geut
- Amsterdam UMC, Vrije Universiteit, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Netherlands Brain Bank, Netherlands Institute of Neurosciences, Amsterdam, The Netherlands
| | | | - Annemieke J M Rozemuller
- Amsterdam UMC, Vrije Universiteit, Department of Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Jon-Anders Tunold
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Eilis Hannon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Paul Francis
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Alan J Thomas
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Seth Love
- Dementia Research Group, Bristol Medical School, University of Bristol, Bristol, UK
| | - Jonathan Mill
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Wilma D J van de Berg
- Amsterdam UMC, Vrije Universiteit, Department of Anatomy and Neurosciences, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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15
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Schaffner SL, Kobor MS. DNA methylation as a mediator of genetic and environmental influences on Parkinson's disease susceptibility: Impacts of alpha-Synuclein, physical activity, and pesticide exposure on the epigenome. Front Genet 2022; 13:971298. [PMID: 36061205 PMCID: PMC9437223 DOI: 10.3389/fgene.2022.971298] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/25/2022] [Indexed: 12/15/2022] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder with a complex etiology and increasing prevalence worldwide. As PD is influenced by a combination of genetic and environment/lifestyle factors in approximately 90% of cases, there is increasing interest in identification of the interindividual mechanisms underlying the development of PD as well as actionable lifestyle factors that can influence risk. This narrative review presents an outline of the genetic and environmental factors contributing to PD risk and explores the possible roles of cytosine methylation and hydroxymethylation in the etiology and/or as early-stage biomarkers of PD, with an emphasis on epigenome-wide association studies (EWAS) of PD conducted over the past decade. Specifically, we focused on variants in the SNCA gene, exposure to pesticides, and physical activity as key contributors to PD risk. Current research indicates that these factors individually impact the epigenome, particularly at the level of CpG methylation. There is also emerging evidence for interaction effects between genetic and environmental contributions to PD risk, possibly acting across multiple omics layers. We speculated that this may be one reason for the poor replicability of the results of EWAS for PD reported to date. Our goal is to provide direction for future epigenetics studies of PD to build upon existing foundations and leverage large datasets, new technologies, and relevant statistical approaches to further elucidate the etiology of this disease.
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Affiliation(s)
- Samantha L. Schaffner
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Michael S. Kobor
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
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16
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Bakhit Y, Schmitt I, Hamed A, Ibrahim EAA, Mohamed IN, El-Sadig SM, Elseed MA, Alebeed MA, Shaheen MT, Ibrahim MO, Elhassan AA, Eltom K, Ali HA, Ibrahim YA, Almak ME, Abubaker R, Ahmed MA, Abugrain AA, Elrasheed SM, Omar MA, Almahal MA, MohamedSharif AA, Tahir MY, Malik SM, Eldirdiri HS, Khidir RJ, Mohamed MT, Abdalla A, Omer FY, Elsayed LEO, Babikir HEH, Bukhari EAA, Seidi O, Wüllner U. Methylation of alpha-synuclein in a Sudanese cohort. Parkinsonism Relat Disord 2022; 101:6-8. [PMID: 35728367 DOI: 10.1016/j.parkreldis.2022.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/02/2022] [Accepted: 05/10/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Several studies suggested a significant role of epigenetic changes, including alterations in miRNA, histone modifications, and DNA methylation of α-synuclein (SNCA) in Parkinson's disease (PD) pathogenicity. As of yet, only very few studies have been carried out in this field in Africa and none in Sudan. MATERIALS AND METHODS We collected DNA from 172 Sudanese individuals (90 cases, 82 controls) who donated saliva for DNA extraction (mean age of onset: 40.6 ± 22.4 years). A family history of PD was evident in 64 patients. DNA preparation and bisulfite sequencing of SNCAintron1 was performed as described earlier. RESULTS Of the fourteen analyzed CpGs of SNCAintron1, CpGs 16-23 were hypomethylated in PD (P-value ranged from 0.023 to 0.003). P-values improved, when sporadic cases were excluded from the analysis. CONCLUSION We identified the presence of a specific pattern of DNA methylation in a young Sudanese cohort of familial PD, which confirms the importance of the methylation of SNCAintron1 for PD. This phenomenon appears to be independent of ethnicity, the impact of environmental factors, drug history, or familial clustering.
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Affiliation(s)
- Yousuf Bakhit
- Department of Neurology, University Hospital Bonn, Germany; Department of Basic Medical Sciences, Faculty of Dentistry, University of Khartoum, Sudan; Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan.
| | - Ina Schmitt
- Department of Neurology, University Hospital Bonn, Germany
| | - Ahlam Hamed
- Department of Paediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Etedal Ahmed A Ibrahim
- Faculty of Medicine, Al Neelain University, Khartoum, Sudan, and The National Centre for Neurological Sciences, Sudan
| | - Inaam N Mohamed
- Department of Paediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Sarah M El-Sadig
- Department of Neurology, Soba Teaching Hospital, And Department of Medicine, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Maha A Elseed
- Department of Paediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Mohamed A Alebeed
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan
| | - Mutaz T Shaheen
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan
| | - Mohamed O Ibrahim
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan; Department of Biochemistry, Faculty of Medicine, Sudan University of Science and Technology, Khartoum, Sudan
| | - Ali A Elhassan
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan
| | - Khalid Eltom
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan
| | - Hiba A Ali
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan
| | - Yousuf A Ibrahim
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan
| | - Murad E Almak
- Department of Physiology, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Rayan Abubaker
- Department of Molecular Medicine, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan; Department of Molecular Biology, National University Biomedical Research Institute (NUBRI), National University, Khartoum, Sudan
| | | | - Ahmed A Abugrain
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan
| | - Salma M Elrasheed
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan
| | - Mawia A Omar
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan
| | - Mohamed A Almahal
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan
| | - Abubaker A MohamedSharif
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan; Department of Anatomy, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Mohamed Y Tahir
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan
| | - Sawazen M Malik
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan
| | - Hazim S Eldirdiri
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan; University of Bordeaux, INSERM, U1215, Neurocentre Magendie, Bordeaux, France
| | - Reem J Khidir
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan
| | - Malaz T Mohamed
- Sudan Neuroscience Projects, University of Khartoum, Khartoum, Sudan
| | | | - Farouk Yassen Omer
- Department of Medicine, Neurology, Omdurman Islamic University, Khartoum, Sudan
| | - Liena E O Elsayed
- Department of Basic Sciences, College of Medicine, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Haydar El Hadi Babikir
- Department of Paediatrics and Child Health, Faculty of Medicine, University of Gezira, Sudan
| | - Elfateh Abd-Allah Bukhari
- Department of Neurology, Bashaier University Hospital, And Khartoum Teaching Hospital. Department of Medicine, Faculty of Medicine, Al-Neelain University, Khartoum, Sudan
| | - Osheik Seidi
- Department of Neurology, Soba Teaching Hospital, And Department of Medicine, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Ullrich Wüllner
- Department of Neurology, University Hospital Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.
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17
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Monayo SM, Liu X. The Prospective Application of Melatonin in Treating Epigenetic Dysfunctional Diseases. Front Pharmacol 2022; 13:867500. [PMID: 35668933 PMCID: PMC9163742 DOI: 10.3389/fphar.2022.867500] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/14/2022] [Indexed: 01/09/2023] Open
Abstract
In the past, different human disorders were described by scientists from the perspective of either environmental factors or just by genetically related mechanisms. The rise in epigenetic studies and its modifications, i.e., heritable alterations in gene expression without changes in DNA sequences, have now been confirmed in diseases. Modifications namely, DNA methylation, posttranslational histone modifications, and non-coding RNAs have led to a better understanding of the coaction between epigenetic alterations and human pathologies. Melatonin is a widely-produced indoleamine regulator molecule that influences numerous biological functions within many cell types. Concerning its broad spectrum of actions, melatonin should be investigated much more for its contribution to the upstream and downstream mechanistic regulation of epigenetic modifications in diseases. It is, therefore, necessary to fill the existing gaps concerning corresponding processes associated with melatonin with the physiological abnormalities brought by epigenetic modifications. This review outlines the findings on melatonin’s action on epigenetic regulation in human diseases including neurodegenerative diseases, diabetes, cancer, and cardiovascular diseases. It summarizes the ability of melatonin to act on molecules such as proteins and RNAs which affect the development and progression of diseases.
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18
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Iakovenko EV, Abramycheva NY, Fedotova EY, Illarioshkin SN. Methylation of MAPT Gene in Neurodegenerative Synucleinopathies. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422050118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Schaffner SL, Wassouf Z, Lazaro DF, Xylaki M, Gladish N, Lin DTS, MacIsaac J, Ramadori K, Hentrich T, Schulze-Hentrich JM, Outeiro TF, Kobor MS. Alpha-synuclein overexpression induces epigenomic dysregulation of glutamate signaling and locomotor pathways. Hum Mol Genet 2022; 31:3694-3714. [PMID: 35567546 PMCID: PMC9616577 DOI: 10.1093/hmg/ddac104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 04/15/2022] [Accepted: 05/03/2022] [Indexed: 11/26/2022] Open
Abstract
Parkinson’s disease (PD) is a neurological disorder with complex interindividual etiology that is becoming increasingly prevalent worldwide. Elevated alpha-synuclein levels can increase risk of PD and may influence epigenetic regulation of PD pathways. Here, we report genome-wide DNA methylation and hydroxymethylation alterations associated with overexpression of two PD-linked alpha-synuclein variants (wild-type and A30P) in LUHMES cells differentiated to dopaminergic neurons. Alpha-synuclein altered DNA methylation at thousands of CpGs and DNA hydroxymethylation at hundreds of CpGs in both genotypes, primarily in locomotor behavior and glutamate signaling pathway genes. In some cases, epigenetic changes were associated with transcription. SMITE network analysis incorporating H3K4me1 ChIP-seq to score DNA methylation and hydroxymethylation changes across promoters, enhancers, and gene bodies confirmed epigenetic and transcriptional deregulation of glutamate signaling modules in both genotypes. Our results identify distinct and shared impacts of alpha-synuclein variants on the epigenome, and associate alpha-synuclein with the epigenetic etiology of PD.
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Affiliation(s)
- Samantha L Schaffner
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Zinah Wassouf
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37073 Göttingen, Germany.,German Centre for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany
| | - Diana F Lazaro
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Mary Xylaki
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Nicole Gladish
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - David T S Lin
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Julia MacIsaac
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Katia Ramadori
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Thomas Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Julia M Schulze-Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37073 Göttingen, Germany.,German Centre for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany.,Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
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20
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Epigenome-Wide Analysis of DNA Methylation in Parkinson's Disease Cortex. Life (Basel) 2022; 12:life12040502. [PMID: 35454993 PMCID: PMC9025601 DOI: 10.3390/life12040502] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 12/27/2022] Open
Abstract
Background: Epigenetic factors including DNA methylation contribute to specific patterns of gene expression. Gene−environment interactions can change the methylation status in the brain, and accumulation of these epigenetic changes over a lifespan may be co-responsible for a neurodegenerative disease like Parkinson’s disease, which that is characterised by a late onset in life. Aims: To determine epigenetic modifications in the brains of Parkinson’s disease patients. Patients and Methods: DNA methylation patterns were compared in the cortex tissue of 14 male PD patients and 10 male healthy individuals using the Illumina Methylation 450 K chip. Subsequently, DNA methylation of candidate genes was evaluated using bisulphite pyrosequencing, and DNA methylation of cytochrome P450 2E1 (CYP2E1) was characterized in DNA from blood mononuclear cells (259 PD patients and 182 healthy controls) and skin fibroblasts (10 PD patients and 5 healthy controls). Protein levels of CYP2E1 were analysed using Western blot in human cortex and knock-out mice brain samples. Results: We found 35 hypomethylated and 22 hypermethylated genes with a methylation M-value difference >0.5. Decreased methylation of cytochrome P450 2E1 (CYP2E1) was associated with increased protein levels in PD brains, but in peripheral tissues, i.e., in blood cells and skin fibroblasts, DNA methylation of CYP2E1 was unchanged. In CYP2E1 knock-out mice brain alpha-synuclein (SNCA) protein levels were down-regulated compared to wild-type mice, whereas treatment with trichloroethylene (TCE) up-regulated CYP2E1 protein in a dose-dependent manner in cultured cells. We further identified an interconnected group of genes associated with oxidative stress, such as Methionine sulfoxide reductase A (MSRA) and tumour protein 73 (TP73) in the brain, which again were not paralleled in other tissues and appeared to indicate brain-specific changes. Conclusions: Our study revealed surprisingly few dysmethylated genes in a brain region less affected in PD. We confirmed hypomethylation of CYP2E1.
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21
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Crocin Protects Malathion-Induced Striatal Biochemical Deficits by Inhibiting Apoptosis and Increasing α-Synuclein in Rats' Striatum. J Mol Neurosci 2022; 72:983-993. [PMID: 35274200 DOI: 10.1007/s12031-022-01990-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/24/2022] [Indexed: 10/18/2022]
Abstract
Long-term exposure to organophosphates might result in neurodegenerative diseases, comprising Parkinson's disease. Malathion is an organophosphate pesticide with high neurotoxicity. Oxidative stress, apoptosis, and α-synuclein accumulation are important underlying mechanisms in Parkinson's disease. According to studies, crocin, an active constituent of saffron, has anti-apoptotic, anti-inflammatory, and antioxidant properties. Thus, the effect of crocin on malathion-induced striatal biochemical deficits in rats was investigated in this study. Six groups of male Wistar rats were used: 1. control (normal saline); 2. malathion (100 mg/kg/day, i.p.); 3. crocin (10 mg/kg/day, i.p.) + malathion; 4. levodopa (10 mg/kg/day, i.p.) + malathion; 5. crocin (40 mg/kg/day, i.p.); and 6. polyethylene glycol (PEG) (vehicle of levodopa) groups. The drugs were administered for 28 days. The amounts of Bcl-2, Bax, and caspases 3, 8, and 9 proteins in the striatum were measured by western blotting. Also, the amounts of protein and mRNA level of the α-synuclein in striatum tissue were measured by western blotting and RT-qPCR methods. Malathion induced apoptosis by increasing the amount of Bax/Bcl2 ratio and caspases 3 and 9 proteins in rat striatum tissue. It also increased the protein and mRNA level of α-synuclein in striatal tissue. Co-administration of crocin or levodopa with malathion inhibited the toxic effects of malathion on striatal tissue. Crocin ameliorates the neurotoxic effect of malathion by its anti-apoptotic activity and regulating the expression of proteins involved in Parkinson's disease pathogenesis. As a result, crocin has the potential to be used as a treatment for malathion-induced neurotoxicity.
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22
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Does the Expression and Epigenetics of Genes Involved in Monogenic Forms of Parkinson’s Disease Influence Sporadic Forms? Genes (Basel) 2022; 13:genes13030479. [PMID: 35328033 PMCID: PMC8951612 DOI: 10.3390/genes13030479] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 12/25/2022] Open
Abstract
Parkinson’s disease (PD) is a disorder characterized by a triad of motor symptoms (akinesia, rigidity, resting tremor) related to loss of dopaminergic neurons mainly in the Substantia nigra pars compacta. Diagnosis is often made after a substantial loss of neurons has already occurred, and while dopamine replacement therapies improve symptoms, they do not modify the course of the disease. Although some biological mechanisms involved in the disease have been identified, such as oxidative stress and accumulation of misfolded proteins, they do not explain entirely PD pathophysiology, and a need for a better understanding remains. Neurodegenerative diseases, including PD, appear to be the result of complex interactions between genetic and environmental factors. The latter can alter gene expression by causing epigenetic changes, such as DNA methylation, post-translational modification of histones and non-coding RNAs. Regulation of genes responsible for monogenic forms of PD may be involved in sporadic PD. This review will focus on the epigenetic mechanisms regulating their expression, since these are the genes for which we currently have the most information available. Despite technical challenges, epigenetic epidemiology offers new insights on revealing altered biological pathways and identifying predictive biomarkers for the onset and progression of PD.
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23
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Qu W, Zhuang Y, Li X. The roles of epigenetic modifications in neurodegenerative diseases. Zhejiang Da Xue Xue Bao Yi Xue Ban 2021; 50:642-650. [PMID: 34986527 PMCID: PMC8732261 DOI: 10.3724/zdxbyxb-2021-0160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/30/2021] [Indexed: 06/14/2023]
Abstract
In neuronal system, epigenetic modifications are essential for neuronal development, the fate determination of neural stem cells and neuronal function. The dysfunction of epigenetic regulation is closely related to occurrence and development of neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, Huntington's disease. Abnormally elevated DNA methylation inhibits the expression of some DNA repair-related genes and affects the progression of Huntington's disease. In the brain of Alzheimer's disease patients, the levels of H3K27ac and H3K9ac histone modifications increased. In addition, the alteration of RNA methylation in animal models of Alzheimer's disease and Parkinson's disease showed discrepancy trends. Therefore, epigenetic modifications may serve as potential therapeutic targets for neurodegenerative diseases. Here, we summarize the recent progress of the roles of epigenetic modifications in neurodegenerative diseases.
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Affiliation(s)
- Wenzheng Qu
- of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| | - Yingliang Zhuang
- of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| | - Xuekun Li
- of Translational Medicine, Zhejiang University, Hangzhou 310029, China
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24
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Emelyanov A, Usenko T, Nikolaev M, Senkevich K, Kulabukhova D, Lavrinova A, Andoskin P, Miliukhina I, Pchelina S. Increased α-Synuclein Level in CD45+ Blood Cells in Asymptomatic Carriers of GBA Mutations. Mov Disord 2021; 36:1997-1998. [PMID: 34409693 DOI: 10.1002/mds.28688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/17/2021] [Accepted: 04/20/2021] [Indexed: 11/10/2022] Open
Affiliation(s)
- Anton Emelyanov
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute,", St. Petersburg, Russian Federation.,First Pavlov State Medical University of St. Petersburg, St. Petersburg, Russian Federation
| | - Tatiana Usenko
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute,", St. Petersburg, Russian Federation.,First Pavlov State Medical University of St. Petersburg, St. Petersburg, Russian Federation
| | - Mikhail Nikolaev
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute,", St. Petersburg, Russian Federation.,First Pavlov State Medical University of St. Petersburg, St. Petersburg, Russian Federation
| | - Konstantin Senkevich
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute,", St. Petersburg, Russian Federation.,First Pavlov State Medical University of St. Petersburg, St. Petersburg, Russian Federation
| | - Darya Kulabukhova
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute,", St. Petersburg, Russian Federation
| | - Anna Lavrinova
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute,", St. Petersburg, Russian Federation
| | - Pavel Andoskin
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute,", St. Petersburg, Russian Federation.,First Pavlov State Medical University of St. Petersburg, St. Petersburg, Russian Federation
| | - Irina Miliukhina
- First Pavlov State Medical University of St. Petersburg, St. Petersburg, Russian Federation
| | - Sofya Pchelina
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Centre "Kurchatov Institute,", St. Petersburg, Russian Federation.,First Pavlov State Medical University of St. Petersburg, St. Petersburg, Russian Federation.,Institute of Experimental Medicine, St. Petersburg, Russian Federation
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25
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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: 30] [Impact Index Per Article: 10.0] [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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26
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Sarangi SC, Sopory P, Reeta KH. Chronic Neurological Disorders: Genetic and Epigenetic Markers for Monitoring of Pharmacotherapy. Neurol India 2021; 69:252-259. [PMID: 33904433 DOI: 10.4103/0028-3886.314522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Introduction Chronic neurological diseases are a major cause of mortality and morbidity in the world. With increasing life expectancy in the developing world, the incidence and prevalence of these diseases are predicted to rise even further. This has also contributed to an increase in disability-adjusted life years (DALYs) for noncommunicable diseases. Treatment for such diseases also poses a challenge with multiple genetic and epigenetic factors leading to a varied outcome. Personalization of treatment is one way that treatment outcome/prognosis of disease can be improved, and pharmacogenomics plays a significant role in this context. Methodology This article reviewed the evidence pertaining to the association of genetic and epigenetic markers with major neurological disorders like multiple sclerosis (MS), Alzheimer's disease (AD), and Parkinson's disease (PD), which are a major source of burden among neurological disorders. Types of studies included are peer-reviewed original research articles from the PubMed database (1999-2018). Results This study compiled data regarding specific genetic and epigenetic markers with a significant correlation between the clinical diagnosis of the disease and prognosis of therapy from 65 studies. In a single platform, this review highlights the clues to some vital questions, such as why interferon beta (IFN-β) therapy fails to improve symptoms in all MS patients? why cholinesterase inhibitors fail to improve cognitive impairment in a subset of people suffering from AD? or why some individuals on levodopa (L-DOPA) for PD suffer from side-effects ranging from dyskinesia to hallucination while others do not? Conclusion This article summarizes the genetic and epigenetic factors that may either require monitoring or help in deciding future pharmacotherapy in a patient suffering from MS, AD, and PD. As the health care system develops and reaches newer heights, we expect more and more of these biomarkers to be used as pharmacotherapeutic outcome indicators.
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Affiliation(s)
| | - Pranav Sopory
- Department of Pharmacology, All India Institute of Medical Sciences, New Delhi, India
| | - K H Reeta
- Department of Pharmacology, All India Institute of Medical Sciences, New Delhi, India
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Stoccoro A, Smith AR, Baldacci F, Del Gamba C, Lo Gerfo A, Ceravolo R, Lunnon K, Migliore L, Coppedè F. Mitochondrial D-Loop Region Methylation and Copy Number in Peripheral Blood DNA of Parkinson's Disease Patients. Genes (Basel) 2021; 12:genes12050720. [PMID: 34065874 PMCID: PMC8151519 DOI: 10.3390/genes12050720] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/30/2021] [Accepted: 05/10/2021] [Indexed: 02/07/2023] Open
Abstract
Altered mitochondrial DNA (mtDNA) methylation has been detected in several human pathologies, although little attention has been given to neurodegenerative diseases. Recently, altered methylation levels of the mitochondrial displacement loop (D-loop) region, which regulates mtDNA replication, were observed in peripheral blood cells of Alzheimer’s disease and amyotrophic lateral sclerosis patients. However, nothing is yet known about D-loop region methylation levels in peripheral blood of Parkinson’s disease (PD) patients. In the current study, we investigated D-loop methylation levels and mtDNA copy number in peripheral blood of 30 PD patients and 30 age- and sex-matched control subjects. DNA methylation analyses have been performed by means of methylation-sensitive high-resolution melting (MS-HRM) and pyrosequencing techniques, while mtDNA copy number was analyzed by quantitative PCR. MS-HRM and pyrosequencing analyses provided very similar D-loop methylation levels in PD patients and control subjects, and no differences between the two groups have been observed. Treatment with L-dopa and duration of the disease had no effect on D-loop methylation levels in PD patients. Additionally, mtDNA copy number did not differ between PD patients and control subjects. Current results suggest that D-loop methylation levels are not altered in peripheral blood of PD patients nor influenced by dopaminergic treatment.
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Affiliation(s)
- Andrea Stoccoro
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy; (A.S.); (L.M.)
| | - Adam R. Smith
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK; (A.R.S.); (K.L.)
| | - Filippo Baldacci
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (F.B.); (C.D.G.); (A.L.G.); (R.C.)
| | - Claudia Del Gamba
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (F.B.); (C.D.G.); (A.L.G.); (R.C.)
| | - Annalisa Lo Gerfo
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (F.B.); (C.D.G.); (A.L.G.); (R.C.)
| | - Roberto Ceravolo
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (F.B.); (C.D.G.); (A.L.G.); (R.C.)
| | - Katie Lunnon
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK; (A.R.S.); (K.L.)
| | - Lucia Migliore
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy; (A.S.); (L.M.)
- Department of Laboratory Medicine, Azienda Ospedaliero Universitaria Pisana, 56124 Pisa, Italy
| | - Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy; (A.S.); (L.M.)
- Correspondence:
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Epigenetic Modulation in Parkinson's Disease and Potential Treatment Therapies. Neurochem Res 2021; 46:1618-1626. [PMID: 33900517 DOI: 10.1007/s11064-021-03334-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/17/2021] [Accepted: 04/20/2021] [Indexed: 12/11/2022]
Abstract
In the recent past, huge emphasis has been given to the epigenetic alterations of the genes responsible for the cause of neurological disorders. Earlier, the scientists believed somatic changes and modifications in the genetic makeup of DNA to be the main cause of the neurodegenerative diseases. With the increase in understanding of the neural network and associated diseases, it was observed that alterations in the gene expression were not always originated by the change in the genetic sequence. For this reason, extensive research has been conducted to understand the role of epigenetics in the pathophysiology of several neurological disorders including Alzheimer's disease, Parkinson's disease and, Huntington's disease. In a healthy person, the epigenetic modifications play a crucial role in maintaining the homeostasis of a cell by either up-regulating or down-regulating the genes. Therefore, improved understanding of these modifications may provide better insight about the diseases and may serve as potential therapeutic targets for their treatment. The present review describes various epigenetic modifications involved in the pathology of Parkinson's Disease (PD) backed by multiple researches carried out to study the gene expression regulation related to the epigenetic alterations. Additionally, we will briefly go through the current scenario about the various treatment therapies including small molecules and multiple phytochemicals potent enough to reverse these alterations and the future directions for a better management of PD.
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Salas-Leal AC, Salas-Pacheco SM, Gavilán-Ceniceros JAP, Castellanos-Juárez FX, Méndez-Hernández EM, La Llave-León O, Camacho-Luis A, Quiñones-Canales G, Romero-Gutiérrez E, Arias-Carrión O, Salas-Pacheco JM, Sandoval-Carrillo AA. α-syn and SNP rs356219 as a potential biomarker in blood for Parkinson's disease in Mexican Mestizos. Neurosci Lett 2021; 754:135901. [PMID: 33865938 DOI: 10.1016/j.neulet.2021.135901] [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: 03/10/2021] [Revised: 04/02/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
Clinical criteria diagnose Parkinson's disease (PD), therefore, it is crucial to find biological elements that could support diagnosis or even act as prognostic tools of PD. The SNCA gene codifies a protein called α - synuclein; several studies associate genetic and biochemical factors of SNCA with PD, including transcript and plasmatic protein levels, however, contradictory evidence indicates inconclusive results. We aim to compare SNCA mRNA expression, plasmatic α-syn protein and rs356219 SNP between PD cases and a control group, and to identify a potential biomarker in Mexican mestizos', focusing on these three components determined in blood. We included 88 PD patients and 88 age-matched controls. We observed higher α-syn protein and decreased SNCA mRNA levels in PD subjects, compared to control group (p = 0.044 and p < 0.001, respectively). A statistically significant difference was found in allelic and genotypic frequencies of SNP rs356219 between PD patients and normal subjects (p = 0.006 and p = 0.023, respectively). Logistic regression analysis determined as optimal predictors of PD the GG genotype of SNP rs356219 (OR 2.49; p = 0.006) in a recessive model and α-syn protein (OR 1.057; p = 0.033). Furthermore, the G allele of SNP rs356219 was associated with higher plasmatic α-syn and mRNA levels in PD subjects. The receiver operating curves (ROC) distinguished PD from healthy controls with good sensitivity and specificity considering the plasmatic α-syn protein (AUC = 0.693, Sensitivity = 66.7 %, Specificity = 63.9 %) or a predictive probability of plasmatic α-syn protein and SNP rs356219 in a single model (AUC = 0.692, Sensitivity = 62.3 %, Specificity = 62.5 %). The performance of this classifier model in PD at early stage (n = 31) increase the discriminant power in both, plasmatic α-syn protein (AUC = 0.779, Sensitivity = 72.7 %, Specificity = 73.9 %) and predictive probability (AUC = 0.707, Sensitivity = 63.6 %, Specificity = 62.5 %). We propose that α-syn protein and SNP rs356219 together may work as a good signature of PD, and they can be suggested as a non-invasive biomarker of PD risk.
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Affiliation(s)
- Alma Cristina Salas-Leal
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, 34000, Mexico
| | - Sergio M Salas-Pacheco
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, 34000, Mexico
| | | | | | - Edna M Méndez-Hernández
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, 34000, Mexico
| | - Osmel La Llave-León
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, 34000, Mexico
| | - Abelardo Camacho-Luis
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Durango, 34000, Mexico
| | | | - Elizabeth Romero-Gutiérrez
- Unidad de Trastornos del Movimiento y Sueño, Hospital General Dr. Manuel Gea González, Ciudad de México, 14080, Mexico
| | - Oscar Arias-Carrión
- Unidad de Trastornos del Movimiento y Sueño, Hospital General Dr. Manuel Gea González, Ciudad de México, 14080, Mexico
| | - José M Salas-Pacheco
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, 34000, Mexico.
| | - Ada A Sandoval-Carrillo
- Instituto de Investigación Científica, Universidad Juárez del Estado de Durango, Durango, 34000, Mexico.
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30
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Wei X, Cai M, Jin L. The Function of the Metals in Regulating Epigenetics During Parkinson's Disease. Front Genet 2021; 11:616083. [PMID: 33603768 PMCID: PMC7884633 DOI: 10.3389/fgene.2020.616083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/30/2020] [Indexed: 11/13/2022] Open
Abstract
Parkinson's means Parkinson's disease, a chronic degenerative disease of central nervous system. The main area which is affected by this disease is motor system. Since it firstly founded by James Parkinson in his 1817 publication, nowadays, people still have lots of questions about this disease. This review mainly summarizes the epigenetics of Parkinson's. DNA methylation is one of the epigenetic mechanisms of Parkinson's. During the development of disease, global hypomethylation, and hypermethylation happen in different areas of patients. Another epigenetic mechanism is histone modification. People believe that some metals can induce Parkinson's disease by modulating epigenetic mechanisms. This review summarizes the relationships between different metals and Parkinson's disease. However, the specific roles of most metals in epigenetics are still unknown, which need further research.
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Affiliation(s)
- Xiangzhen Wei
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Menghua Cai
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Lifang Jin
- Department of Biological Sciences, Shaoxing University, Shaoxing, China
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31
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Li Y, Hao S, Zhang H, Mao W, Xue J, Zhang Y, Cai Y, Chan P. Hypomethylation of SNCA in Idiopathic REM Sleep Behavior Disorder Associated With Phenoconversion. Mov Disord 2020; 36:955-962. [PMID: 33340152 DOI: 10.1002/mds.28421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/21/2020] [Accepted: 11/20/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Hypomethylation of intron 1 of the α-synuclein (SNCA) gene has been extensively reported in the blood of patients with α-synucleinopathies. Idiopathic rapid eye movement sleep behavior disorder represents a prodromal stage of α-synucleinopathies. Methylation of α-synuclein intron 1 in idiopathic rapid eye movement sleep behavior disorder patients is largely unexplored. The objective of the current study was to assess blood α-synuclein intron 1 methylation in patients and to explore it as a potential biomarker to predict phenoconversion and monitor disease progression. METHODS Seventy-eight polysomnography-confirmed patients and 74 healthy controls were enrolled. After an average of 3.75 years of follow up, 16 patients converted to neurodegenerative diseases (converters), whereas 59 did not (nonconverters). Blood DNA was obtained at baseline from all participants, as well as at the follow-up visit for 27 patients. DNA methylation levels were determined using bisulfite pyrosequencing methods and were compared between patients and healthy controls, converters and nonconverters, and baseline and follow-up visits. RESULTS Hypomethylation at cytosine-phosphate-guanine 10, 11, 12, 13, and 17 was found in patients compared with healthy controls. Hypomethylation at cytosine-phosphate-guanine 17 was associated with an increased risk of clinical phenoconversion, which was further enhanced with the presence of subtle motor abnormalities. In addition, it appeared that later reduction in methylation levels at cytosine-phosphate-guanine 14, 15, and 16 was associated with disease progression. CONCLUSIONS Peripheral blood α-synuclein intron 1 was hypomethylated in idiopathic rapid eye movement sleep behavior disorder patients. α-Synuclein methylation levels may be useful biomarkers to screen patients, predict phenoconversion, and monitor disease progression. © 2020 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Yuan Li
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China.,Department of Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Shuwen Hao
- Department of Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China.,Key Laboratory for Neurodegenerative Diseases of the Ministry of Education, Beijing Key Laboratory on Parkinson's Disease, Parkinson's Disease Center for Beijing Institute on Brain Disorders, Clinical and Research Center for Parkinson's Disease of Capital Medical University, Beijing, China
| | - Hui Zhang
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China.,Department of Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Wei Mao
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Jinhua Xue
- Department of Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China.,Key Laboratory for Neurodegenerative Diseases of the Ministry of Education, Beijing Key Laboratory on Parkinson's Disease, Parkinson's Disease Center for Beijing Institute on Brain Disorders, Clinical and Research Center for Parkinson's Disease of Capital Medical University, Beijing, China
| | - Yanli Zhang
- Department of Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China.,Key Laboratory for Neurodegenerative Diseases of the Ministry of Education, Beijing Key Laboratory on Parkinson's Disease, Parkinson's Disease Center for Beijing Institute on Brain Disorders, Clinical and Research Center for Parkinson's Disease of Capital Medical University, Beijing, China
| | - Yanning Cai
- Department of Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China.,Key Laboratory for Neurodegenerative Diseases of the Ministry of Education, Beijing Key Laboratory on Parkinson's Disease, Parkinson's Disease Center for Beijing Institute on Brain Disorders, Clinical and Research Center for Parkinson's Disease of Capital Medical University, Beijing, China.,Department of Biobank, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Piu Chan
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China.,Department of Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China.,Key Laboratory for Neurodegenerative Diseases of the Ministry of Education, Beijing Key Laboratory on Parkinson's Disease, Parkinson's Disease Center for Beijing Institute on Brain Disorders, Clinical and Research Center for Parkinson's Disease of Capital Medical University, Beijing, China.,National Clinical Research Center for Geriatric Disorders, Beijing, China
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32
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Tafani X, Pascale E, Fattapposta F, Pucci M, D'Addario C, Adriani W. Cross-correlations between motifs in the 5'-UTR of DAT1 gene: Findings from Parkinson's disease. Adv Biol Regul 2020; 78:100753. [PMID: 33022465 DOI: 10.1016/j.jbior.2020.100753] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/28/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
Parkinson's disease (PD) is a neuro-degenerative disorder affecting the striatal motor system, caused by the loss of neuronal cells in the mid-brain, where reduced amounts of dopamine do cause involuntary movements and others symptoms. Alterations of methylome have been reported in PD epigenomic studies, and also human dopamine transporter gene (DAT1, SLC6A3) is considered as a candidate risk factor for PD. Since the DNA methylation on DAT promoter may well have a role in the development of this disease, we aimed to further assess the epigenetic control, by focusing on specific CpG sites located in the 5'-untranslated region (5'-UTR) of the DAT1 gene. Significant changes in DAT 5'-UTR methylation were already found in peripheral blood mononuclear cells (PBMCs) of PD subjects (Rubino et al., 2020). Of note, methylation values at the CpG 5 were increased. We run on same data a novel statistical approach: cross-correlation between pairs of loci. CpG 5 was the only always-differing variable but, alternatively, CpGs 2 and 6 or CpGs 1 and 3 were also significantly correlated with CpG 5. Interestingly, this picture emerged for those patients whose M2xM6 index was above-median; loci were rather independent for below-median patients. Present data may shed light into dynamics occurring at 5'-UTR of DAT1, a gene involved in PD but also in many psycho-physiological pathologies.
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Affiliation(s)
- Xhensina Tafani
- Faculty of Psychology - UTIU Università Telematica Internazionale "Uninettuno", Rome, Italy
| | - Esterina Pascale
- Department of Medical-Surgical Sciences and Biotechnologies, Sapienza University, Rome, Italy
| | | | - Mariangela Pucci
- Faculty of Bioscience & Technology for Food, for Agriculture and for Environment - University of Teramo, Teramo, Italy
| | - Claudio D'Addario
- Faculty of Bioscience & Technology for Food, for Agriculture and for Environment - University of Teramo, Teramo, Italy
| | - Walter Adriani
- Faculty of Psychology - UTIU Università Telematica Internazionale "Uninettuno", Rome, Italy; Reference Center for Behavioral Science and Mental Health - Istituto Superiore di Sanità, Rome, Italy.
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Rubino A, D'Addario C, Di Bartolomeo M, Michele Salamone E, Locuratolo N, Fattapposta F, Vanacore N, Pascale E. DNA methylation of the 5'-UTR DAT 1 gene in Parkinson's disease patients. Acta Neurol Scand 2020; 142:275-280. [PMID: 32415851 DOI: 10.1111/ane.13279] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/30/2020] [Accepted: 05/11/2020] [Indexed: 12/27/2022]
Abstract
OBJECTIVES The involvement of epigenetics mechanisms in the transcriptional regulation of key genes has been investigated in the initiation and progression of neurodegenerative disorders, including Parkinson's disease (PD). Among others, we, here, focused the attention on the dopamine transporter (DAT) gene playing a critical role in maintaining the integrity of dopaminergic neurons. MATERIALS AND METHODS We performed bisulfite pyrosequencing to examine DNA methylation levels of six CpG sites in the 5'-UTR of DAT1 gene in human peripheral blood mononuclear cells (PBMCs) obtained from 101 sporadic PD patients and 59 healthy controls. RESULTS We selectively report for CpG5 an increase in DNA methylation levels in PD subjects respect to controls, that almost reaches statistical significance (30.06 ± 12.4 vs 26.58 ± 7.6, P = .052). Of interest, a significantly higher methylation at specific CpG sites (ANOVA: P = .029) was observed in PD subjects with advanced stage of illness. Namely, a multivariate regression analysis showed that a higher methylation level at specific CpG sites in the group of PD patients was associated with increased methylation at CpG2, CpG3, and with H&Y stage but not with age and gender. This regression model explains the 38% of the variance of methylation at CpG5. CONCLUSION Our results do seem to suggest that the methylation level of CpG5 is different between PD patients and controls. Moreover, this methylation level for CpG5 may be associated also with the stage of disease.
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Affiliation(s)
- Alfonso Rubino
- Department of Human NeurosciencesSapienza University Rome Italy
| | - Claudio D'Addario
- Faculty of Bioscience and Technology for Food, Agriculture and EnvironmentUniversity of Teramo Teramo Italy
- Department of Clinical NeuroscienceKarolinska Institute Stockholm Stockholm Sweden
| | - Martina Di Bartolomeo
- Faculty of Bioscience and Technology for Food, Agriculture and EnvironmentUniversity of Teramo Teramo Italy
| | | | | | | | - Nicola Vanacore
- National Centre for Disease Prevention and Health PromotionNational Institute of Health Rome Italy
| | - Esterina Pascale
- Department of Medical‐Surgical Sciences and BiotechnologiesSapienza University Rome Italy
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Lee D, Choi YH, Seo J, Kim JK, Lee SB. Discovery of new epigenomics-based biomarkers and the early diagnosis of neurodegenerative diseases. Ageing Res Rev 2020; 61:101069. [PMID: 32416267 DOI: 10.1016/j.arr.2020.101069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 03/02/2020] [Accepted: 04/06/2020] [Indexed: 12/12/2022]
Abstract
Treatment options for many neurodegenerative diseases are limited due to the lack of early diagnostic procedures that allow timely delivery of therapeutic agents to affected neurons prior to cell death. While notable advances have been made in neurodegenerative disease biomarkers, whether or not the biomarkers discovered to date are useful for early diagnosis remains an open question. Additionally, the reliability of these biomarkers has been disappointing, due in part to the large dissimilarities between the tissues traditionally used to source biomarkers and primarily diseased neurons. In this article, we review the potential viability of atypical epigenetic and/or consequent transcriptional alterations (ETAs) as biomarkers of early-stage neurodegenerative disease, and present our perspectives on the discovery and practical use of such biomarkers in patient-derived neural samples using single-cell level analyses, thereby greatly enhancing the reliability of biomarker application.
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35
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Zhao A, Li Y, Niu M, Li G, Luo N, Zhou L, Kang W, Liu J. SNCA Hypomethylation in Rapid Eye Movement Sleep Behavior Disorder Is a Potential Biomarker for Parkinson’s Disease. JOURNAL OF PARKINSONS DISEASE 2020; 10:1023-1031. [PMID: 32444558 DOI: 10.3233/jpd-201912] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Aonan Zhao
- Department of Neurology and Institute of Neurology, Ruijin Hospital affiliated with the Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuanyuan Li
- Department of Neurology and Institute of Neurology, Ruijin Hospital affiliated with the Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mengyue Niu
- Department of Neurology and Institute of Neurology, Ruijin Hospital affiliated with the Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guanglu Li
- Department of Neurology and Institute of Neurology, Ruijin Hospital affiliated with the Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ningdi Luo
- Department of Neurology and Institute of Neurology, Ruijin Hospital affiliated with the Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liche Zhou
- Department of Neurology and Institute of Neurology, Ruijin Hospital affiliated with the Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenyan Kang
- Department of Neurology, Ruijin Hospital North affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jun Liu
- Department of Neurology and Institute of Neurology, Ruijin Hospital affiliated with the Shanghai Jiao Tong University School of Medicine, Shanghai, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Ruijin Hospital affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
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Epigenetics in Lewy Body Diseases: Impact on Gene Expression, Utility as a Biomarker, and Possibilities for Therapy. Int J Mol Sci 2020; 21:ijms21134718. [PMID: 32630630 PMCID: PMC7369933 DOI: 10.3390/ijms21134718] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 02/07/2023] Open
Abstract
Lewy body disorders (LBD) include Parkinson's disease (PD) and dementia with Lewy bodies (DLB). They are synucleinopathies with a heterogeneous clinical manifestation. As a cause of neuropathological overlap with other neurodegenerative diseases, the establishment of a correct clinical diagnosis is still challenging, and clinical management may be difficult. The combination of genetic variation and epigenetic changes comprising gene expression-modulating DNA methylation and histone alterations modifies the phenotype, disease course, and susceptibility to disease. In this review, we summarize the results achieved in the deciphering of the LBD epigenome. To provide an appropriate context, first LBD genetics is briefly outlined. Afterwards, a detailed review of epigenetic modifications identified for LBD in human cells, postmortem, and peripheral tissues is provided. We also focus on the difficulty of identifying epigenome-related biomarker candidates and discuss the results obtained so far. Additionally, epigenetic changes as therapeutic targets, as well as different epigenome-based treatments, are revised. The number of studies focusing on PD is relatively limited and practically inexistent for DLB. There is a lack of replication studies, and some results are even contradictory, probably due to differences in sample collection and analytical techniques. In summary, we show the current achievements and directions for future research.
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Kanzato N, Nakachi K, Naka T, Mochizuki S, Miyamae Y, Okada Y. Parkinson's disease therapy with Istradefylline and blood biomarkers of epigenetics. ACTA ACUST UNITED AC 2020. [DOI: 10.1111/ncn3.12415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Naomi Kanzato
- Department of Neurology Okinawa Prefectural Southern Medical Center & Children's Medical Center Okinawa Japan
| | - Kou Nakachi
- Department of Neurology Okinawa Prefectural Southern Medical Center & Children's Medical Center Okinawa Japan
| | - Taro Naka
- Department of Neurology Okinawa Prefectural Southern Medical Center & Children's Medical Center Okinawa Japan
| | - Satsuki Mochizuki
- Department of Surgery National Defense Medical College Saitama Japan
| | - Yuka Miyamae
- Department of Pathophysiology for Locomotive and Neoplastic Diseases Juntendo University Graduate School of Medicine Tokyo Japan
| | - Yasunori Okada
- Department of Pathophysiology for Locomotive and Neoplastic Diseases Juntendo University Graduate School of Medicine Tokyo Japan
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Iakovenko EV, Abramycheva NY, Fedotova EY, Illarioshkin SN. The SNCA-Rep1 Polymorphic Locus: Association with the Risk of Parkinson's Disease and SNCA Gene Methylation. Acta Naturae 2020; 12:105-110. [PMID: 32742734 PMCID: PMC7385090 DOI: 10.32607/actanaturae.10956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Neurodegeneration in Parkinson’s disease is characterized by the
accumulation of alpha-synuclein, a protein encoded by the SNCA
gene, in neurons. In addition to mutations, many polymorphisms have
been identified in this gene, and one of these is a dinucleotide
microsatellite: SNCA-Rep1. The mechanisms by
which specific configurations of SNCA-Rep1 may contribute to
the development of this disease have yet to be clarified. In our study, a
relationship between long SNCA-Rep1 alleles and
Parkinson’s was confirmed in the Russian population. Long allelic
variants of SNCA-Rep1 were shown to be associated with the
hypomethylation of the CpG-sites in intron 1 of the SNCA gene.
Long variants of SNCA-Rep1 are supposed to exert their effect
through the hypomethylation of a transcriptionally significant region of this
gene. Hypomethylation is usually associated with increased expression, which,
in turn, contributes to alpha-synuclein accumulation in neuronal cytoplasm,
with the latter being the main molecular marker of Parkinson’s disease.
Further studies are needed to establish a relationship between our finding and
SNCA gene expression.
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Young JI, Sivasankaran SK, Wang L, Ali A, Mehta A, Davis DA, Dykxhoorn DM, Petito CK, Beecham GW, Martin ER, Mash DC, Pericak-Vance M, Scott WK, Montine TJ, Vance JM. Genome-wide brain DNA methylation analysis suggests epigenetic reprogramming in Parkinson disease. NEUROLOGY-GENETICS 2019; 5:e342. [PMID: 31403079 PMCID: PMC6659138 DOI: 10.1212/nxg.0000000000000342] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 05/09/2019] [Indexed: 12/13/2022]
Abstract
Objective Given the known strong relationship of DNA methylation with environmental exposure, we investigated whether brain regions affected in Parkinson disease (PD) were differentially methylated between PD cases and controls. Methods DNA chip arrays were used to perform a genome-wide screen of DNA methylation on the dorsal motor nucleus of the vagus (DMV), substantia nigra (SN), and cingulate gyrus (CG) of pathologically confirmed PD cases and controls selected using the criteria of Beecham et al. Analysis examined differentially methylated regions (DMRs) between cases and controls for each brain area. RNA sequencing and pathway analysis were also performed for each brain area. Results Thirty-eight PD cases and 41 controls were included in the analysis. Methylation studies revealed 234 significant DMR in the DMV, 44 in the SN, and 141 in the CG between cases and controls (Sidak p < 0.05). Pathway analysis of these genes showed significant enrichment for the Wnt signaling pathway (FDR < 0.01). Conclusions Our data suggest that significant DNA methylation changes exist between cases and controls in PD, especially in the DMV, one of the areas affected earliest in PD. The etiology of these methylation changes is not yet known, but the predominance of methylation changes occurring in the DMV supports the hypothesis that vagus nerve function, perhaps involving the gastrointestinal system, is important in PD pathogenesis. These data also give independent support that genes involved in Wnt signaling are a likely factor in the neurodegenerative processes of PD.
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Affiliation(s)
- Juan I Young
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Sathesh K Sivasankaran
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Lily Wang
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Aleena Ali
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Arpit Mehta
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - David A Davis
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Carol K Petito
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Deborah C Mash
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Margaret Pericak-Vance
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - William K Scott
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Thomas J Montine
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics (J.I.Y., S.K.S., A.A., A.M., D.M.D., G.W.B., E.R.M., M.P.-V., W.K.S., J.M.V.), Miller School of Medicine, University of Miami; Department of Public Health Sciences (L.W.), Division of Biostatistics, Miller School of Medicine, University of Miami; Department of Neurology (D.A.D., D.C.M.), Miller School of Medicine, University of Miami; Department of Pathology (C.K.P.), Miller School of Medicine, University of Miami, FL; and Department of Pathology (T.J.M.), Stanford University, CA
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Henderson-Smith A, Fisch KM, Hua J, Liu G, Ricciardelli E, Jepsen K, Huentelman M, Stalberg G, Edland SD, Scherzer CR, Dunckley T, Desplats P. DNA methylation changes associated with Parkinson's disease progression: outcomes from the first longitudinal genome-wide methylation analysis in blood. Epigenetics 2019; 14:365-382. [PMID: 30871403 DOI: 10.1080/15592294.2019.1588682] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Parkinson's Disease (PD) is a common neurodegenerative disorder currently diagnosed based on the presentation of characteristic movement symptoms. Unfortunately, patients exhibiting these symptoms have already undergone significant dopaminergic neuronal loss. Earlier diagnosis, aided by molecular biomarkers specific to PD, would improve overall patient care. Epigenetic mechanisms, which are modified by both environment and disease pathophysiology, are emerging as important components of neurodegeneration. Alterations to the PD methylome have been reported in epigenome-wide association studies. However, the extent to which methylation changes correlate with disease progression has not yet been reported; nor the degree to which methylation is affected by PD medication. We performed a longitudinal genome-wide methylation study surveying ~850,000 CpG sites in whole blood from 189 well-characterized PD patients and 191 control individuals obtained at baseline and at a follow-up visit ~2 y later. We identified distinct patterns of methylation in PD cases versus controls. Importantly, we identified genomic sites where methylation changes longitudinally as the disease progresses. Moreover, we identified methylation changes associated with PD pathology through the analysis of PD cases that were not exposed to anti-parkinsonian therapy. In addition, we identified methylation sites modulated by exposure to dopamine replacement drugs. These results indicate that DNA methylation is dynamic in PD and changes over time during disease progression. To the best of our knowledge, this is the first longitudinal epigenome-wide methylation analysis for Parkinson's disease and reveals changes associated with disease progression and in response to dopaminergic medications in the blood methylome.
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Affiliation(s)
- Adrienne Henderson-Smith
- a Biodesign Institute , Arizona State University , Tempe , AZ , USA.,b Neurogenomics Division , Translational Genomics Research Institute , Phoenix , AZ , USA
| | - Kathleen M Fisch
- c Center for Computational Biology & Bioinformatics, Department of Medicine , University of California San Diego , La Jolla , CA , USA
| | - Jianping Hua
- d Center for Bioinformatics and Genomics Systems Engineering, Texas A&M Engineering Experiment Station , Texas A&M University , College Station , TX , USA
| | - Ganqiang Liu
- e Advanced Center for Parkinson's Disease Research and Precision Neurology Program, Harvard Medical School , Brigham & Women's Hospital , Boston , MA , USA
| | - Eugenia Ricciardelli
- f Genomics Center, Institute for Genomics Medicine , University of California San Diego , La Jolla , CA , USA
| | - Kristen Jepsen
- f Genomics Center, Institute for Genomics Medicine , University of California San Diego , La Jolla , CA , USA
| | - Mathew Huentelman
- b Neurogenomics Division , Translational Genomics Research Institute , Phoenix , AZ , USA
| | - Gabriel Stalberg
- e Advanced Center for Parkinson's Disease Research and Precision Neurology Program, Harvard Medical School , Brigham & Women's Hospital , Boston , MA , USA.,g Harvard Biomarkers Study investigators are listed in the Acknowledgement section
| | - Steven D Edland
- h Department of Neurosciences , University of California San Diego , La Jolla , CA , USA
| | - Clemens R Scherzer
- e Advanced Center for Parkinson's Disease Research and Precision Neurology Program, Harvard Medical School , Brigham & Women's Hospital , Boston , MA , USA
| | - Travis Dunckley
- a Biodesign Institute , Arizona State University , Tempe , AZ , USA
| | - Paula Desplats
- h Department of Neurosciences , University of California San Diego , La Jolla , CA , USA.,i Department of Pathology , University of California San Diego , La Jolla , CA , USA
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Kaut O, Kuchelmeister K, Moehl C, Wüllner U. 5-methylcytosine and 5-hydroxymethylcytosine in brains of patients with multiple system atrophy and patients with Parkinson’s disease. J Chem Neuroanat 2019; 96:41-48. [DOI: 10.1016/j.jchemneu.2018.12.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 12/14/2018] [Indexed: 12/26/2022]
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Wang C, Chen L, Yang Y, Zhang M, Wong G. Identification of potential blood biomarkers for Parkinson's disease by gene expression and DNA methylation data integration analysis. Clin Epigenetics 2019; 11:24. [PMID: 30744671 PMCID: PMC6371578 DOI: 10.1186/s13148-019-0621-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/24/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Blood-based gene expression or epigenetic biomarkers of Parkinson's disease (PD) are highly desirable. However, accuracy and specificity need to be improved, and methods for the integration of gene expression with epigenetic data need to be developed in order to make this feasible. METHODS Whole blood gene expression data and DNA methylation data were downloaded from Gene Expression Omnibus (GEO) database. A linear model was used to identify significantly differentially expressed genes (DEGs) and differentially methylated genes (DMGs) according to specific gene regions 5'-C-phosphate-G-3' (CpGs) or all gene regions CpGs in PD. Gene set enrichment analysis was then applied to DEGs and DMGs. Subsequently, data integration analysis was performed to identify robust PD-associated blood biomarkers. Finally, the random forest algorithm and a leave-one-out cross validation method were performed to construct classifiers based on gene expression data integrated with methylation data. RESULTS Eighty-five (85) significantly hypo-methylated and upregulated genes in PD patients compared to healthy controls were identified. The dominant hypo-methylated regions of these genes were significantly different. Some genes had a single dominant hypo-methylated region, while others had multiple dominant hypo-methylated regions. One gene expression classifier and two gene methylation classifiers based on all or dominant methylation-altered region CpGs were constructed. All have a good prediction power for PD. CONCLUSIONS Gene expression and methylation data integration analysis identified a blood-based 53-gene signature, which could be applied as a biomarker for PD.
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Affiliation(s)
- Changliang Wang
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R., Macau, China
| | - Liang Chen
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R., Macau, China
| | - Yang Yang
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R., Macau, China
| | - Menglei Zhang
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R., Macau, China
| | - Garry Wong
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R., Macau, China.
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Li X, Liu Q, Zhu D, Che Y, Feng X. Preparation of levodopa-loaded crystalsomes through thermally induced crystallization reverses functional deficits in Parkinsonian mice. Biomater Sci 2019; 7:1623-1631. [DOI: 10.1039/c8bm01098f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The prepared levodopa loaded crystalsomes are nanoscale crystals and controlling levodopa release which improving MPTP-induced behavioral impairments and pathological features of mice.
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Affiliation(s)
- Xinyu Li
- State Key Laboratory of Medicinal Chemical Biology
- Key Laboratory of Bioactive Materials
- Ministry of Education
- College of Life Sciences
- Nankai University
| | - Qianqian Liu
- State Key Laboratory of Medicinal Chemical Biology
- Key Laboratory of Bioactive Materials
- Ministry of Education
- College of Life Sciences
- Nankai University
| | - Dashuai Zhu
- Nankai University
- School of medicine
- Tianjin
- China
| | - Yongzhe Che
- Nankai University
- School of medicine
- Tianjin
- China
| | - Xizeng Feng
- State Key Laboratory of Medicinal Chemical Biology
- Key Laboratory of Bioactive Materials
- Ministry of Education
- College of Life Sciences
- Nankai University
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SNCA variants and alpha-synuclein level in CD45+ blood cells in Parkinson’s disease. J Neurol Sci 2018; 395:135-140. [DOI: 10.1016/j.jns.2018.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 08/30/2018] [Accepted: 10/02/2018] [Indexed: 11/23/2022]
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Navarro-Sánchez L, Águeda-Gómez B, Aparicio S, Pérez-Tur J. Epigenetic Study in Parkinson's Disease: A Pilot Analysis of DNA Methylation in Candidate Genes in Brain. Cells 2018; 7:cells7100150. [PMID: 30261625 PMCID: PMC6210421 DOI: 10.3390/cells7100150] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/15/2018] [Accepted: 09/21/2018] [Indexed: 01/08/2023] Open
Abstract
Efforts have been made to understand the pathophysiology of Parkinson’s disease (PD). A significant number of studies have focused on genetics, despite the fact that the described pathogenic mutations have been observed only in around 10% of patients; this observation supports the fact that PD is a multifactorial disorder. Lately, differences in miRNA expression, histone modification, and DNA methylation levels have been described, highlighting the importance of epigenetic factors in PD etiology. Taking all this into consideration, we hypothesized that an alteration in the level of methylation in PD-related genes could be related to disease pathogenesis, possibly due to alterations in gene expression. After analysing promoter regions of five PD-related genes in three brain regions by pyrosequencing, we observed some differences in DNA methylation levels (hypo and hypermethylation) in substantia nigra in some CpG dinucleotides that, possibly through an alteration in Sp1 binding, could alter their expression.
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Affiliation(s)
- Luis Navarro-Sánchez
- Unitat de Genètica Molecular, Instituto de Biomedicina de Valencia, CSIC, 46010 València, Spain.
| | - Beatriz Águeda-Gómez
- Unitat de Genètica Molecular, Instituto de Biomedicina de Valencia, CSIC, 46010 València, Spain.
| | - Silvia Aparicio
- Unitat de Genètica Molecular, Instituto de Biomedicina de Valencia, CSIC, 46010 València, Spain.
| | - Jordi Pérez-Tur
- Unitat de Genètica Molecular, Instituto de Biomedicina de Valencia, CSIC, 46010 València, Spain.
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), 46010 València, Spain.
- Unidad Mixta de Genética y Neurología, Instituto de Investigación Sanitaria La Fe, 46026 València, Spain.
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Epigenetic mechanisms in amyotrophic lateral sclerosis: A short review. Mech Ageing Dev 2018; 174:103-110. [DOI: 10.1016/j.mad.2018.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 03/08/2018] [Accepted: 03/11/2018] [Indexed: 12/13/2022]
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Piper DA, Sastre D, Schüle B. Advancing Stem Cell Models of Alpha-Synuclein Gene Regulation in Neurodegenerative Disease. Front Neurosci 2018; 12:199. [PMID: 29686602 PMCID: PMC5900030 DOI: 10.3389/fnins.2018.00199] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 03/13/2018] [Indexed: 12/15/2022] Open
Abstract
Alpha-synuclein (non A4 component of amyloid precursor, SNCA, NM_000345.3) plays a central role in the pathogenesis of Parkinson's disease (PD) and related Lewy body disorders such as Parkinson's disease dementia, Lewy body dementia, and multiple system atrophy. Since its discovery as a disease-causing gene in 1997, alpha-synuclein has been a central point of scientific interest both at the protein and gene level. Mutations, including copy number variants, missense mutations, short structural variants, and single nucleotide polymorphisms, can be causative for PD and affect conformational changes of the protein, can contribute to changes in expression of alpha-synuclein and its isoforms, and can influence regulation of temporal as well as spatial levels of alpha-synuclein in different tissues and cell types. A lot of progress has been made to understand both the physiological transcriptional and epigenetic regulation of the alpha-synuclein gene and whether changes in transcriptional regulation could lead to disease and neurodegeneration in PD and related alpha-synucleinopathies. Although the histopathological changes in these neurodegenerative disorders are similar, the temporal and spatial presentation and progression distinguishes them which could be in part due to changes or disruption of transcriptional regulation of alpha-synuclein. In this review, we describe different genetic alterations that contribute to PD and neurodegenerative conditions and review aspects of transcriptional regulation of the alpha-synuclein gene in the context of the development of PD. New technologies, advanced gene engineering and stem cell modeling, are on the horizon to shed further light on a better understanding of gene regulatory processes and exploit them for therapeutic developments.
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Affiliation(s)
- Desiree A Piper
- Parkinson's Institute and Clinical Center, Sunnyvale, CA, United States
| | - Danuta Sastre
- Parkinson's Institute and Clinical Center, Sunnyvale, CA, United States
| | - Birgitt Schüle
- Parkinson's Institute and Clinical Center, Sunnyvale, CA, United States
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de Boni L, Gasparoni G, Haubenreich C, Tierling S, Schmitt I, Peitz M, Koch P, Walter J, Wüllner U, Brüstle O. DNA methylation alterations in iPSC- and hESC-derived neurons: potential implications for neurological disease modeling. Clin Epigenetics 2018; 10:13. [PMID: 29422978 PMCID: PMC5789607 DOI: 10.1186/s13148-018-0440-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 01/04/2018] [Indexed: 12/21/2022] Open
Abstract
Background Genetic predisposition and epigenetic alterations are both considered to contribute to sporadic neurodegenerative diseases (NDDs) such as Parkinson's disease (PD). Since cell reprogramming and the generation of induced pluripotent stem cells (iPSCs) are themselves associated with major epigenetic remodeling, it remains unclear to what extent iPSC-derived neurons lend themselves to model epigenetic disease-associated changes. A key question to be addressed in this context is whether iPSC-derived neurons exhibit epigenetic signatures typically observed in neurons derived from non-reprogrammed human embryonic stem cells (hESCs). Results Here, we compare mature neurons derived from hESC and isogenic human iPSC generated from hESC-derived neural stem cells. Genome-wide 450 K-based DNA methylation and HT12v4 gene array expression analyses were complemented by a deep analysis of selected genes known to be involved in NDD. Our studies show that DNA methylation and gene expression patterns of isogenic hESC- and iPSC-derived neurons are markedly preserved on a genome-wide and single gene level. Conclusions Overall, iPSC-derived neurons exhibit similar DNA methylation patterns compared to isogenic hESC-derived neurons. Further studies will be required to explore whether the epigenetic patterns observed in iPSC-derived neurons correspond to those detectable in native brain neurons.
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Affiliation(s)
- Laura de Boni
- Department of Neurology, University Hospital of Bonn, Bonn, Germany
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Gilles Gasparoni
- Institute for Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken, Germany
| | - Carolin Haubenreich
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Sascha Tierling
- Institute for Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken, Germany
| | - Ina Schmitt
- Department of Neurology, University Hospital of Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany
| | - Michael Peitz
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany
| | - Philipp Koch
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Jörn Walter
- Institute for Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken, Germany
| | - Ullrich Wüllner
- Department of Neurology, University Hospital of Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany
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Gámez-Valero A, Beyer K. Alternative Splicing of Alpha- and Beta-Synuclein Genes Plays Differential Roles in Synucleinopathies. Genes (Basel) 2018; 9:genes9020063. [PMID: 29370097 PMCID: PMC5852559 DOI: 10.3390/genes9020063] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/15/2018] [Accepted: 01/17/2018] [Indexed: 11/16/2022] Open
Abstract
The synuclein family is composed of three members, two of which, α- and β-synuclein, play a major role in the development of synucleinopathies, including Parkinson’s disease (PD) as most important movement disorder, dementia with Lewy bodies (DLB) as the second most frequent cause of dementia after Alzheimer’s disease and multiple system atrophy. Whereas abnormal oligomerization and fibrillation of α-synuclein are now well recognized as initial steps in the development of synucleinopathies, β-synuclein is thought to be a natural α-synuclein anti-aggregant. α-synuclein is encoded by the SNCA gene, and β-synuclein by SNCB. Both genes are homologous and undergo complex splicing events. On one hand, in-frame splicing of coding exons gives rise to at least three shorter transcripts, and the functional properties of the corresponding protein isoforms are different. Another type of alternative splicing is the alternative inclusion of at least four initial exons in the case of SNCA, and two in the case of SNCB. Finally, different lengths of 3’ untranslated regions have been also reported for both genes. SNCB only expresses in the brain, but some of the numerous SNCA transcripts are also brain-specific. With the present article, we aim to provide a systematic review of disease related changes in the differential expression of the various SNCA and SNCB transcript variants in brain, blood, and non-neuronal tissue of synucleinopathies, but especially PD and DLB as major neurodegenerative disorders.
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Affiliation(s)
- Ana Gámez-Valero
- Department of Pathology, Germans Trias i Pujol Research Institute, Badalona, 08916 Barcelona, Spain.
| | - Katrin Beyer
- Department of Pathology, Germans Trias i Pujol Research Institute, Badalona, 08916 Barcelona, Spain.
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