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Li L, Chen R, Zhang H, Li J, Huang H, Weng J, Tan H, Guo T, Wang M, Xie J. The epigenetic modification of DNA methylation in neurological diseases. Front Immunol 2024; 15:1401962. [PMID: 39376563 PMCID: PMC11456496 DOI: 10.3389/fimmu.2024.1401962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 09/03/2024] [Indexed: 10/09/2024] Open
Abstract
Methylation, a key epigenetic modification, is essential for regulating gene expression and protein function without altering the DNA sequence, contributing to various biological processes, including gene transcription, embryonic development, and cellular functions. Methylation encompasses DNA methylation, RNA methylation and histone modification. Recent research indicates that DNA methylation is vital for establishing and maintaining normal brain functions by modulating the high-order structure of DNA. Alterations in the patterns of DNA methylation can exert significant impacts on both gene expression and cellular function, playing a role in the development of numerous diseases, such as neurological disorders, cardiovascular diseases as well as cancer. Our current understanding of the etiology of neurological diseases emphasizes a multifaceted process that includes neurodegenerative, neuroinflammatory, and neurovascular events. Epigenetic modifications, especially DNA methylation, are fundamental in the control of gene expression and are critical in the onset and progression of neurological disorders. Furthermore, we comprehensively overview the role and mechanism of DNA methylation in in various biological processes and gene regulation in neurological diseases. Understanding the mechanisms and dynamics of DNA methylation in neural development can provide valuable insights into human biology and potentially lead to novel therapies for various neurological diseases.
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Affiliation(s)
- Linke Li
- The Center of Obesity and Metabolic Diseases, Department of General Surgery, The Third People’s Hospital of Chengdu and The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- College of Medicine, Southwest Jiaotong University, Chengdu, China
| | - Rui Chen
- The Center of Obesity and Metabolic Diseases, Department of General Surgery, The Third People’s Hospital of Chengdu and The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- College of Medicine, Southwest Jiaotong University, Chengdu, China
- Department of Stomatology, The Third People’s Hospital of Chengdu and The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Hui Zhang
- Department of Stomatology, The Third People’s Hospital of Chengdu and The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- College of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Jinsheng Li
- College of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Hao Huang
- College of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Jie Weng
- College of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Huan Tan
- College of Medicine, Southwest Jiaotong University, Chengdu, China
| | - Tailin Guo
- College of Medicine, Southwest Jiaotong University, Chengdu, China
| | - Mengyuan Wang
- The Center of Obesity and Metabolic Diseases, Department of General Surgery, The Third People’s Hospital of Chengdu and The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
- College of Medicine, Southwest Jiaotong University, Chengdu, China
- Department of Stomatology, The Third People’s Hospital of Chengdu and The Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Jiang Xie
- Key Laboratory of Drug Targeting and Drug Delivery of Ministry of Education (MOE), Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital, West China School of Pharmacy, Sichuan University, Chengdu, China
- Department of Pediatrics, Chengdu Third People’s Hospital, Chengdu, China
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Fan Y, Wang P, Jiang C, Chen J, Zhao M, Liu J. Tet1-mediated activation of the Ampk signaling by Trpv1 DNA hydroxymethylation exerts neuroprotective effects in a rat model of Parkinson's disease. Funct Integr Genomics 2024; 24:161. [PMID: 39285026 DOI: 10.1007/s10142-024-01446-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 08/23/2024] [Accepted: 09/05/2024] [Indexed: 09/26/2024]
Abstract
Epigenetic regulation plays a role in Parkinson's disease (PD), and ten-eleven translocation methylcytosine dioxygenase 1 (TET1) catalyzes the first step in DNA demethylation by converting 5-methylcytosine to 5-hydroxymethylcytosine. We investigated whether TET1 binds to the promoter of the transient receptor potential cation channel subfamily V member 1 (TRPV1) and regulates its expression, thereby controlling oxidative stress in PD. TRPV1 was identified as an oxidative stress-associated gene in the GSE20186 dataset including substantia nigra from 14 patients with PD and 14 healthy controls and the Genecards database. Lentiviral vectors were used to manipulate Trpv1 expression in rats, followed by 6-hydroxydopamine hydrochloride (6-OHDA) injection for modeling. Behavioral tests, immunofluorescence, Nissl staining, western blot assays, DHE fluorescent probe, biochemical analysis, and ELISA were conducted to assess oxidative stress and neurotoxicity. Trpv1 expression was significantly reduced in the brain tissues of 6-OHDA-treated Parkinsonian rats. Trpv1 alleviated behavioral dysfunction, oxidative stress, and dopamine neuron loss in rats. TET1 mediated TRPV1 hydroxymethylation to promote its expression, and Trpv1 inhibition reversed the mitigating effect of Tet1 on oxidative stress and behavioral dysfunction in PD. TRPV1 activated the AMPK signaling by promoting AMPK phosphorylation to alleviate neurotoxicity and oxidative stress in SH-SY5Y cells. Tet1-mediated Trpv1 hydroxymethylation modification promotes the Ampk signaling activation, thereby eliciting neuroprotection in 6-OHDA-treated Parkinsonian rats. These findings provide experimental evidence that targeting the TET1/TRPV1 axis may be neuroprotective for PD by acting on the AMPK signaling.
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Affiliation(s)
- Yu Fan
- Department of Neurology, Baotou Central Hospital, Baotou, 014040, Inner Mongolia, People's Republic of China
| | - Po Wang
- Department of Neurology, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou Workers Hospital, Liuzhou, 545005, Guangxi, People's Republic of China
| | - Changchun Jiang
- Department of Neurology, Baotou Central Hospital, Baotou, 014040, Inner Mongolia, People's Republic of China
| | - Jinyu Chen
- Department of Neurology, Baotou Central Hospital, Baotou, 014040, Inner Mongolia, People's Republic of China
| | - Meili Zhao
- Department of Neurology, Baotou Central Hospital, Baotou, 014040, Inner Mongolia, People's Republic of China
| | - Jiahui Liu
- Department of Neurology, Baotou Central Hospital, Baotou, 014040, Inner Mongolia, People's Republic of China.
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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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Sun Z, Kantor B, Chiba-Falek O. Neuronal-type-specific epigenome editing to decrease SNCA expression: Implications for precision medicine in synucleinopathies. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102084. [PMID: 38130373 PMCID: PMC10732167 DOI: 10.1016/j.omtn.2023.102084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
Overexpression of SNCA has been implicated in the pathogenesis of synucleinopathies, particularly Parkinson's disease (PD) and dementia with Lewy bodies (DLB). While PD and DLB share some clinical and pathological similarities, each disease presents distinct characteristics, including the primary affected brain region and neuronal type. We aimed to develop neuronal-type-specific SNCA-targeted epigenome therapies for synucleinopathies. The system is based on an all-in-one lentiviral vector comprised of CRISPR-dSaCas9 and guide RNA (gRNA) targeted at SNCA intron 1 fused with a synthetic repressor molecule of Krüppel-associated box (KRAB)/ methyl CpG binding protein 2 (MeCp2) transcription repression domain (TRD). To achieve neuronal-type specificity for dopaminergic and cholinergic neurons, the system was driven by tyrosine hydroxylase (TH) and choline acetyltransferase (ChAT) promoters, respectively. Delivering the system into human induced pluripotent stem cell (hiPSC)-derived dopaminergic and cholinergic neurons from a patient with the SNCA triplication resulted in efficient and neuronal-type-specific downregulation of SNCA-mRNA and protein. Furthermore, the reduction in SNCA levels by the gRNA-dSaCas9-repressor system rescued disease-related cellular phenotypes including Ser129-phophorylated α-synuclein, neuronal viability, and mitochondrial dysfunction. We established a novel neuronal-type-specific SNCA-targeted epigenome therapy and provided in vitro proof of concept using human-based disease models. Our results support the therapeutic potential of our system for PD and DLB and provide the foundation for further preclinical studies in animal models toward investigational new drug (IND) enablement and clinical trials.
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Affiliation(s)
| | - Boris Kantor
- Viral Vector Core, Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
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Lu Y, Gao X, Mohammed SAD, Wang T, Fu J, Wang Y, Nan Y, Lu F, Liu S. Efficacy and mechanism study of Baichanting compound, a combination of Acanthopanax senticosus (Rupr. and Maxim.) Harms, Paeonia lactiflora Pall and Uncaria rhynchophylla (Miq.) Miq. ex Havil, on Parkinson's disease based on metagenomics and metabolomics. JOURNAL OF ETHNOPHARMACOLOGY 2024; 319:117182. [PMID: 37714224 DOI: 10.1016/j.jep.2023.117182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/30/2023] [Accepted: 09/11/2023] [Indexed: 09/17/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Parkinson's disease (PD) is a rapidly progressing neurological disorder. Currently, Medication for PD has numerous limitations. Baichanting Compound (BCT) is a Chinese herbal prescription, a Combination of Acanthopanax senticosus (Rupr. and Maxim.) Harms, Paeonia lactiflora Pall and Uncaria rhynchophylla (Miq.) Miq. ex Havil, that was developed to treat PD and holds a national patent (ZL, 201110260536.3). AIM OF THE STUDY To clarify the therapeutic effect of BCT on PD and explore its possible mechanism based on metabolomics and metagenomics. MATERIALS AND METHODS C57BL/6 mice were used as a control group, and α-syn transgenic C57BL/6 mice were randomly assigned to the PD (without treatment) or BCT (with BCT treatment) group. UPLC-MS was performed to detect dopamine levels in brain tissue, while ELISA was used to determine inflammatory factors such as IL-1β, IL-6, TNF-α, IFN-γ and NO, and oxidative stress indicators such as malondialdehyde, superoxide dismutase and glutathione peroxidase enzyme activity. Fecal metabolomics was used to detect fecal metabolic profiles, screen differential metabolic markers, and predict metabolic pathways by KEGG enrichment analysis. Metagenomics was used to determine the intestinal microbial composition, and KO enrichment analysis was performed to predict the potential function of different gut microbiota. Finally, Spearman correlation analysis was used to find the possible relationships among intestinal flora, metabolic markers, inflammatory factors, oxidative stress and dopamine levels. RESULTS BCT increased the superoxide dismutase activity of α-Syn transgenic C57BL/6 mice (P < 0.01), decreased the levels of TNF-α, IFN-γ, IL-1β, IL-6, NO and malondialdehyde (P < 0.01, 0.05), and increased the release of dopamine (P < 0.01). Metabolomics results show that BCT could regulate Acetatifactor, Marvinbryantia, Faecalitalea, Anaeromassilibacillus, Anaerobium, Pseudobutyrivibrio and Lachnotalea and Acetatifactor_muris, Marvinbryantia_formatexigens, Lachnotalea_sp_AF33_28, Faecalitalea_sp_Marseille_P3755 and Anaerobium_acetethylicum, Gemmiger_sp_An120 abundance to restore intestinal flora function, and reverse fecal metabolism trend, restoring the content of α-D-glucose, cytidine, L-glutamate, L-glutamine, N-acetyl-L-glutamate, raffinose and uracil. In addition, it regulates arginine biosynthesis, D-glutamine and D-glutamate, pyrimidine, galactose and alanine, aspartate and glutamate metabolic pathways. CONCLUSION BCT may regulate the composition of the gut microbiota to reverse fecal metabolism in PD mice to protect the substantia nigra and striatum from oxidative stress and inflammatory factors and ultimately play an anti-PD role.
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Affiliation(s)
- Yi Lu
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, 150040, China
| | - Xin Gao
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, 150040, China
| | - Shadi A D Mohammed
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, 150040, China; School of Pharmacy, Lebanese International University, Sana'a, 18644, Yemen
| | - Tianyu Wang
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, 150040, China
| | - Jiaqi Fu
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, 150040, China
| | - Yu Wang
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, 150040, China
| | - Yang Nan
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, 150040, China
| | - Fang Lu
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, 150040, China.
| | - Shumin Liu
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, 150040, China.
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Sun X, Kong J, Dong S, Kato H, Sato H, Hirofuji Y, Ito Y, Wang L, Kato TA, Torio M, Sakai Y, Ohga S, Fukumoto S, Masuda K. TRPV4-mediated Ca 2+ deregulation causes mitochondrial dysfunction via the AKT/α-synuclein pathway in dopaminergic neurons. FASEB Bioadv 2023; 5:507-520. [PMID: 38094157 PMCID: PMC10714070 DOI: 10.1096/fba.2023-00057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/03/2023] [Accepted: 09/13/2023] [Indexed: 06/30/2024] Open
Abstract
Mutations in the gene encoding the transient receptor potential vanilloid member 4 (TRPV4), a Ca2+ permeable nonselective cation channel, cause TRPV4-related disorders. TRPV4 is widely expressed in the brain; however, the pathogenesis underlying TRPV4-mediated Ca2+ deregulation in neurodevelopment remains unresolved and an effective therapeutic strategy remains to be established. These issues were addressed by isolating mutant dental pulp stem cells from a tooth donated by a child diagnosed with metatropic dysplasia with neurodevelopmental comorbidities caused by a gain-of-function TRPV4 mutation, c.1855C > T (p.L619F). The mutation was repaired using CRISPR/Cas9 to generate corrected isogenic stem cells. These stem cells were differentiated into dopaminergic neurons and the pharmacological effects of folic acid were examined. In mutant neurons, constitutively elevated cytosolic Ca2+ augmented AKT-mediated α-synuclein (α-syn) induction, resulting in mitochondrial Ca2+ accumulation and dysfunction. The TRPV4 antagonist, AKT inhibitor, or α-syn knockdown, normalizes the mitochondrial Ca2+ levels in mutant neurons, suggesting the importance of mutant TRPV4/Ca2+/AKT-induced α-syn in mitochondrial Ca2+ accumulation. Folic acid was effective in normalizing mitochondrial Ca2+ levels via the transcriptional repression of α-syn and improving mitochondrial reactive oxygen species levels, adenosine triphosphate synthesis, and neurite outgrowth of mutant neurons. This study provides new insights into the neuropathological mechanisms underlying TRPV4-related disorders and related therapeutic strategies.
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Affiliation(s)
- Xiao Sun
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental ScienceKyushu UniversityFukuokaJapan
- Present address:
Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine ResearchCollege of Stomatology, Xi'an Jiaotong UniversityXi'anChina
- Present address:
Department of Pediatric DentistryCollege of Stomatology, Xi'an Jiaotong UniversityXi'anChina
| | - Jun Kong
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental ScienceKyushu UniversityFukuokaJapan
| | - Shuangshan Dong
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental ScienceKyushu UniversityFukuokaJapan
| | - Hiroki Kato
- Department of Molecular Cell Biology and Oral AnatomyKyushu University Graduate School of Dental ScienceFukuokaJapan
| | - Hiroshi Sato
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental ScienceKyushu UniversityFukuokaJapan
| | - Yuta Hirofuji
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental ScienceKyushu UniversityFukuokaJapan
| | - Yosuke Ito
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental ScienceKyushu UniversityFukuokaJapan
| | - Lu Wang
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental ScienceKyushu UniversityFukuokaJapan
| | - Takahiro A. Kato
- Department of Neuropsychiatry, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Michiko Torio
- Department of General Pediatrics, Fukuoka Children's HospitalFukuokaJapan
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Yasunari Sakai
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Shouichi Ohga
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Satoshi Fukumoto
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental ScienceKyushu UniversityFukuokaJapan
| | - Keiji Masuda
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental ScienceKyushu UniversityFukuokaJapan
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Mir FA, Amanullah A, Jain BP, Hyderi Z, Gautam A. Neuroepigenetics of ageing and neurodegeneration-associated dementia: An updated review. Ageing Res Rev 2023; 91:102067. [PMID: 37689143 DOI: 10.1016/j.arr.2023.102067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/11/2023]
Abstract
Gene expression is tremendously altered in the brain during memory acquisition, recall, and forgetfulness. However, non-genetic factors, including environmental elements, epigenetic changes, and lifestyle, have grabbed significant attention in recent years regarding the etiology of neurodegenerative diseases (NDD) and age-associated dementia. Epigenetic modifications are essential in regulating gene expression in all living organisms in a DNA sequence-independent manner. The genes implicated in ageing and NDD-related memory disorders are epigenetically regulated by processes such as DNA methylation, histone acetylation as well as messenger RNA editing machinery. The physiological and optimal state of the epigenome, especially within the CNS of humans, plays an intricate role in helping us adjust to the changing environment, and alterations in it cause many brain disorders, but the mechanisms behind it still need to be well understood. When fully understood, these epigenetic landscapes could act as vital targets for pharmacogenetic rescue strategies for treating several diseases, including neurodegeneration- and age-induced dementia. Keeping this objective in mind, this updated review summarises the epigenetic changes associated with age and neurodegeneration-associated dementia.
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Affiliation(s)
- Fayaz Ahmad Mir
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Zeeshan Hyderi
- Department of Biotechnology, Alagappa University, Karaikudi, India
| | - Akash Gautam
- Centre for Neural and Cognitive Sciences, University of Hyderabad, Hyderabad, India.
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Zhang D, Zhang J, Wang Y, Wang G, Tang P, Liu Y, Zhang Y, Ouyang L. Targeting epigenetic modifications in Parkinson's disease therapy. Med Res Rev 2023; 43:1748-1777. [PMID: 37119043 DOI: 10.1002/med.21962] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 01/10/2023] [Accepted: 04/12/2023] [Indexed: 04/30/2023]
Abstract
Parkinson's disease (PD) is a multifactorial disease due to a complex interplay between genetic and epigenetic factors. Recent efforts shed new light on the epigenetic mechanisms involved in regulating pathways related to the development of PD, including DNA methylation, posttranslational modifications of histones, and the presence of microRNA (miRNA or miR). Epigenetic regulators are potential therapeutic targets for neurodegenerative disorders. In the review, we aim to summarize mechanisms of epigenetic regulation in PD, and describe how the DNA methyltransferases, histone deacetylases, and histone acetyltransferases that mediate the key processes of PD are attractive therapeutic targets. We discuss the use of inhibitors and/or activators of these regulators in PD models or patients, and how these small molecule epigenetic modulators elicit neuroprotective effects. Further more, given the importance of miRNAs in PD, their contributions to the underlying mechanisms of PD will be discussed as well, together with miRNA-based therapies.
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Affiliation(s)
- Dan Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Jifa Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Yuxi Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Guan Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Pan Tang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Yun Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Yiwen Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Liang Ouyang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
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Gladkova MG, Leidmaa E, Anderzhanova EA. Epidrugs in the Therapy of Central Nervous System Disorders: A Way to Drive on? Cells 2023; 12:1464. [PMID: 37296584 PMCID: PMC10253154 DOI: 10.3390/cells12111464] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 05/01/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023] Open
Abstract
The polygenic nature of neurological and psychiatric syndromes and the significant impact of environmental factors on the underlying developmental, homeostatic, and neuroplastic mechanisms suggest that an efficient therapy for these disorders should be a complex one. Pharmacological interventions with drugs selectively influencing the epigenetic landscape (epidrugs) allow one to hit multiple targets, therefore, assumably addressing a wide spectrum of genetic and environmental mechanisms of central nervous system (CNS) disorders. The aim of this review is to understand what fundamental pathological mechanisms would be optimal to target with epidrugs in the treatment of neurological or psychiatric complications. To date, the use of histone deacetylases and DNA methyltransferase inhibitors (HDACis and DNMTis) in the clinic is focused on the treatment of neoplasms (mainly of a glial origin) and is based on the cytostatic and cytotoxic actions of these compounds. Preclinical data show that besides this activity, inhibitors of histone deacetylases, DNA methyltransferases, bromodomains, and ten-eleven translocation (TET) proteins impact the expression of neuroimmune inflammation mediators (cytokines and pro-apoptotic factors), neurotrophins (brain-derived neurotropic factor (BDNF) and nerve growth factor (NGF)), ion channels, ionotropic receptors, as well as pathoproteins (β-amyloid, tau protein, and α-synuclein). Based on this profile of activities, epidrugs may be favorable as a treatment for neurodegenerative diseases. For the treatment of neurodevelopmental disorders, drug addiction, as well as anxiety disorders, depression, schizophrenia, and epilepsy, contemporary epidrugs still require further development concerning a tuning of pharmacological effects, reduction in toxicity, and development of efficient treatment protocols. A promising strategy to further clarify the potential targets of epidrugs as therapeutic means to cure neurological and psychiatric syndromes is the profiling of the epigenetic mechanisms, which have evolved upon actions of complex physiological lifestyle factors, such as diet and physical exercise, and which are effective in the management of neurodegenerative diseases and dementia.
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Affiliation(s)
- Marina G. Gladkova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Este Leidmaa
- Institute of Molecular Psychiatry, Medical Faculty, University of Bonn, 53127 Bonn, Germany
- Institute of Biomedicine and Translational Medicine, Department of Physiology, University of Tartu, 50411 Tartu, Estonia
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10
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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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11
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Li D, Huang LT, Zhang CP, Li Q, Wang JH. Insights Into the Role of Platelet-Derived Growth Factors: Implications for Parkinson’s Disease Pathogenesis and Treatment. Front Aging Neurosci 2022; 14:890509. [PMID: 35847662 PMCID: PMC9283766 DOI: 10.3389/fnagi.2022.890509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Parkinson’s disease (PD), the second most common neurodegenerative disease after Alzheimer’s disease, commonly occurs in the elderly population, causing a significant medical and economic burden to the aging society worldwide. At present, there are few effective methods that achieve satisfactory clinical results in the treatment of PD. Platelet-derived growth factors (PDGFs) and platelet-derived growth factor receptors (PDGFRs) are important neurotrophic factors that are expressed in various cell types. Their unique structures allow for specific binding that can effectively regulate vital functions in the nervous system. In this review, we summarized the possible mechanisms by which PDGFs/PDGFRs regulate the occurrence and development of PD by affecting oxidative stress, mitochondrial function, protein folding and aggregation, Ca2+ homeostasis, and cell neuroinflammation. These modes of action mainly depend on the type and distribution of PDGFs in different nerve cells. We also summarized the possible clinical applications and prospects for PDGF in the treatment of PD, especially in genetic treatment. Recent advances have shown that PDGFs have contradictory roles within the central nervous system (CNS). Although they exert neuroprotective effects through multiple pathways, they are also associated with the disruption of the blood–brain barrier (BBB). Our recommendations based on our findings include further investigation of the contradictory neurotrophic and neurotoxic effects of the PDGFs acting on the CNS.
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Affiliation(s)
- Dan Li
- Department of Family Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Le-Tian Huang
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Cheng-pu Zhang
- Department of Family Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qiang Li
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Qiang Li,
| | - Jia-He Wang
- Department of Family Medicine, Shengjing Hospital of China Medical University, Shenyang, China
- Jia-He Wang,
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12
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Environmental Impact on the Epigenetic Mechanisms Underlying Parkinson’s Disease Pathogenesis: A Narrative Review. Brain Sci 2022; 12:brainsci12020175. [PMID: 35203939 PMCID: PMC8870303 DOI: 10.3390/brainsci12020175] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/17/2022] [Accepted: 01/22/2022] [Indexed: 02/04/2023] Open
Abstract
Parkinson’s disease (PD) is the second most common neurodegenerative disorder with an unclear etiology and no disease-modifying treatment to date. PD is considered a multifactorial disease, since both genetic and environmental factors contribute to its pathogenesis, although the molecular mechanisms linking these two key disease modifiers remain obscure. In this context, epigenetic mechanisms that alter gene expression without affecting the DNA sequence through DNA methylation, histone post-transcriptional modifications, and non-coding RNAs may represent the key mediators of the genetic–environmental interactions underlying PD pathogenesis. Environmental exposures may cause chemical alterations in several cellular functions, including gene expression. Emerging evidence has highlighted that smoking, coffee consumption, pesticide exposure, and heavy metals (manganese, arsenic, lead, etc.) may potentially affect the risk of PD development at least partially via epigenetic modifications. Herein, we discuss recent accumulating pre-clinical and clinical evidence of the impact of lifestyle and environmental factors on the epigenetic mechanisms underlying PD development, aiming to shed more light on the pathogenesis and stimulate future research.
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13
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Coppede F. Targeting the epigenome to treat neurodegenerative diseases or delay their onset: a perspective. Neural Regen Res 2022; 17:1745-1747. [PMID: 35017429 PMCID: PMC8820689 DOI: 10.4103/1673-5374.332145] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Fabio Coppede
- Department of Translational Research and of New Surgical and Medical Technologies, Interdepartmental Research Center Nutrafood "Nutraceuticals and Food for Health", University of Pisa, Pisa, Italy
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14
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Kaur G, Rathod SSS, Ghoneim MM, Alshehri S, Ahmad J, Mishra A, Alhakamy NA. DNA Methylation: A Promising Approach in Management of Alzheimer's Disease and Other Neurodegenerative Disorders. BIOLOGY 2022; 11:90. [PMID: 35053088 PMCID: PMC8773419 DOI: 10.3390/biology11010090] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/13/2022]
Abstract
DNA methylation, in the mammalian genome, is an epigenetic modification that involves the transfer of a methyl group on the C5 position of cytosine to derive 5-methylcytosine. The role of DNA methylation in the development of the nervous system and the progression of neurodegenerative diseases such as Alzheimer's disease has been an interesting research area. Furthermore, mutations altering DNA methylation affect neurodevelopmental functions and may cause the progression of several neurodegenerative diseases. Epigenetic modifications in neurodegenerative diseases are widely studied in different populations to uncover the plausible mechanisms contributing to the development and progression of the disease and detect novel biomarkers for early prognosis and future pharmacotherapeutic targets. In this manuscript, we summarize the association of DNA methylation with the pathogenesis of the most common neurodegenerative diseases, such as, Alzheimer's disease, Parkinson's disease, Huntington diseases, and amyotrophic lateral sclerosis, and discuss the potential of DNA methylation as a potential biomarker and therapeutic tool for neurogenerative diseases.
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Affiliation(s)
- Gagandeep Kaur
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, Punjab, India; (G.K.); (S.S.S.R.)
| | - Suraj Singh S. Rathod
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, Punjab, India; (G.K.); (S.S.S.R.)
| | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia;
| | - Sultan Alshehri
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Javed Ahmad
- Department of Pharmaceutics, College of Pharmacy, Najran University, Najran 11001, Saudi Arabia;
| | - Awanish Mishra
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, Kamrup 781101, Assam, India
| | - Nabil A. Alhakamy
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
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15
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Inhibitors of DNA Methylation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:471-513. [DOI: 10.1007/978-3-031-11454-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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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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17
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Melnik BC, Stremmel W, Weiskirchen R, John SM, Schmitz G. Exosome-Derived MicroRNAs of Human Milk and Their Effects on Infant Health and Development. Biomolecules 2021; 11:biom11060851. [PMID: 34200323 PMCID: PMC8228670 DOI: 10.3390/biom11060851] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 05/29/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022] Open
Abstract
Multiple biologically active components of human milk support infant growth, health and development. Milk provides a wide spectrum of mammary epithelial cell-derived extracellular vesicles (MEVs) for the infant. Although the whole spectrum of MEVs appears to be of functional importance for the growing infant, the majority of recent studies report on the MEV subfraction of milk exosomes (MEX) and their miRNA cargo, which are in the focus of this review. MEX and the dominant miRNA-148a play a key role in intestinal maturation, barrier function and suppression of nuclear factor-κB (NF-κB) signaling and may thus be helpful for the prevention and treatment of necrotizing enterocolitis. MEX and their miRNAs reach the systemic circulation and may impact epigenetic programming of various organs including the liver, thymus, brain, pancreatic islets, beige, brown and white adipose tissue as well as bones. Translational evidence indicates that MEX and their miRNAs control the expression of global cellular regulators such as DNA methyltransferase 1-which is important for the up-regulation of developmental genes including insulin, insulin-like growth factor-1, α-synuclein and forkhead box P3-and receptor-interacting protein 140, which is important for the regulation of multiple nuclear receptors. MEX-derived miRNA-148a and miRNA-30b may stimulate the expression of uncoupling protein 1, the key inducer of thermogenesis converting white into beige/brown adipose tissue. MEX have to be considered as signalosomes derived from the maternal lactation genome emitted to promote growth, maturation, immunological and metabolic programming of the offspring. Deeper insights into milk's molecular biology allow the conclusion that infants are both "breast-fed" and "breast-programmed". In this regard, MEX miRNA-deficient artificial formula is not an adequate substitute for breastfeeding, the birthright of all mammals.
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Affiliation(s)
- Bodo C. Melnik
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, D-49076 Osnabrück, Germany;
- Correspondence: ; Tel.: +49-5241-988060
| | - Wolfgang Stremmel
- Private Praxis for Internal Medicine, Beethovenstraße 2, D-76530 Baden-Baden, Germany;
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, D-52074 Aachen, Germany;
| | - Swen Malte John
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, D-49076 Osnabrück, Germany;
- Institute for Interdisciplinary Dermatological Prevention and Rehabilitation (iDerm), University of Osnabrück, D-49076 Osnabrück, Germany
| | - Gerd Schmitz
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital of Regensburg, University of Regensburg, D-93053 Regensburg, Germany;
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18
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Hyeon JW, Kim AH, Yano H. Epigenetic regulation in Huntington's disease. Neurochem Int 2021; 148:105074. [PMID: 34038804 DOI: 10.1016/j.neuint.2021.105074] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/23/2021] [Accepted: 05/17/2021] [Indexed: 12/25/2022]
Abstract
Huntington's disease (HD) is a devastating and fatal monogenic neurodegenerative disorder characterized by progressive loss of selective neurons in the brain and is caused by an abnormal expansion of CAG trinucleotide repeats in a coding exon of the huntingtin (HTT) gene. Progressive gene expression changes that begin at premanifest stages are a prominent feature of HD and are thought to contribute to disease progression. Increasing evidence suggests the critical involvement of epigenetic mechanisms in abnormal transcription in HD. Genome-wide alterations of a number of epigenetic modifications, including DNA methylation and multiple histone modifications, are associated with HD, suggesting that mutant HTT causes complex epigenetic abnormalities and chromatin structural changes, which may represent an underlying pathogenic mechanism. The causal relationship of specific epigenetic changes to early transcriptional alterations and to disease pathogenesis require further investigation. In this article, we review recent studies on epigenetic regulation in HD with a focus on DNA and histone modifications. We also discuss the contribution of epigenetic modifications to HD pathogenesis as well as potential mechanisms linking mutant HTT and epigenetic alterations. Finally, we discuss the therapeutic potential of epigenetic-based treatments.
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Affiliation(s)
- Jae Wook Hyeon
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hiroko Yano
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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19
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Gu J, Barrera J, Yun Y, Murphy SK, Beach TG, Woltjer RL, Serrano GE, Kantor B, Chiba-Falek O. Cell-Type Specific Changes in DNA Methylation of SNCA Intron 1 in Synucleinopathy Brains. Front Neurosci 2021; 15:652226. [PMID: 33994928 PMCID: PMC8113398 DOI: 10.3389/fnins.2021.652226] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/06/2021] [Indexed: 11/26/2022] Open
Abstract
Parkinson's disease (PD) and dementia with Lewy body (DLB) are the most common synucleinopathies. SNCA gene is a major genetic risk factor for these diseases group, and dysregulation of its expression has been implicated in the genetic etiologies of several synucleinopathies. DNA methylation at CpG island (CGI) within SNCA intron 1 has been suggested as a regulatory mechanism of SNCA expression, and changes in methylation levels at this region were associated with PD and DLB. However, the role of DNA methylation in the regulation of SNCA expression in a cell-type specific manner and its contribution to the pathogenesis of PD and DLB remain poorly understood, and the data are conflicting. Here, we employed a bisulfite pyrosequencing technique to profile the DNA methylation across SNCA intron 1 CGI in PD and DLB compared to age- and sex-matched normal control subjects. We analyzed homogenates of bulk post-mortem frozen frontal cortex samples and a subset of neuronal and glia nuclei sorted by the fluorescence-activated nuclei sorting (FANS) method. Bulk brain tissues showed no significant difference in the overall DNA methylation across SNCA intron 1 CGI region between the neuropathological groups. Sorted neuronal nuclei from PD frontal cortex showed significant lower levels of DNA methylation at this region compared to normal controls, but no differences between DLB and control, while sorted glia nuclei exhibited trends of decreased overall DNA methylation in DLB only. In conclusion, our data suggested disease-dependent cell-type specific differential DNA methylation within SNCA intron 1 CGI. These changes may affect SNCA dysregulation that presumably mediates disease-specific risk. Our results can be translated into the development of the SNCA intron 1 CGI region as an attractive therapeutics target for gene therapy in patients who suffer from synucleinopathies due to SNCA dysregulation.
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Affiliation(s)
- Jeffrey Gu
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, United States
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, United States
| | - Julio Barrera
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, United States
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, United States
| | - Young Yun
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, United States
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, United States
| | - Susan K. Murphy
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, United States
| | - Thomas G. Beach
- Banner Sun Health Research Institute, Sun City, AZ, United States
| | - Randy L. Woltjer
- Layton Aging and Alzheimer’s Disease Center, Department of Pathology, Oregon Health & Science University, Portland, OR, United States
| | - Geidy E. Serrano
- Banner Sun Health Research Institute, Sun City, AZ, United States
| | - Boris Kantor
- Viral Vector Core, Duke University Medical Center, Durham, NC, United States
- Department of Neurobiology, Duke University Medical Center, Durham, NC, United States
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, Durham, NC, United States
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, United States
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20
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Melnik BC. Lifetime Impact of Cow's Milk on Overactivation of mTORC1: From Fetal to Childhood Overgrowth, Acne, Diabetes, Cancers, and Neurodegeneration. Biomolecules 2021; 11:404. [PMID: 33803410 PMCID: PMC8000710 DOI: 10.3390/biom11030404] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 02/07/2023] Open
Abstract
The consumption of cow's milk is a part of the basic nutritional habits of Western industrialized countries. Recent epidemiological studies associate the intake of cow's milk with an increased risk of diseases, which are associated with overactivated mechanistic target of rapamycin complex 1 (mTORC1) signaling. This review presents current epidemiological and translational evidence linking milk consumption to the regulation of mTORC1, the master-switch for eukaryotic cell growth. Epidemiological studies confirm a correlation between cow's milk consumption and birthweight, body mass index, onset of menarche, linear growth during childhood, acne vulgaris, type 2 diabetes mellitus, prostate cancer, breast cancer, hepatocellular carcinoma, diffuse large B-cell lymphoma, neurodegenerative diseases, and all-cause mortality. Thus, long-term persistent consumption of cow's milk increases the risk of mTORC1-driven diseases of civilization. Milk is a highly conserved, lactation genome-controlled signaling system that functions as a maternal-neonatal relay for optimized species-specific activation of mTORC1, the nexus for regulation of eukaryotic cell growth, and control of autophagy. A deeper understanding of milk´s impact on mTORC1 signaling is of critical importance for the prevention of common diseases of civilization.
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Affiliation(s)
- Bodo C Melnik
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, Am Finkenhügel 7a, D-49076 Osnabrück, Germany
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21
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Melnik BC. Synergistic Effects of Milk-Derived Exosomes and Galactose on α-Synuclein Pathology in Parkinson's Disease and Type 2 Diabetes Mellitus. Int J Mol Sci 2021; 22:1059. [PMID: 33494388 PMCID: PMC7865729 DOI: 10.3390/ijms22031059] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/14/2021] [Accepted: 01/19/2021] [Indexed: 12/11/2022] Open
Abstract
Epidemiological studies associate milk consumption with an increased risk of Parkinson's disease (PD) and type 2 diabetes mellitus (T2D). PD is an α-synucleinopathy associated with mitochondrial dysfunction, oxidative stress, deficient lysosomal clearance of α-synuclein (α-syn) and aggregation of misfolded α-syn. In T2D, α-syn promotes co-aggregation with islet amyloid polypeptide in pancreatic β-cells. Prion-like vagal nerve-mediated propagation of exosomal α-syn from the gut to the brain and pancreatic islets apparently link both pathologies. Exosomes are critical transmitters of α-syn from cell to cell especially under conditions of compromised autophagy. This review provides translational evidence that milk exosomes (MEX) disturb α-syn homeostasis. MEX are taken up by intestinal epithelial cells and accumulate in the brain after oral administration to mice. The potential uptake of MEX miRNA-148a and miRNA-21 by enteroendocrine cells in the gut, dopaminergic neurons in substantia nigra and pancreatic β-cells may enhance miRNA-148a/DNMT1-dependent overexpression of α-syn and impair miRNA-148a/PPARGC1A- and miRNA-21/LAMP2A-dependent autophagy driving both diseases. MiRNA-148a- and galactose-induced mitochondrial oxidative stress activate c-Abl-mediated aggregation of α-syn which is exported by exosome release. Via the vagal nerve and/or systemic exosomes, toxic α-syn may spread to dopaminergic neurons and pancreatic β-cells linking the pathogenesis of PD and T2D.
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Affiliation(s)
- Bodo C Melnik
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, D-49076 Osnabrück, Germany
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22
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Okechukwu C. Deciphering and manipulating the epigenome for the treatment of Parkinson’s and Alzheimer’s disease. MGM JOURNAL OF MEDICAL SCIENCES 2021. [DOI: 10.4103/mgmj.mgmj_90_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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23
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Mohd Murshid N, Aminullah Lubis F, Makpol S. Epigenetic Changes and Its Intervention in Age-Related Neurodegenerative Diseases. Cell Mol Neurobiol 2020; 42:577-595. [DOI: 10.1007/s10571-020-00979-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023]
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24
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Cantelmo RA, Dos Santos NAG, Dos Santos AC, Joca SRL. Dual effects of S-adenosyl-methyonine on PC12 cells exposed to the dopaminergic neurotoxin MPP . J Pharm Pharmacol 2020; 72:1427-1435. [PMID: 32602113 DOI: 10.1111/jphp.13323] [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] [Received: 12/14/2019] [Revised: 05/22/2020] [Accepted: 05/30/2020] [Indexed: 12/21/2022]
Abstract
OBJECTIVES To investigate S-adenosyl-methyonine (SAM) effects on PC12 cells viability and neuritogenesis treated with MPP+ (1-methyl-4-phenylpyridinium). METHODS PC12 cell viability test (MTT assay) in DMEM medium with SAM and/or MPP+; PC12 cell neuritogenesis test in F-12K medium with nerve growth factor (NGF); DNMT activity in PC12 cells (DNMT Activity Assay Kit) with SAM and/or MPP+. KEY FINDINGS (1) MPP+ decreased cell viability; (2) SAM did not affect cell viability per se, but it increased MPP+ neurotoxicity when co-incubated with the neurotoxin, an effect abolished by DNA methyltransferases (DNMT) inhibitors; (3) pretreatment with SAM for 30 min or 24 h before MPP+ addition had no effect on cell viability. Neuritogenesis: Treatment with SAM for 30 min or 24 h (1) increased cell differentiation per se, (2) increased NGF differentiating effects (additive effect) and (3) blocked the neuritogenesis impairment induced by MPP+. SAM with MPP+ increased the DNMT activity, whereas SAM alone or MPP+ alone did not. CONCLUSIONS (1) SAM might induce neurotoxic or neuroprotective effects on PC12 cells, depending on the exposure conditions; (2) DNMT inhibitors might attenuate the MPP+ exacerbation toxicity induced by SAM; (3) DNA methylation might be involved in the observed effects of SAM (needs further investigation).
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Affiliation(s)
- Rebeca Araujo Cantelmo
- Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto (FCFRP), University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Neife Aparecida G Dos Santos
- Department of Clinical, Toxicological and Bromatological Analyses, School of Pharmaceutical Sciences of Ribeirão Preto (FCFRP), University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Antonio Cardozo Dos Santos
- Department of Clinical, Toxicological and Bromatological Analyses, School of Pharmaceutical Sciences of Ribeirão Preto (FCFRP), University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Sâmia Regiane Lourenço Joca
- Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto (FCFRP), University of São Paulo (USP), Ribeirão Preto, SP, Brazil
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25
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Safari F, Hatam G, Behbahani AB, Rezaei V, Barekati-Mowahed M, Petramfar P, Khademi F. CRISPR System: A High-throughput Toolbox for Research and Treatment of Parkinson's Disease. Cell Mol Neurobiol 2020; 40:477-493. [PMID: 31773362 DOI: 10.1007/s10571-019-00761-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/14/2019] [Indexed: 12/13/2022]
Abstract
In recent years, the innovation of gene-editing tools such as the CRISPR/Cas9 system improves the translational gap of treatments mediated by gene therapy. The privileges of CRISPR/Cas9 such as working in living cells and organs candidate this technology for using in research and treatment of the central nervous system (CNS) disorders. Parkinson's disease (PD) is a common, debilitating, neurodegenerative disorder which occurs due to loss of dopaminergic neurons and is associated with progressive motor dysfunction. Knowledge about the pathophysiological basis of PD has altered the classification system of PD, which manifests in familial and sporadic forms. The first genetic linkage studies in PD demonstrated the involvement of Synuclein alpha (SNCA) mutations and SNCA genomic duplications in the pathogenesis of PD familial forms. Subsequent studies have also insinuated mutations in leucine repeat kinase-2 (LRRK2), Parkin, PTEN-induced putative kinase 1 (PINK1), as well as DJ-1 causing familial forms of PD. This review will attempt to discuss the structure, function, and development in genome editing mediated by CRISP/Cas9 system. Further, it describes the genes involved in the pathogenesis of PD and the pertinent alterations to them. We will pursue this line by delineating the PD linkage studies in which CRISPR system was employed. Finally, we will discuss the pros and cons of CRISPR employment vis-à-vis the process of genome editing in PD patients' iPSCs.
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Affiliation(s)
- Fatemeh Safari
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Gholamreza Hatam
- Basic Sciences in Infectious Diseases Research Center, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Behzad Behbahani
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Vahid Rezaei
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mazyar Barekati-Mowahed
- Department of Physiology & Biophysics, School of Medicine, Case Western Reserve University, Ohio, USA
| | - Peyman Petramfar
- Clinical Neurology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farzaneh Khademi
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
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Renani PG, Taheri F, Rostami D, Farahani N, Abdolkarimi H, Abdollahi E, Taghizadeh E, Gheibi Hayat SM. Involvement of aberrant regulation of epigenetic mechanisms in the pathogenesis of Parkinson's disease and epigenetic-based therapies. J Cell Physiol 2019; 234:19307-19319. [PMID: 30968426 DOI: 10.1002/jcp.28622] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 03/07/2019] [Accepted: 03/14/2019] [Indexed: 12/26/2022]
Abstract
Parkinson's disease (PD) is known as a progressive neurodegenerative disorder associated with the reduction of dopamine-secreting neurons and the formation of Lewy bodies in the substantia nigra and basal ganglia routes. Aging, as well as environmental and genetic factors, are considered as disease risk factors that can make PD as a complex one. Epigenetics means studying heritable changes in gene expression or function, without altering the underlying DNA sequence. Multiple studies have shown the association of epigenetic variations with onset or progression of various types of diseases. DNA methylation, posttranslational modifications of histones and presence of microRNA (miRNA) are among epigenetic processes involved in regulating pathways related to the development of PD. Unlike genetic mutations, most epigenetic variations may be reversible or preventable. Therefore, the return of aberrant epigenetic events in different cells is a growing therapeutic approach to treatment or prevention. Currently, there are several methods for treating PD patients, the most important of which are drug therapies. However, detection of genes and epigenetic mechanisms involved in the disease can develop appropriate diagnosis and treatment of the disease before the onset of disabilities and resulting complications. The main purpose of this study was to review the most important epigenetic molecular mechanisms, epigenetic variations in PD, and epigenetic-based therapies.
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Affiliation(s)
- Pedram G Renani
- Genetic Department, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Forogh Taheri
- Genetic Department, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Daryoush Rostami
- Department of School Allied, Zabol University of Medical Sciences, Zabol, Iran
| | - Najmeh Farahani
- Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hamed Abdolkarimi
- Department of Biology, Marvdasht Branch, Islamic Azad University, Marvdasht, Iran
| | - Elahe Abdollahi
- Department of Medical Genetics, Faculty of Medicine, Tarbiat Modares University, Tehran, Iran
| | - Eskandar Taghizadeh
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mohammad Gheibi Hayat
- Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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Tagliafierro L, Ilich E, Moncalvo M, Gu J, Sriskanda A, Grenier C, Murphy SK, Chiba-Falek O, Kantor B. Lentiviral Vector Platform for the Efficient Delivery of Epigenome-editing Tools into Human Induced Pluripotent Stem Cell-derived Disease Models. J Vis Exp 2019. [PMID: 30985756 DOI: 10.3791/59241] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The use of hiPSC-derived cells represents a valuable approach to study human neurodegenerative diseases. Here, we describe an optimized protocol for the differentiation of hiPSCs derived from a patient with the triplication of the alpha-synuclein gene (SNCA) locus into Parkinson's disease (PD)-relevant dopaminergic neuronal populations. Accumulating evidence has shown that high levels of SNCA are causative for the development of PD. Recognizing the unmet need to establish novel therapeutic approaches for PD, especially those targeting the regulation of SNCA expression, we recently developed a CRISPR/dCas9-DNA-methylation-based system to epigenetically modulate SNCA transcription by enriching methylation levels at the SNCA intron 1 regulatory region. To deliver the system, consisting of a dead (deactivated) version of Cas9 (dCas9) fused with the catalytic domain of the DNA methyltransferase enzyme 3A (DNMT3A), a lentiviral vector is used. This system is applied to cells with the triplication of the SNCA locus and reduces the SNCA-mRNA and protein levels by about 30% through the targeted DNA methylation of SNCA intron 1. The fine-tuned downregulation of the SNCA levels rescues disease-related cellular phenotypes. In the current protocol, we aim to describe a step-by-step procedure for differentiating hiPSCs into neural progenitor cells (NPCs) and the establishment and validation of pyrosequencing assays for the evaluation of the methylation profile in the SNCA intron 1. To outline in more detail the lentivirus-CRISPR/dCas9 system used in these experiments, this protocol describes how to produce, purify, and concentrate lentiviral vectors and to highlight their suitability for epigenome- and genome-editing applications using hiPSCs and NPCs. The protocol is easily adaptable and can be used to produce high titer lentiviruses for in vitro and in vivo applications.
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Affiliation(s)
- Lidia Tagliafierro
- Department of Neurology, Duke University Medical Center; Center for Genomic and Computational Biology, Duke University Medical Center
| | | | | | - Jeffrey Gu
- Department of Neurology, Duke University Medical Center
| | - Ahila Sriskanda
- Department of Neurology, Duke University Medical Center; Center for Genomic and Computational Biology, Duke University Medical Center
| | - Carole Grenier
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center
| | - Susan K Murphy
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center
| | - Ornit Chiba-Falek
- Department of Neurology, Duke University Medical Center; Center for Genomic and Computational Biology, Duke University Medical Center;
| | - Boris Kantor
- Viral Vector Core, Duke University Medical Center;
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Kantor B, Tagliafierro L, Gu J, Zamora ME, Ilich E, Grenier C, Huang ZY, Murphy S, Chiba-Falek O. Downregulation of SNCA Expression by Targeted Editing of DNA Methylation: A Potential Strategy for Precision Therapy in PD. Mol Ther 2018; 26:2638-2649. [PMID: 30266652 PMCID: PMC6224806 DOI: 10.1016/j.ymthe.2018.08.019] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/21/2018] [Accepted: 08/23/2018] [Indexed: 01/04/2023] Open
Abstract
Elevated levels of SNCA have been implicated in the pathogenesis of Parkinson's disease (PD), while normal physiological levels of SNCA are needed to maintain neuronal function. We ought to develop new therapeutic strategies targeting the regulation of SNCA expression. DNA methylation at SNCA intron 1 regulates SNCA transcription, and PD brains showed differential methylation levels compared to controls. Thus, DNA methylation at SNCA intron 1 is an attractive target for fine-tuned downregulation of SNCA levels. Here we developed a system, comprising an all-in-one lentiviral vector, for targeted DNA methylation editing within intron 1. The system is based on CRISPR-deactivated Cas9 (dCas9) fused with the catalytic domain of DNA-methyltransferase 3A (DNMT3A). Applying the system to human induced pluripotent stem cell (hiPSC)-derived dopaminergic neurons from a PD patient with the SNCA triplication resulted in fine downregulation of SNCA mRNA and protein mediated by targeted DNA methylation at intron 1. Furthermore, the reduction in SNCA levels by the guide RNA (gRNA)-dCas9-DMNT3A system rescued disease-related cellular phenotype characteristics of the SNCA triplication hiPSC-derived dopaminergic neurons, e.g., mitochondrial ROS production and cellular viability. We established that DNA hypermethylation at SNCA intron 1 allows an effective and sufficient tight downregulation of SNCA expression levels, suggesting the potential of this target sequence combined with the CRISPR-dCas9 technology as a novel epigenetic-based therapeutic approach for PD.
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Affiliation(s)
- Boris Kantor
- Viral Vector Core, Duke University Medical Center, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Lidia Tagliafierro
- Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA; Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Jeffrey Gu
- Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA; Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Madison E Zamora
- Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA; Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Ekaterina Ilich
- Viral Vector Core, Duke University Medical Center, Durham, NC 27710, USA; Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Carole Grenier
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC 27710, USA
| | - Zhiqing Y Huang
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC 27710, USA
| | - Susan Murphy
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC 27710, USA
| | - Ornit Chiba-Falek
- Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA; Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27710, USA.
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Singh S, Gupta SK, Seth PK. Biomarkers for detection, prognosis and therapeutic assessment of neurological disorders. Rev Neurosci 2018; 29:771-789. [PMID: 29466244 DOI: 10.1515/revneuro-2017-0097] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 12/17/2017] [Indexed: 10/24/2023]
Abstract
Neurological disorders have aroused a significant concern among the health scientists globally, as diseases such as Parkinson's, Alzheimer's and dementia lead to disability and people have to live with them throughout the life. Recent evidence suggests that a number of environmental chemicals such as pesticides (paraquat) and metals (lead and aluminum) are also the cause of these diseases and other neurological disorders. Biomarkers can help in detecting the disorder at the preclinical stage, progression of the disease and key metabolomic alterations permitting identification of potential targets for intervention. A number of biomarkers have been proposed for some neurological disorders based on laboratory and clinical studies. In silico approaches have also been used by some investigators. Yet the ideal biomarker, which can help in early detection and follow-up on treatment and identifying the susceptible populations, is not available. An attempt has therefore been made to review the recent advancements of in silico approaches for discovery of biomarkers and their validation. In silico techniques implemented with multi-omics approaches have potential to provide a fast and accurate approach to identify novel biomarkers.
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Affiliation(s)
- Sarita Singh
- Distinguished Scientist Laboratory, Biotech Park, Sector-G Jankipram, Kursi Road, Lucknow 226021, Uttar Pradesh, India
| | - Sunil Kumar Gupta
- Distinguished Scientist Laboratory, Biotech Park, Lucknow 226021, Uttar Pradesh, India
| | - Prahlad Kishore Seth
- Distinguished Scientist Laboratory, Biotech Park, Lucknow 226021, Uttar Pradesh, India
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30
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Kular L, Kular S. Epigenetics applied to psychiatry: Clinical opportunities and future challenges. Psychiatry Clin Neurosci 2018; 72:195-211. [PMID: 29292553 DOI: 10.1111/pcn.12634] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/12/2017] [Accepted: 12/26/2017] [Indexed: 12/11/2022]
Abstract
Psychiatric disorders are clinically heterogeneous and debilitating chronic diseases resulting from a complex interplay between gene variants and environmental factors. Epigenetic processes, such as DNA methylation and histone posttranslational modifications, instruct the cell/tissue to correctly interpret external signals and adjust its functions accordingly. Given that epigenetic modifications are sensitive to environment, stable, and reversible, epigenetic studies in psychiatry could represent a promising approach to better understanding and treating disease. In the present review, we aim to discuss the clinical opportunities and challenges arising from the epigenetic research in psychiatry. Using selected examples, we first recapitulate key findings supporting the role of adverse life events, alone or in combination with genetic risk, in epigenetic programming of neuropsychiatric systems. Epigenetic studies further report encouraging findings about the use of methylation changes as diagnostic markers of disease phenotype and predictive tools of progression and response to treatment. Then we discuss the potential of using targeted epigenetic pharmacotherapy, combined with psychosocial interventions, for future personalized medicine for patients. Finally, we review the methodological limitations that could hinder interpretation of epigenetic data in psychiatry. They mainly arise from heterogeneity at the individual and tissue level and require future strategies in order to reinforce the biological relevance of epigenetic data and its translational use in psychiatry. Overall, we suggest that epigenetics could provide new insights into a more comprehensive interpretation of mental illness and might eventually improve the nosology, treatment, and prevention of psychiatric disorders.
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Affiliation(s)
- Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sonia Kular
- Adult Psychiatry Unit of Laval Secteur Est, Laval, France
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31
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Yang J, Yang Z, Wang X, Sun M, Wang Y, Wang X. CpG demethylation in the neurotoxicity of 1-methyl-4-phenylpyridinium might mediate transcriptional up-regulation of α-synuclein in SH-SY5Y cells. Neurosci Lett 2017; 659:124-132. [PMID: 28807729 DOI: 10.1016/j.neulet.2017.08.023] [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: 01/22/2017] [Revised: 04/10/2017] [Accepted: 08/08/2017] [Indexed: 11/19/2022]
Abstract
The accumulation of α-synuclein is the primary pathological hallmark of Parkinson's disease (PD). In PD patients, CpG demethylation of intron-1 has been reported to be associated with α-synuclein up-regulation. Environmental factor, for example neurotoxin, is a major etiological risk factor in PD pathogenesis. However, the role of CpG methylation in neurotoxin-induced PD has not been addressed completely yet. To explore CpG methylation associating with α-synuclein transcription and its underlying mechanisms in the neurotoxin-induced PD pathology, human neuroblastoma SH-SY5Y cells were treated with neurotoxins 6-hydroxydopamine (6-OHDA) and 1-methyl-4-phenylpyridinium (MPP+). Results showed that MPP+ induced demethylation of the whole length of the CpG island around SNCA promoter, and both 6-OHDA and MPP+ resulted in up-regulation of SNCA transcription. The CpG demethylation around promoter resulted in up-regulation of SNCA transcriptional activity. In addition, 6-OHDA and MPP+ induced the reduced levels of DNA methyltransferase (DNMT) 3a and DNMT3b but not DNMT1. These data suggested that CpG demethylation was induced by MPP+ and might mediate up-regulation of SNCA transcription in neurotoxin-induced PD. And down-regulation of both DNMT3a and DNMT3b, but not DNMT1, might contribute to CpG demethylation of the SNCA promoter.
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Affiliation(s)
- Jian Yang
- Department of Neurobiology, Capital Medical University, Beijing, China
| | - Zhaofei Yang
- Department of Neurobiology, Capital Medical University, Beijing, China; Center for Clinical Research on Neurological Diseases, 1st Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Xuan Wang
- Department of Physiology, Capital Medical University, Beijing, China
| | - Min Sun
- Department of Neurobiology, Capital Medical University, Beijing, China; Beijing Institute for Brain Disorders, Beijing, China; Key Laboratory for the Neurodegenerative Disorders of the Chinese Ministry of Education, Beijing, China
| | - Yong Wang
- Department of Physiology, Capital Medical University, Beijing, China; Beijing Institute for Brain Disorders, Beijing, China; Key Laboratory for the Neurodegenerative Disorders of the Chinese Ministry of Education, Beijing, China.
| | - Xiaomin Wang
- Department of Neurobiology, Capital Medical University, Beijing, China; Beijing Institute for Brain Disorders, Beijing, China; Key Laboratory for the Neurodegenerative Disorders of the Chinese Ministry of Education, Beijing, China.
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32
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Ponomarev I, Stelly CE, Morikawa H, Blednov YA, Mayfield RD, Harris RA. Mechanistic insights into epigenetic modulation of ethanol consumption. Alcohol 2017; 60:95-101. [PMID: 28433417 DOI: 10.1016/j.alcohol.2017.01.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 01/26/2017] [Accepted: 01/26/2017] [Indexed: 12/16/2022]
Abstract
There is growing evidence that small-molecule inhibitors of epigenetic modulators, such as histone deacetylases (HDAC) and DNA methyltransferases (DNMT), can reduce voluntary ethanol consumption in animal models, but molecular and cellular processes underlying this behavioral effect are poorly understood. We used C57BL/6J male mice to investigate the effects of two FDA-approved drugs, decitabine (a DNMT inhibitor) and SAHA (an HDAC inhibitor), on ethanol consumption using two tests: binge-like drinking in the dark (DID) and chronic intermittent every other day (EOD) drinking. Decitabine but not SAHA reduced ethanol consumption in both tests. We further investigated decitabine's effects on the brain's reward pathway by gene expression profiling in the ventral tegmental area (VTA), using RNA sequencing and electrophysiological recordings from VTA dopaminergic neurons. Decitabine-induced decreases in EOD drinking were associated with global changes in gene expression, implicating regulation of cerebral blood flow, extracellular matrix organization, and neuroimmune functions in decitabine actions. In addition, an in vivo administration of decitabine shortened ethanol-induced excitation of VTA dopaminergic neurons in vitro, suggesting that decitabine reduces ethanol drinking via changes in the reward pathway. Taken together, our data suggest a contribution of both neuronal and non-neuronal mechanisms in the VTA in the regulation of ethanol consumption. Decitabine and other epigenetic compounds have been approved for cancer treatment, and understanding their mechanisms of actions in the brain may assist in repurposing these drugs and developing novel therapies for central disorders, including drug addiction.
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Affiliation(s)
- Igor Ponomarev
- Waggoner Center for Alcohol and Addiction Research, USA; The College of Pharmacy, The University of Texas at Austin, 2500 Speedway A4800, Austin, TX, 78712, USA.
| | | | | | | | | | - R Adron Harris
- Waggoner Center for Alcohol and Addiction Research, USA; The College of Pharmacy, The University of Texas at Austin, 2500 Speedway A4800, Austin, TX, 78712, USA
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33
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Deregulation of α-synuclein in Parkinson's disease: Insight from epigenetic structure and transcriptional regulation of SNCA. Prog Neurobiol 2017; 154:21-36. [PMID: 28445713 DOI: 10.1016/j.pneurobio.2017.04.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 01/19/2023]
Abstract
Understanding regulation of α-synuclein has long been a central focus for Parkinson's disease (PD) researchers. Accumulation of this protein in the Lewy body or neurites, mutations in the coding region of the gene and strong association of α-synuclein encoding gene multiplication (duplication/triplication) with familial form of PD have indicated the importance of this molecule in pathogenesis of the disease. Several years of research identified many potential faulty pathways associated with accumulation of α-synuclein inside dopaminergic neurons and its transmission to neighboring ones. Concurrently, an appreciable body of research is growing to understand the epigenetic and genetic deregulation of α-synuclein that might contribute to the disease pathology. Completion of the ENCODE (Encyclopedia of DNA Elements) project and recent advancement made in the epigenetic and trans factor mediated regulation of each gene, has tremendously accelerated the need to carefully understand the epigenetic structure of the gene (SNCA) encoding α-synuclein protein in order to decipher the regulation and contribution of α-synuclein to the pathogenesis of PD. We have also analyzed the detailed epigenetic structure of this gene with knowledge from ENCODE database, which may open new avenues in α-synuclein research. Interestingly, we have found that the gene contains several transcriptionally activate histone modifications and associated potential transcription factor binding sites in the non-coding areas that strongly suggest alternative regulatory pathways. Altogether this review will provide interesting insight of α-synuclein gene regulation from epigenetic, genetic and post-transcriptional perspectives and their potential implication in the PD pathogenesis.
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34
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A novel tool for monitoring endogenous alpha-synuclein transcription by NanoLuciferase tag insertion at the 3'end using CRISPR-Cas9 genome editing technique. Sci Rep 2017; 8:45883. [PMID: 28374838 PMCID: PMC5379209 DOI: 10.1038/srep45883] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 03/06/2017] [Indexed: 01/19/2023] Open
Abstract
α-synuclein (α-SYN) is a major pathologic contributor to Parkinson's disease (PD). Multiplication of α-SYN encoding gene (SNCA) is correlated with early onset of the disease underlining the significance of its transcriptional regulation. Thus, monitoring endogenous transcription of SNCA is of utmost importance to understand PD pathology. We developed a stable cell line expressing α-SYN endogenously tagged with NanoLuc luciferase reporter using CRISPR/Cas9-mediated genome editing. This allows efficient measurement of transcriptional activity of α-SYN in its native epigenetic landscape which is not achievable using exogenous transfection-based luciferase reporter assays. The NanoLuc activity faithfully monitored the transcriptional regulation of SNCA following treatment with different drugs known to regulate α-SYN expression; while exogenous promoter-reporter assays failed to reproduce the similar outcomes. To our knowledge, this is the first report showing endogenous monitoring of α-SYN transcription, thus making it an efficient drug screening tool that can be used for therapeutic intervention in PD.
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35
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Yang Z, Wang X, Yang J, Sun M, Wang Y, Wang X. Aberrant CpG Methylation Mediates Abnormal Transcription of MAO-A Induced by Acute and Chronic l-3,4-Dihydroxyphenylalanine Administration in SH-SY5Y Neuronal Cells. Neurotox Res 2016; 31:334-347. [DOI: 10.1007/s12640-016-9686-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 11/27/2016] [Accepted: 12/01/2016] [Indexed: 01/07/2023]
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36
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Differential regulation of expression of RNA-editing enzymes, ADAR1 and ADAR2, by 5-aza-2'-deoxycytidine and trichostatin A in human neuronal SH-SY5Y cells. Neuroreport 2016; 26:1089-94. [PMID: 26485095 DOI: 10.1097/wnr.0000000000000474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Adenosine deaminase acting on RNA (ADAR) enzymes, ADAR1 and ADAR2, mediates adenosine-to-inosine RNA editing, and their mRNA expressions are altered during developmental, physiological, and pathophysiological processes in the nervous system. The present study attempted to investigate the involvement of epigenetic modifying enzymes, such as DNA methyltransferase (DNMT) and histone deacetylase (HDAC), in the regulation of ADAR1 and ADAR2 mRNA expressions in neuronal cells. Using human neuronal SH-SY5Y cells, we found that the DNMT inhibitor 5-aza-2'-deoxycytidine led to an increase in ADAR2, but not ADAR1, mRNA expression in a concentration-dependent and time-dependent manner. However, treatment with HDAC inhibitor trichostatin A elicited an increase in ADAR2 mRNA expression and a decrease in ADAR1 mRNA expression, and these changes were blocked by actinomycin D, a transcription inhibitor. Taken together, these findings suggest that ADAR1 and ADAR2 expressions are subject to different regulations by DNMT and HDAC enzymes in neuronal SH-SY5Y cells.
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37
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Wüllner U, Kaut O, deBoni L, Piston D, Schmitt I. DNA methylation in Parkinson's disease. J Neurochem 2016; 139 Suppl 1:108-120. [DOI: 10.1111/jnc.13646] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/21/2016] [Accepted: 04/15/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Ullrich Wüllner
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
| | - Oliver Kaut
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
| | - Laura deBoni
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
| | - Dominik Piston
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
| | - Ina Schmitt
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
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38
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Dermentzaki G, Paschalidis N, Politis PK, Stefanis L. Complex Effects of the ZSCAN21 Transcription Factor on Transcriptional Regulation of α-Synuclein in Primary Neuronal Cultures and in Vivo. J Biol Chem 2016; 291:8756-72. [PMID: 26907683 DOI: 10.1074/jbc.m115.704973] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Indexed: 11/06/2022] Open
Abstract
α-Synuclein, a presynaptic neuronal protein encoded by the SNCA gene, is strongly implicated in Parkinson disease (PD). PD pathogenesis is linked to increased SNCA levels; however, the transcriptional elements that control SNCA expression are still elusive. Previous experiments in PC12 cells demonstrated that the transcription factor zinc finger and SCAN domain containing 21 (ZSCAN21) plays an important regulatory role in SNCA transcription. Currently, we characterized the role of ZSCAN21 in SNCA transcription in primary neuronal cultures and in vivo We found that ZSCAN21 is developmentally expressed in neurons in different rat brain regions. We confirmed its binding in the intron 1 region of SNCA in rat cortical cultures. Lentivirus-mediated silencing of ZSCAN21 increased significantly SNCA promoter activity, mRNA, and protein levels in such cultures. In contrast, ZSCAN21 silencing reduced SNCA in neurosphere cultures. Interestingly, ZSCAN21 overexpression in cortical neurons led to robust mRNA but negligible protein expression, suggesting that ZSCAN21 protein levels are tightly regulated post-transcriptionally and/or post-translationally in primary neurons. Efficient adeno-associated virus-mediated knockdown of ZSCAN21 in the postnatal and adult hippocampus, an area linked with non-motor PD symptoms, revealed no significant alterations in SNCA levels. Overall, our study demonstrates that ZSCAN21 is involved in the transcriptional regulation of SNCA in primary neuronal cultures, but the direction of the effect is variable, likely depending on neuronal maturation. However, the unaltered SNCA levels observed following ZSCAN21 down-regulation in the rat brain, possibly due to compensatory mechanisms, imply that ZSCAN21 is not a master regulator of SNCA in vivo.
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Affiliation(s)
- Georgia Dermentzaki
- From the Biomedical Research Foundation of the Academy of Athens, Athens 11527 and
| | - Nikolaos Paschalidis
- From the Biomedical Research Foundation of the Academy of Athens, Athens 11527 and
| | - Panagiotis K Politis
- From the Biomedical Research Foundation of the Academy of Athens, Athens 11527 and
| | - Leonidas Stefanis
- From the Biomedical Research Foundation of the Academy of Athens, Athens 11527 and the Second Department of Neurology, National and Kapodistrian University of Athens Medical School, Hospital Attikon, Athens 12462, Greece,
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Lopez M, Halby L, Arimondo PB. DNA Methyltransferase Inhibitors: Development and Applications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:431-473. [DOI: 10.1007/978-3-319-43624-1_16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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40
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Epigenetic Research of Neurodegenerative Disorders Using Patient iPSC-Based Models. Stem Cells Int 2015; 2016:9464591. [PMID: 26697081 PMCID: PMC4677257 DOI: 10.1155/2016/9464591] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 06/18/2015] [Indexed: 01/15/2023] Open
Abstract
Epigenetic mechanisms play a role in human disease but their involvement in pathologies from the central nervous system has been hampered by the complexity of the brain together with its unique cellular architecture and diversity. Until recently, disease targeted neural types were only available as postmortem materials after many years of disease evolution. Current in vitro systems of induced pluripotent stem cells (iPSCs) generated by cell reprogramming of somatic cells from patients have provided valuable disease models recapitulating key pathological molecular events. Yet whether cell reprogramming on itself implies a truly epigenetic reprogramming, the epigenetic mechanisms governing this process are only partially understood. Moreover, elucidating epigenetic regulation using patient-specific iPSC-derived neural models is expected to have a great impact to unravel the pathophysiology of neurodegenerative diseases and to hopefully expand future therapeutic possibilities. Here we will critically review current knowledge of epigenetic involvement in neurodegenerative disorders focusing on the potential of iPSCs as a promising tool for epigenetic research of these diseases.
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Calligaris R, Banica M, Roncaglia P, Robotti E, Finaurini S, Vlachouli C, Antonutti L, Iorio F, Carissimo A, Cattaruzza T, Ceiner A, Lazarevic D, Cucca A, Pangher N, Marengo E, di Bernardo D, Pizzolato G, Gustincich S. Blood transcriptomics of drug-naïve sporadic Parkinson's disease patients. BMC Genomics 2015; 16:876. [PMID: 26510930 PMCID: PMC4625854 DOI: 10.1186/s12864-015-2058-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 10/02/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Parkinson's disease (PD) is a chronic progressive neurodegenerative disorder that is clinically defined in terms of motor symptoms. These are preceded by prodromal non-motor manifestations that prove the systemic nature of the disease. Identifying genes and pathways altered in living patients provide new information on the diagnosis and pathogenesis of sporadic PD. METHODS Changes in gene expression in the blood of 40 sporadic PD patients and 20 healthy controls ("Discovery set") were analyzed by taking advantage of the Affymetrix platform. Patients were at the onset of motor symptoms and before initiating any pharmacological treatment. Data analysis was performed by applying Ranking-Principal Component Analysis, PUMA and Significance Analysis of Microarrays. Functional annotations were assigned using GO, DAVID, GSEA to unveil significant enriched biological processes in the differentially expressed genes. The expressions of selected genes were validated using RT-qPCR and samples from an independent cohort of 12 patients and controls ("Validation set"). RESULTS Gene expression profiling of blood samples discriminates PD patients from healthy controls and identifies differentially expressed genes in blood. The majority of these are also present in dopaminergic neurons of the Substantia Nigra, the key site of neurodegeneration. Together with neuronal apoptosis, lymphocyte activation and mitochondrial dysfunction, already found in previous analysis of PD blood and post-mortem brains, we unveiled transcriptome changes enriched in biological terms related to epigenetic modifications including chromatin remodeling and methylation. Candidate transcripts as CBX5, TCF3, MAN1C1 and DOCK10 were validated by RT-qPCR. CONCLUSIONS Our data support the use of blood transcriptomics to study neurodegenerative diseases. It identifies changes in crucial components of chromatin remodeling and methylation machineries as early events in sporadic PD suggesting epigenetics as target for therapeutic intervention.
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Affiliation(s)
- Raffaella Calligaris
- Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy.
| | - Mihaela Banica
- Department of Medical Sciences, Neurology Unit, University of Trieste, Strada di Fiume 447, 34100, Trieste, Italy.
| | - Paola Roncaglia
- Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy. .,Present Address: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), CB10 1SD Hinxton, Cambridge, UK.
| | - Elisa Robotti
- Department of Environmental and Life Sciences, University of Eastern Piedmont, Viale T. Michel 11, 15121, Alessandria, Italy.
| | - Sara Finaurini
- Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy.
| | - Christina Vlachouli
- Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy.
| | - Lucia Antonutti
- Department of Medical Sciences, Neurology Unit, University of Trieste, Strada di Fiume 447, 34100, Trieste, Italy.
| | - Francesco Iorio
- Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino 111, Naples, 80131, Italy. .,Present Address: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), CB10 1SD Hinxton, Cambridge, UK.
| | - Annamaria Carissimo
- Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino 111, Naples, 80131, Italy.
| | - Tatiana Cattaruzza
- Department of Medical Sciences, Neurology Unit, University of Trieste, Strada di Fiume 447, 34100, Trieste, Italy.
| | - Andrea Ceiner
- ITALTBS S.p.A., AREA Science Park, Padriciano, 99, 34149, Trieste, Italy.
| | - Dejan Lazarevic
- Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy. .,CBM Scrl - Consorzio per il Centro di Biomedicina Molecolare, Area Science Park, S.S.14, km 163.5, Basovizza, 34149, Trieste, Italy.
| | - Alberto Cucca
- Department of Medical Sciences, Neurology Unit, University of Trieste, Strada di Fiume 447, 34100, Trieste, Italy.
| | - Nicola Pangher
- ITALTBS S.p.A., AREA Science Park, Padriciano, 99, 34149, Trieste, Italy.
| | - Emilio Marengo
- Department of Environmental and Life Sciences, University of Eastern Piedmont, Viale T. Michel 11, 15121, Alessandria, Italy.
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino 111, Naples, 80131, Italy. .,Department Computer Science & Systems, School of Engineering, University of Naples "Federico II", via Claudio 21, 80125, Naples, Italy.
| | - Gilberto Pizzolato
- Department of Medical Sciences, Neurology Unit, University of Trieste, Strada di Fiume 447, 34100, Trieste, Italy.
| | - Stefano Gustincich
- Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy.
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Li R, Wang Y, Yang Z, He Y, Zhao T, Fan M, Wang X, Zhu L, Wang X. Hypoxia-inducible factor-1α regulates the expression of L-type voltage-dependent Ca(2+) channels in PC12 cells under hypoxia. Cell Stress Chaperones 2015; 20:507-16. [PMID: 25648081 PMCID: PMC4406929 DOI: 10.1007/s12192-015-0575-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 01/16/2015] [Accepted: 01/23/2015] [Indexed: 10/24/2022] Open
Abstract
Hypoxia is an important factor in regulation of cell behavior both under physiological and pathological conditions. The mechanisms of hypoxia-induced cell death have not been completely elucidated yet. It is well known that Ca(2+) is critically related to cell survival. Hypoxia-inducible factor-1α (HIF-1α) is a core regulatory factor during hypoxia, and L-type voltage-dependent Ca(2+) channels (L-VDCCs) have been reported to play a critical role in cell survival. This study was conducted to explore the relationship between L-VDCC expression and HIF-1α regulation in PC12 cells under hypoxia. PC12 cells were treated at 20 or 3 % O2 to observe its proliferation and the intracellular calcium concentration. Then, we detected the protein expression of HIF-1α and L-VDCCs subtypes, Cav1.2 and Cav1.3. At last, to verify the relationship between HIF-1α and Cav1.2 and Cav1.3, we got the expression of Cav1.2 and Cav1.3 with Western blot and luciferase report gene assays after PC12 cells were treated by echinomycin, which is an HIF-1α inhibitor. Compared with 20 % O2 (normoxia), 3 % O2 (hypoxia) inhibited cell proliferation, increased the intracellular calcium concentration, and induced protein expression of HIF-1α. The protein expression of two L-VDCCs subtypes expressed in the nervous system, Cav1.2 and Cav1.3, was upregulated by hypoxia and reduced dose dependently by treatment with echinomycin, a HIF-1α inhibitor. Luciferase report gene assays showed that the expression of Cav1.2 and Cav1.3 genes was augmented under 3 % O2. However, echinomycin only slightly and dose dependently decreased expression of the Cav1.2 gene, but not that of the Cav1.3 gene. These data indicated that Cav1.2 might be regulated by HIF-1α as one of its downstream target genes and involved in regulation of PC12 cells death under hypoxia.
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Affiliation(s)
- Ran Li
- />Department of Physiology, Key Laboratory for Neurodegenerative Disorders of the Ministry of Education, Capital Medical University, 10# You An Men, Beijing, 100069 People’s Republic of China
- />Department of Rehabilitation Medicine, Xuan Xu Hospital, Capital Medical University, 45# Changchun Street, Beijing, 100053 People’s Republic of China
| | - Yong Wang
- />Department of Physiology, Key Laboratory for Neurodegenerative Disorders of the Ministry of Education, Capital Medical University, 10# You An Men, Beijing, 100069 People’s Republic of China
| | - Zhaofei Yang
- />Department of Physiology, Key Laboratory for Neurodegenerative Disorders of the Ministry of Education, Capital Medical University, 10# You An Men, Beijing, 100069 People’s Republic of China
| | - Yunling He
- />Department of Brain Protection and Plasticity, Institute of Basic Medical Sciences, 27# Taiping Road, Beijing, 100850 People’s Republic of China
| | - Tong Zhao
- />Department of Brain Protection and Plasticity, Institute of Basic Medical Sciences, 27# Taiping Road, Beijing, 100850 People’s Republic of China
| | - Ming Fan
- />Department of Brain Protection and Plasticity, Institute of Basic Medical Sciences, 27# Taiping Road, Beijing, 100850 People’s Republic of China
| | - Xuan Wang
- />Department of Physiology, Key Laboratory for Neurodegenerative Disorders of the Ministry of Education, Capital Medical University, 10# You An Men, Beijing, 100069 People’s Republic of China
| | - Lingling Zhu
- />Department of Brain Protection and Plasticity, Institute of Basic Medical Sciences, 27# Taiping Road, Beijing, 100850 People’s Republic of China
| | - Xiaomin Wang
- />Department of Physiology, Key Laboratory for Neurodegenerative Disorders of the Ministry of Education, Capital Medical University, 10# You An Men, Beijing, 100069 People’s Republic of China
- />Beijing Institute for Brain Disorder, 10# You An Men, Beijing, 100069 People’s Republic of China
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Chin-Chan M, Navarro-Yepes J, Quintanilla-Vega B. Environmental pollutants as risk factors for neurodegenerative disorders: Alzheimer and Parkinson diseases. Front Cell Neurosci 2015; 9:124. [PMID: 25914621 PMCID: PMC4392704 DOI: 10.3389/fncel.2015.00124] [Citation(s) in RCA: 344] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 03/17/2015] [Indexed: 12/21/2022] Open
Abstract
Neurodegenerative diseases including Alzheimer (AD) and Parkinson (PD) have attracted attention in last decades due to their high incidence worldwide. The etiology of these diseases is still unclear; however the role of the environment as a putative risk factor has gained importance. More worryingly is the evidence that pre- and post-natal exposures to environmental factors predispose to the onset of neurodegenerative diseases in later life. Neurotoxic metals such as lead, mercury, aluminum, cadmium and arsenic, as well as some pesticides and metal-based nanoparticles have been involved in AD due to their ability to increase beta-amyloid (Aβ) peptide and the phosphorylation of Tau protein (P-Tau), causing senile/amyloid plaques and neurofibrillary tangles (NFTs) characteristic of AD. The exposure to lead, manganese, solvents and some pesticides has been related to hallmarks of PD such as mitochondrial dysfunction, alterations in metal homeostasis and aggregation of proteins such as α-synuclein (α-syn), which is a key constituent of Lewy bodies (LB), a crucial factor in PD pathogenesis. Common mechanisms of environmental pollutants to increase Aβ, P-Tau, α-syn and neuronal death have been reported, including the oxidative stress mainly involved in the increase of Aβ and α-syn, and the reduced activity/protein levels of Aβ degrading enzyme (IDE)s such as neprilysin or insulin IDE. In addition, epigenetic mechanisms by maternal nutrient supplementation and exposure to heavy metals and pesticides have been proposed to lead phenotypic diversity and susceptibility to neurodegenerative diseases. This review discusses data from epidemiological and experimental studies about the role of environmental factors in the development of idiopathic AD and PD, and their mechanisms of action.
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44
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Epigenetic mechanisms in Parkinson's disease. J Neurol Sci 2014; 349:3-9. [PMID: 25553963 DOI: 10.1016/j.jns.2014.12.017] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 12/01/2014] [Accepted: 12/10/2014] [Indexed: 12/21/2022]
Abstract
Parkinson's disease (PD) is the second most common age-related neurodegenerative disease, but its pathogenesis is not fully understood. The selective neuronal cell death in PD has been considered to result from a complex interaction between genetic and environmental factors, but the nature of the relationship between the two chief modifiers remains to be elucidated. There is a growing body of evidence supporting the role of epigenetics in the development and progression of many neurodegenerative diseases including PD. Epigenetic modification refers to changes in gene expression or function without changes in DNA sequence, which mainly includes DNA methylation, post-modifications of histone, and non-coding RNAs. In this review, we will focus on the abnormal epigenetic modifications involved in the pathogenesis of PD and their implications for the development of future diagnostic and therapeutic strategies.
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45
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Farinelli P, Perera A, Arango-Gonzalez B, Trifunovic D, Wagner M, Carell T, Biel M, Zrenner E, Michalakis S, Paquet-Durand F, Ekström PAR. DNA methylation and differential gene regulation in photoreceptor cell death. Cell Death Dis 2014; 5:e1558. [PMID: 25476906 PMCID: PMC4649831 DOI: 10.1038/cddis.2014.512] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 10/17/2014] [Accepted: 10/21/2014] [Indexed: 01/09/2023]
Abstract
Retinitis pigmentosa (RP) defines a group of inherited degenerative retinal diseases causing progressive loss of photoreceptors. To this day, RP is still untreatable and rational treatment development will require a thorough understanding of the underlying cell death mechanisms. Methylation of the DNA base cytosine by DNA methyltransferases (DNMTs) is an important epigenetic factor regulating gene expression, cell differentiation, cell death, and survival. Previous studies suggested an involvement of epigenetic mechanisms in RP, and in this study, increased cytosine methylation was detected in dying photoreceptors in the rd1, rd2, P23H, and S334ter rodent models for RP. Ultrastructural analysis of photoreceptor nuclear morphology in the rd1 mouse model for RP revealed a severely altered chromatin structure during retinal degeneration that coincided with an increased expression of the DNMT isozyme DNMT3a. To identify disease-specific differentially methylated DNA regions (DMRs) on a genomic level, we immunoprecipitated methylated DNA fragments and subsequently analyzed them with a targeted microarray. Genome-wide comparison of DMRs between rd1 and wild-type retina revealed hypermethylation of genes involved in cell death and survival as well as cell morphology and nervous system development. When correlating DMRs with gene expression data, we found that hypermethylation occurred alongside transcriptional repression. Consistently, motif analysis showed that binding sites of several important transcription factors for retinal physiology were hypermethylated in the mutant model, which also correlated with transcriptional silencing of their respective target genes. Finally, inhibition of DNMTs in rd1 organotypic retinal explants using decitabine resulted in a substantial reduction of photoreceptor cell death, suggesting inhibition of DNA methylation as a potential novel treatment in RP.
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Affiliation(s)
- P Farinelli
- 1] Division of Ophthalmology, Department of Clinical Sciences, University of Lund, BMC-B11, Lund 22184, Sweden [2] Division of Experimental Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen 72076, Germany
| | - A Perera
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - B Arango-Gonzalez
- Division of Experimental Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen 72076, Germany
| | - D Trifunovic
- Division of Experimental Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen 72076, Germany
| | - M Wagner
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - T Carell
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - M Biel
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - E Zrenner
- Division of Experimental Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen 72076, Germany
| | - S Michalakis
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - F Paquet-Durand
- Division of Experimental Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen 72076, Germany
| | - P A R Ekström
- Division of Ophthalmology, Department of Clinical Sciences, University of Lund, BMC-B11, Lund 22184, Sweden
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46
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Jiang W, Li J, Zhang Z, Wang H, Wang Z. Epigenetic upregulation of alpha-synuclein in the rats exposed to methamphetamine. Eur J Pharmacol 2014; 745:243-8. [PMID: 25445041 DOI: 10.1016/j.ejphar.2014.10.043] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 10/23/2014] [Accepted: 10/23/2014] [Indexed: 11/20/2022]
Abstract
Abuse of methamphetamine (METH) increases the risk of occurrence of Parkinson׳s disease (PD) in the individuals. Increased expression of synaptic protein α-synuclein (encoded by gene Snca) is remarkably associated with the neuronal loss and motor dysfunction in the patients with PD. The present study aimed to explore the epigenetic mechanism underlying the altered expression of α-synuclein in substantia nigra in the rats previously exposed to METH. Exposure to METH induced significant behavioral impairments in the rotarod test and open field test, as well as the upregulation of cytokine synthesis in the substantia nigra. Significantly increased expression of α-synuclein was also observed in the substantia nigra in the rats exposed to METH. Further chromatin immunoprecipitation and bisulfite sequencing studies revealed a significantly decreased cytosine methylation in the Snca promoter region in the rats exposed to METH. It was found that the occupancy of methyl CpG binding protein 2 and DNA methyltransferase 1 in Snca promoter region was also significantly decreased in the substantia nigra in the modeled rats. These results advanced our understanding on the mechanism of the increased incidence of PD in the individuals with history use of METH, and shed novel lights on the development of therapeutic approaches for the patients conflicted with this neurological disorder.
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Affiliation(s)
- Wenda Jiang
- Department of Neurology Fist Affiliated Hospital of Liaoning Medical University, 5-2 Renmin Street, Jinzhou, Liaoning 121000, China.
| | - Ji Li
- Department of Neurology Fist Affiliated Hospital of Liaoning Medical University, 5-2 Renmin Street, Jinzhou, Liaoning 121000, China
| | - Zhuang Zhang
- Department of Neurology Fist Affiliated Hospital of Liaoning Medical University, 5-2 Renmin Street, Jinzhou, Liaoning 121000, China
| | - Hongxin Wang
- Institute of Medicine Liaoning Medical University, Jinzhou 121000, China
| | - Zhejian Wang
- Dalian Medical University, Dalian, Liaoning 116044, China
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Song Y, Ding H, Yang J, Lin Q, Xue J, Zhang Y, Chan P, Cai Y. Pyrosequencing analysis of SNCA methylation levels in leukocytes from Parkinson's disease patients. Neurosci Lett 2014; 569:85-8. [DOI: 10.1016/j.neulet.2014.03.076] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 03/29/2014] [Indexed: 12/20/2022]
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48
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Lu H, Liu X, Deng Y, Qing H. DNA methylation, a hand behind neurodegenerative diseases. Front Aging Neurosci 2013; 5:85. [PMID: 24367332 PMCID: PMC3851782 DOI: 10.3389/fnagi.2013.00085] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 11/17/2013] [Indexed: 12/13/2022] Open
Abstract
Epigenetic alterations represent a sort of functional modifications related to the genome that are not responsible for changes in the nucleotide sequence. DNA methylation is one of such epigenetic modifications that have been studied intensively for the past several decades. The transfer of a methyl group to the 5 position of a cytosine is the key feature of DNA methylation. A simple change as such can be caused by a variety of factors, which can be the cause of many serious diseases including several neurodegenerative diseases. In this review, we have reviewed and summarized recent progress regarding DNA methylation in four major neurodegenerative diseases: Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS). The studies of these four major neurodegenerative diseases conclude the strong suggestion of the important role DNA methylation plays in these diseases. However, each of these diseases has not yet been understood completely as details in some areas remain unclear, and will be investigated in future studies. We hope this review can provide new insights into the understanding of neurodegenerative diseases from the epigenetic perspective.
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Affiliation(s)
| | | | | | - Hong Qing
- School of Life Science, Beijing Institute of TechnologyBeijing, China
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