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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 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] [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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Shadrina MI, Slominsky PA. Genetic Architecture of Parkinson's Disease. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:417-433. [PMID: 37076287 DOI: 10.1134/s0006297923030100] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 03/28/2023]
Abstract
Year 2022 marks 25 years since the first mutation in familial autosomal dominant Parkinson's disease was identified. Over the years, our understanding of the role of genetic factors in the pathogenesis of familial and idiopathic forms of Parkinson's disease has expanded significantly - a number of genes for the familial form of the disease have been identified, and DNA markers for an increased risk of developing its sporadic form have been found. But, despite all the success achieved, we are far from an accurate assessment of the contribution of genetic and, even more so, epigenetic factors to the disease development. The review summarizes the information accumulated to date on the genetic architecture of Parkinson's disease and formulates issues that need to be addressed, which are primarily related to the assessment of epigenetic factors in the disease pathogenesis.
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Affiliation(s)
- Maria I Shadrina
- Institute of Molecular Genetics, Kurchatov Institute National Research Centre, Moscow, 123182, Russia.
| | - Petr A Slominsky
- Institute of Molecular Genetics, Kurchatov Institute National Research Centre, Moscow, 123182, Russia
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Fu MP, Merrill SM, Sharma M, Gibson WT, Turvey SE, Kobor MS. Rare diseases of epigenetic origin: Challenges and opportunities. Front Genet 2023; 14:1113086. [PMID: 36814905 PMCID: PMC9939656 DOI: 10.3389/fgene.2023.1113086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023] Open
Abstract
Rare diseases (RDs), more than 80% of which have a genetic origin, collectively affect approximately 350 million people worldwide. Progress in next-generation sequencing technology has both greatly accelerated the pace of discovery of novel RDs and provided more accurate means for their diagnosis. RDs that are driven by altered epigenetic regulation with an underlying genetic basis are referred to as rare diseases of epigenetic origin (RDEOs). These diseases pose unique challenges in research, as they often show complex genetic and clinical heterogeneity arising from unknown gene-disease mechanisms. Furthermore, multiple other factors, including cell type and developmental time point, can confound attempts to deconvolute the pathophysiology of these disorders. These challenges are further exacerbated by factors that contribute to epigenetic variability and the difficulty of collecting sufficient participant numbers in human studies. However, new molecular and bioinformatics techniques will provide insight into how these disorders manifest over time. This review highlights recent studies addressing these challenges with innovative solutions. Further research will elucidate the mechanisms of action underlying unique RDEOs and facilitate the discovery of treatments and diagnostic biomarkers for screening, thereby improving health trajectories and clinical outcomes of affected patients.
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Affiliation(s)
- Maggie P. Fu
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Sarah M. Merrill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Mehul Sharma
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada,Department of Pediatrics, Faculty of Medicine, BC Children’s Hospital, University of British Columbia, Vancouver, BC, Canada
| | - William T. Gibson
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Stuart E. Turvey
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada,Department of Pediatrics, Faculty of Medicine, BC Children’s Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Michael S. Kobor
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada,*Correspondence: Michael S. Kobor,
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Wang JY, Cui L, Shi HY, Chen LH, Jin RW, Jiang XX, Chen ZL, Zhu JH, Zhang X. Gene-wide significant association analyses of DNMT1 genetic variants with Parkinson's disease. Front Genet 2023; 14:1112388. [PMID: 36950137 PMCID: PMC10025298 DOI: 10.3389/fgene.2023.1112388] [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: 01/20/2023] [Accepted: 02/24/2023] [Indexed: 03/08/2023] Open
Abstract
Background: DNA methylation plays an important role in Parkinson's disease (PD) pathogenesis. DNA methyltransferase 1 (DNMT1) is critical for maintaining DNA methylation in mammals. The link between DNMT1 polymorphisms and PD remains elusive. Methods: The DNMT1 gene contained a total of 28 single nucleotide polymorphisms (SNPs). Four representing tag-SNPs (rs16999593, rs2162560, rs11880553, and rs9305012) were identified and genotyped in a Han Chinese population comprising 712 PD patients and 696 controls. Association analyses were performed at gene-wide significance (p < 1.8 × 10-3). Results: Rs9305012, but not the other 3 tag-SNPs, was gene-wide significantly associated with PD risk (p = 0.8 × 10-3). The rs9305012/C was a protective allele against PD (p = 1.5 × 10-3, OR 0.786, 95% CI 0.677-0.912). No significant association was observed in individual genders or PD subtypes. Haplotypes of the 4 tag-SNPs showed a significant overall distribution difference between PD patients and controls (p < 1 × 10-4). The 3-allele ACC module in the order of rs2162560, rs11880553, and rs9305012 was the highest-risk haplotype associated with PD (p < 1 × 10-4, OR 2.439, 95% CI 1.563-3.704). Rs9305012 displayed certain probability to affect transcription factor binding and target gene expression based on functional annotation analyses. Conclusion: The DNMT1 variant rs9305012 together with its haplotypes may gene-wide significantly modulate PD susceptibility. Our results support a role of DNMT1 in PD pathogenesis and provide novel insights into the genetic connection in between.
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Affiliation(s)
- Jian-Yong Wang
- Department of Neurology, Institute of Geriatric Neurology, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lei Cui
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Hong-Yi Shi
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ling-Hao Chen
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ren-Wei Jin
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiao-Xia Jiang
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhu-Ling Chen
- Department of Neurology, Institute of Geriatric Neurology, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jian-Hong Zhu
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, Zhejiang, China
- *Correspondence: Jian-Hong Zhu, ; Xiong Zhang,
| | - Xiong Zhang
- Department of Neurology, Institute of Geriatric Neurology, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, Zhejiang, China
- *Correspondence: Jian-Hong Zhu, ; Xiong Zhang,
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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: 0] [Impact Index Per Article: 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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Fan L, Qin JC, Li CR, Yang ZY. Two similar Schiff-base receptor based quinoline derivate: Highly selective fluorescent probe for Zn(II). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 236:118347. [PMID: 32305837 DOI: 10.1016/j.saa.2020.118347] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/31/2020] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
As is known, Zn2+ plays a vital role in a variety of biological processes but excessive exposure of Zn2+ to human beings can cause toxicity, inducing a series of overt poisoning symptoms and neurodegenerative disorders. Thus, we designed and synthesized two quinoline-derived Schiff-bases HL1 and HL2, and investigated the fluorescence emission responses of these two Schiff-bases to various metal ions. A significant enhancement in fluorescence emission band centered at 450 nm was observed in the ethanolic solution of HL1 with addition of Zn2+, while remarkably lower fluorescence emission enhancement was obtained in the case of HL2 in which one methyl group was introduced to the azomethine carbon. In addition, HL1 showed good selectivity and high sensitivity towards Zn2+ in the existence of other various interfering metal ions, and the reversibility and regeneration of HL1 were also perfect for extending its applications in environmental and biological systems. Therefore, HL1 could be identified as a fluorescent probe for sensing Zn2+ environmentally and biologically.
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Affiliation(s)
- Long Fan
- College of Chemistry and Chemical Engineering, State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, PR China; Quality and Technical Supervision and Inspection of Jin Chang, Jin Chang 737100, PR China
| | - Jing-Can Qin
- College of Chemistry and Chemical Engineering, State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, PR China
| | - Chao-Rui Li
- College of Chemistry and Chemical Engineering, State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, PR China
| | - Zheng-Yin Yang
- College of Chemistry and Chemical Engineering, State Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, PR China.
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Saravanaraman P, Selvam M, Ashok C, Srijyothi L, Baluchamy S. De novo methyltransferases: Potential players in diseases and new directions for targeted therapy. Biochimie 2020; 176:85-102. [PMID: 32659446 DOI: 10.1016/j.biochi.2020.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 06/06/2020] [Accepted: 07/07/2020] [Indexed: 12/16/2022]
Abstract
Epigenetic modifications govern gene expression by guiding the human genome on 'what to express and what not to'. DNA methyltransferases (DNMTs) establish methylation patterns on DNA, particularly in CpG islands, and such patterns play a major role in gene silencing. DNMTs are a family of proteins/enzymes (DNMT1, 2, 3A, 3B, and 3L), among which, DNMT1 (maintenance methyltransferase) and DNMT3 (de novo methyltransferases) that direct mammalian development and genome imprinting are highly investigated. In recent decades, many studies revealed a strong association of DNA methylation patterns with gene expression in various clinical conditions. Differential expression of DNMT3 family proteins and their splice variants result in changes in methylation patterns and such alterations have been associated with the initiation and progression of various diseases, especially cancer. This review will discuss the aberrant modifications generated by DNMT3 proteins under various clinical conditions, suggesting a potential signature for de novo methyltransferases in targeted disease therapy. Further, this review discusses the possibility of using 'CpG island methylation signatures' as promising biomarkers and emphasizes 'targeted hypomethylation' by disrupting the interaction of specific DNMT-protein complexes as the future of cancer therapeutics.
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Affiliation(s)
- Ponne Saravanaraman
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Murugan Selvam
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Cheemala Ashok
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Loudu Srijyothi
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Sudhakar Baluchamy
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India.
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Stoccoro A, Tannorella P, Migliore L, Coppedè F. Polymorphisms of genes required for methionine synthesis and DNA methylation influence mitochondrial DNA methylation. Epigenomics 2020; 12:1003-1012. [PMID: 32393056 DOI: 10.2217/epi-2020-0041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aim: Impaired methylation of the mitochondrial DNA and particularly in the regulatory displacement loop (D-loop) region, is increasingly observed in patients with neurodegenerative disorders. The present study aims to investigate if common polymorphisms of genes required for one-carbon metabolism (MTHFR, MTRR, MTR and RFC-1) and DNA methylation reactions (DNMT1, DNMT3A and DNMT3B) influence D-loop methylation levels. Materials & methods: D-loop methylation data were available from 133 late-onset Alzheimer's disease patients and 130 matched controls. Genotyping was performed with PCR-RFLP or high resolution melting techniques. Results: Both MTRR 66A > G and DNMT3A -448A > G polymorphisms were significantly associated with D-loop methylation levels. Conclusion: This exploratory study suggests that MTRR and DNMT3A polymorphisms influence mitochondrial DNA methylation; further research is required to better address this issue.
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Affiliation(s)
- Andrea Stoccoro
- Department of Translational Research & of New Surgical & Medical Technologies, University of Pisa, Via Roma 55, 56126, Pisa, Italy
| | - Pierpaola Tannorella
- Department of Translational Research & of New Surgical & Medical Technologies, University of Pisa, Via Roma 55, 56126, Pisa, Italy
- Current address: Unit of Genetics of Neurodegenerative & Metabolic Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Lucia Migliore
- Department of Translational Research & of New Surgical & Medical Technologies, University of Pisa, Via Roma 55, 56126, Pisa, Italy
| | - Fabio Coppedè
- Department of Translational Research & of New Surgical & Medical Technologies, University of Pisa, Via Roma 55, 56126, Pisa, Italy
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Coppedè F, Stoccoro A, Tannorella P, Gallo R, Nicolì V, Migliore L. Association of Polymorphisms in Genes Involved in One-Carbon Metabolism with MTHFR Methylation Levels. Int J Mol Sci 2019; 20:E3754. [PMID: 31370354 PMCID: PMC6696388 DOI: 10.3390/ijms20153754] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/26/2019] [Accepted: 07/30/2019] [Indexed: 12/11/2022] Open
Abstract
Methylenetetrahydrofolate reductase (MTHFR) is a pivotal enzyme in the one-carbon metabolism, a metabolic pathway required for DNA synthesis and methylation reactions. MTHFR hypermethylation, resulting in reduced gene expression, can contribute to several human disorders, but little is still known about the factors that regulate MTHFR methylation levels. We performed the present study to investigate if common polymorphisms in one-carbon metabolism genes contribute to MTHFR methylation levels. MTHFR methylation was assessed in peripheral blood DNA samples from 206 healthy subjects with methylation-sensitive high-resolution melting (MS-HRM); genotyping was performed for MTHFR 677C>T (rs1801133) and 1298A>C (rs1801131), MTRR 66A>G (rs1801394), MTR 2756A>G (rs1805087), SLC19A1 (RFC1) 80G>A (rs1051266), TYMS 28-bp tandem repeats (rs34743033) and 1494 6-bp ins/del (rs34489327), DNMT3A -448A>G (rs1550117), and DNMT3B -149C>T (rs2424913) polymorphisms. We observed a statistically significant effect of the DNMT3B -149C>T polymorphism on mean MTHFR methylation levels, and particularly CT and TT carriers showed increased methylation levels than CC carriers. The present study revealed an association between a functional polymorphism of DNMT3B and MTHFR methylation levels that could be of relevance in those disorders, such as inborn defects, metabolic disorders and cancer, that have been linked to impaired DNA methylation.
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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.
| | - Andrea Stoccoro
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Via Roma 55, 56126 Pisa, Italy
| | - Pierpaola Tannorella
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Via Roma 55, 56126 Pisa, Italy
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Roberta Gallo
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Via Roma 55, 56126 Pisa, Italy
- Doctoral School in Genetics, Oncology and Clinical Medicine, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Vanessa Nicolì
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Via Roma 55, 56126 Pisa, Italy
- Doctoral School in Genetics, Oncology and Clinical Medicine, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Lucia Migliore
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Via Roma 55, 56126 Pisa, Italy
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Fernández-Santiago R, Merkel A, Castellano G, Heath S, Raya Á, Tolosa E, Martí MJ, Consiglio A, Ezquerra M. Whole-genome DNA hyper-methylation in iPSC-derived dopaminergic neurons from Parkinson's disease patients. Clin Epigenetics 2019; 11:108. [PMID: 31337434 PMCID: PMC6651999 DOI: 10.1186/s13148-019-0701-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 07/08/2019] [Indexed: 12/31/2022] Open
Abstract
Background Parkinson’s disease (PD) is characterized by the loss of midbrain dopaminergic neurons (DAn). Previously, we described the presence of DNA hyper- and hypo-methylation alterations in induced pluripotent stem cells (iPSC)-derived DAn from PD patients using the Illumina 450K array which prominently covers gene regulatory regions. Methods To expand and contextualize previous findings, we performed the first whole-genome DNA bisulfite sequencing (WGBS) using iPSC-derived DAn from representative PD subjects: one sporadic PD (sPD) patient, one monogenic LRRK2-associated PD patient (L2PD), and one control. Results At the whole-genome level, we detected global DNA hyper-methylation in the PD which was similarly spread across the genome in both sPD and L2PD and mostly affected intergenic regions. Conclusion This study implements previous epigenetic knowledge in PD at a whole genome level providing the first comprehensive and unbiased CpG DNA methylation data using iPSC-derived DAn from PD patients. Our results indicate that DAn from monogenic or sporadic PD exhibit global DNA hyper-methylation changes. Findings from this exploratory study are to be validated in further studies analyzing other PD cell models and patient tissues. Electronic supplementary material The online version of this article (10.1186/s13148-019-0701-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rubén Fernández-Santiago
- Department of Neurology, Lab of Parkinson Disease and Other Neurodegenerative Movement Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Faculty of Medicine (UB), University of Barcelona, Casanova 143, Floor 3B, 08036, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain.
| | - Angelika Merkel
- Statistical Genomics Team at the Centro Nacional de Análisis Genómico (CNAG-CRG), Centre de Regulacio Genómico (CRG), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Giancarlo Castellano
- Dept. of Anatomic Pathology, Pharmacology and Microbiology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036, Barcelona, Spain
| | - Simon Heath
- Statistical Genomics Team at the Centro Nacional de Análisis Genómico (CNAG-CRG), Centre de Regulacio Genómico (CRG), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Ángel Raya
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Hospitalet de Llobregat, 08908, Barcelona, Spain.,Centre for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029, Madrid, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - Eduard Tolosa
- Department of Neurology, Lab of Parkinson Disease and Other Neurodegenerative Movement Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Faculty of Medicine (UB), University of Barcelona, Casanova 143, Floor 3B, 08036, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain.,Movement Disorders Unit, Dept. of Neurology, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036, Barcelona, Spain
| | - María-José Martí
- Department of Neurology, Lab of Parkinson Disease and Other Neurodegenerative Movement Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Faculty of Medicine (UB), University of Barcelona, Casanova 143, Floor 3B, 08036, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain.,Movement Disorders Unit, Dept. of Neurology, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036, Barcelona, Spain
| | - Antonella Consiglio
- Department of Pathology and Experimental Therapeutics, Faculty of Medicine, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), University of Barcelona, 08907, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), 08028, Barcelona, Spain.,Department of Molecular and Translational Medicine, University of Brescia, 25123, Brescia, Italy
| | - Mario Ezquerra
- Department of Neurology, Lab of Parkinson Disease and Other Neurodegenerative Movement Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Faculty of Medicine (UB), University of Barcelona, Casanova 143, Floor 3B, 08036, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain.
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11
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Shu L, Qin L, Min S, Pan H, Zhong J, Guo J, Sun Q, Yan X, Chen C, Tang B, Xu Q. Genetic analysis of DNA methylation and hydroxymethylation genes in Parkinson's disease. Neurobiol Aging 2019; 84:242.e13-242.e16. [PMID: 30948140 DOI: 10.1016/j.neurobiolaging.2019.02.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 02/04/2019] [Accepted: 02/27/2019] [Indexed: 01/15/2023]
Abstract
DNA methylation is an important regulatory mechanism of Parkinson's disease (PD). To investigate the relationship between DNA methylation and hydroxymethylation genes and PD, we performed gene-targeted sequencing using molecular inversion probes in a Chinese PD population. We sequenced 12 genes related to DNA methylation and hydroxymethylation in 1657 patients and 1394 control subjects. We conducted genewise association analyses of rare variants detected in the present study and identified the TET1 gene as important in PD (p = 0.0037738, 0.013, 0.019521 (b.collapse test, variable threshold test, and skat-o test, respectively; sex + age as covariates). However, no positive results were observed when conducting association analyses on common variants in these genes. We performed a comprehensive analysis of associations between variants of DNA methylation and hydroxymethylation genes and PD, resulting in determination that TET1 might play a role in PD.
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Affiliation(s)
- Li Shu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lixia Qin
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shishi Min
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
| | - Hongxu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Junfei Zhong
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China; Parkinson's Disease Center of Beijing Institute for Brain Disorders, Beijing, China; Collaborative Innovation Center for Brain Science, Shanghai, China; Collaborative Innovation Center for Genetics and Development, Shanghai, China
| | - Qiying Sun
- National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China; Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xinxiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
| | - Chao Chen
- Center for Medical Genetics, Central South University, Changsha, Hunan, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Center for Medical Genetics, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China; Parkinson's Disease Center of Beijing Institute for Brain Disorders, Beijing, China; Collaborative Innovation Center for Brain Science, Shanghai, China; Collaborative Innovation Center for Genetics and Development, Shanghai, China; Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Changsha, Hunan, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China.
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Gagliardi M, Strazzullo M, Matarazzo MR. DNMT3B Functions: Novel Insights From Human Disease. Front Cell Dev Biol 2018; 6:140. [PMID: 30406101 PMCID: PMC6204409 DOI: 10.3389/fcell.2018.00140] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 10/02/2018] [Indexed: 11/13/2022] Open
Abstract
DNA methylation plays important roles in gene expression regulation and chromatin structure. Its proper establishment and maintenance are essential for mammalian development and cellular differentiation. DNMT3B is the major de novo DNA methyltransferase expressed and active during the early stage of embryonic development, including implantation. In addition to its well-known role to methylate centromeric, pericentromeric, and subtelomeric repeats, recent observations suggest that DNMT3B acts as the main enzyme methylating intragenic regions of active genes. Although largely studied, much remains unknown regarding how these specific patterns of de novo CpG methylation are established in mammalian cells, and which are the rules governing DNMT3B recruitment and activity. Latest evidence indicates that DNMT3B recruitment is regulated by numerous mechanisms including chromatin modifications, transcription levels, non-coding RNAs, and the presence of DNA-binding factors. DNA methylation abnormalities are a common mark of human diseases involving chromosomal and genomic instabilities, such as inherited disease and cancer. The autosomal recessive Immunodeficiency, Centromeric instability and Facial anomalies syndrome, type I (ICF-1), is associated to hypomorphic mutations in DNMT3B gene, while its altered expression has been correlated with the development of tumors. In both cases, this implies that abnormal DNA hypomethylation and hypermethylation patterns affect gene expression and genomic architecture contributing to the pathological states. We will provide an overview of the most recent research aimed at deciphering the molecular mechanisms by which DNMT3B abnormalities are associated with the onset and progression of these pathologies.
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Affiliation(s)
- Miriam Gagliardi
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy.,Max Planck Institute of Psychiatry, Munich, Germany
| | - Maria Strazzullo
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy
| | - Maria R Matarazzo
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy
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Pan H, Shen JY, Du JJ, Cui SS, Liu J, Lin YQ, He YX, Fu Y, Gao C, Li G, Chen SD, Ma JF. Lack of Association Between DNMT3B Polymorphisms and Sporadic Parkinson's Disease in a Han Chinese Population. Neurosci Bull 2018; 34:867-869. [PMID: 29761417 PMCID: PMC6129251 DOI: 10.1007/s12264-018-0233-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/03/2018] [Indexed: 11/24/2022] Open
Affiliation(s)
- Hong Pan
- Laboratory of Neurodegenerative Diseases, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jun-Yi Shen
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Juan-Juan Du
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Shi-Shuang Cui
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jin Liu
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yi-Qi Lin
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yi-Xi He
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yang Fu
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chao Gao
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Gen Li
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Sheng-Di Chen
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jian-Fang Ma
- Department of Neurology and Collaborative Innovation Center for Brain Science, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Chen X, Xiao Y, Wei L, Wu Y, Lu J, Guo W, Huang S, Zhou M, Mo M, Li Z, Cen L, Li S, Yang C, Wu Z, Hu S, Pei Z, Yang X, Qu S, Xu P. Association of DNMT3b gene variants with sporadic Parkinson's disease in a Chinese Han population. J Gene Med 2017; 19:360-365. [PMID: 28990350 DOI: 10.1002/jgm.2991] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 09/11/2017] [Accepted: 09/27/2017] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Parkinson's disease (PD) is the second most common neurodegenerative disorder worldwide. Epigenetic modifications, specifically DNA methylation, have been implicated in the development of this disease. Genetic variants of DNA methyltransferase 3b (DNMT3b), one of the most important DNA methyltransferases, were shown to be associated with PD in a Brazilian population. However, it is unclear whether genetic variants of DNMT3b increase the risk of PD in the Chinese Han people. The present study aimed to investigate the association of the DNMT3b variants rs2424913, rs998382 and rs2424932 with PD in a Chinese Han population. METHODS We studied 487 Chinese Han patients with sporadic PD and 485 healthy age-, sex- and ethnicity-matched controls. DNA was extracted from peripheral blood leukocytes and the individual genotypes were determined using the SNaPshot method. RESULTS We found that the rs2424932 and rs998382 variants were significantly associated with an increased risk of PD compared to the controls [rs2424932: odds ratio (OR) = 1.632, 95% confidence interval (CI) = 1.108-2.406, p = 0.013; rs998382: OR = 1.612, 95% CI = 1.103-2.382, p = 0.014]. Subgroup analysis suggested that female patients carrying the rs2424932 or rs998382 variants were more likely to develop PD than female controls (rs2424932: OR = 3.863, 95% CI = 2.004-7.445, p < 0.001; rs998382: OR = 3.679, 95% CI = 1.943-6.964, p < 0.001). Haplotype analysis indicated that the three variants comprised one block and that the Trs2424913 -Crs998382 -A rs2424932 haplotype was correlated with an increased risk of PD (p = 0.0046), especially for Chinese Han females (p < 0.0001). CONCLUSIONS The results of the present study strongly suggest that DNMT3b variants are associated with PD in the Chinese Han people, especially females.
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Affiliation(s)
- Xiang Chen
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yousheng Xiao
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Guangxi, China
| | - Lei Wei
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yijuan Wu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Disease of the First Affiliated Hospital of Guangzhou Medical University, Guangdong, China
| | - Jianjun Lu
- Department of Neurology, Guangdong 999 Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenyuan Guo
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shuxuan Huang
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Miaomiao Zhou
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Mingshu Mo
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhe Li
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Luan Cen
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Guangxi, China
| | - Shaomin Li
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chaohao Yang
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhuohua Wu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Sophie Hu
- Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Zhong Pei
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - XinLing Yang
- Department of Neurology, The Second Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Shaogang Qu
- Clinical Medicine Research Centre, ShunDe Hospital of Southern Medical University, Foshan, Guangdong, China
| | - Pingyi Xu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- State Key Laboratory of Respiratory Disease of the First Affiliated Hospital of Guangzhou Medical University, Guangdong, China
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