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Wang J, Ran Y, Li Z, Zhao T, Zhang F, Wang J, Liu Z, Chen X. Salsolinol as an RNA m6A methylation inducer mediates dopaminergic neuronal death by regulating YAP1 and autophagy. Neural Regen Res 2025; 20:887-899. [PMID: 38886960 DOI: 10.4103/nrr.nrr-d-23-01592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/18/2024] [Indexed: 06/20/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202503000-00032/figure1/v/2024-06-17T092413Z/r/image-tiff Salsolinol (1-methyl-6,7-dihydroxy-1,2,3,4-tetrahydroisoquinoline, Sal) is a catechol isoquinoline that causes neurotoxicity and shares structural similarity with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, an environmental toxin that causes Parkinson's disease. However, the mechanism by which Sal mediates dopaminergic neuronal death remains unclear. In this study, we found that Sal significantly enhanced the global level of N6-methyladenosine (m6A) RNA methylation in PC12 cells, mainly by inducing the downregulation of the expression of m6A demethylases fat mass and obesity-associated protein (FTO) and alkB homolog 5 (ALKBH5). RNA sequencing analysis showed that Sal downregulated the Hippo signaling pathway. The m6A reader YTH domain-containing family protein 2 (YTHDF2) promoted the degradation of m6A-containing Yes-associated protein 1 (YAP1) mRNA, which is a downstream key effector in the Hippo signaling pathway. Additionally, downregulation of YAP1 promoted autophagy, indicating that the mutual regulation between YAP1 and autophagy can lead to neurotoxicity. These findings reveal the role of Sal on m6A RNA methylation and suggest that Sal may act as an RNA methylation inducer mediating dopaminergic neuronal death through YAP1 and autophagy. Our results provide greater insights into the neurotoxic effects of catechol isoquinolines compared with other studies and may be a reference for assessing the involvement of RNA methylation in the pathogenesis of Parkinson's disease.
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Affiliation(s)
- Jianan Wang
- Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life, Beijing University of Technology, Beijing, China
| | - Yuanyuan Ran
- Department of Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China
| | - Zihan Li
- Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life, Beijing University of Technology, Beijing, China
| | - Tianyuan Zhao
- Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life, Beijing University of Technology, Beijing, China
| | - Fangfang Zhang
- Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life, Beijing University of Technology, Beijing, China
| | - Juan Wang
- Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life, Beijing University of Technology, Beijing, China
| | - Zongjian Liu
- Department of Rehabilitation, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China
| | - Xuechai Chen
- Beijing International Science and Technology Cooperation Base for Antiviral Drugs, College of Chemistry and Life, Beijing University of Technology, Beijing, China
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Soraci L, Corsonello A, Paparazzo E, Montesanto A, Piacenza F, Olivieri F, Gambuzza ME, Savedra EV, Marino S, Lattanzio F, Biscetti L. Neuroinflammaging: A Tight Line Between Normal Aging and Age-Related Neurodegenerative Disorders. Aging Dis 2024; 15:1726-1747. [PMID: 38300639 PMCID: PMC11272206 DOI: 10.14336/ad.2023.1001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 10/01/2023] [Indexed: 02/02/2024] Open
Abstract
Aging in the healthy brain is characterized by a low-grade, chronic, and sterile inflammatory process known as neuroinflammaging. This condition, mainly consisting in an up-regulation of the inflammatory response at the brain level, contributes to the pathogenesis of age-related neurodegenerative disorders. Development of this proinflammatory state involves the interaction between genetic and environmental factors, able to induce age-related epigenetic modifications. Indeed, the exposure to environmental compounds, drugs, and infections, can contribute to epigenetic modifications of DNA methylome, histone fold proteins, and nucleosome positioning, leading to epigenetic modulation of neuroinflammatory responses. Furthermore, some epigenetic modifiers, which combine and interact during the life course, can contribute to modeling of epigenome dynamics to sustain, or dampen the neuroinflammatory phenotype. The aim of this review is to summarize current knowledge about neuroinflammaging with a particular focus on epigenetic mechanisms underlying the onset and progression of neuroinflammatory cascades in the central nervous system; furthermore, we describe some diagnostic biomarkers that may contribute to increase diagnostic accuracy and help tailor therapeutic strategies in patients with neurodegenerative diseases.
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Affiliation(s)
- Luca Soraci
- Unit of Geriatric Medicine, Italian National Research Center of Aging (IRCCS INRCA), Cosenza, Italy.
| | - Andrea Corsonello
- Unit of Geriatric Medicine, Italian National Research Center of Aging (IRCCS INRCA), Cosenza, Italy.
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy.
| | - Ersilia Paparazzo
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy.
| | - Alberto Montesanto
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy.
| | - Francesco Piacenza
- Advanced Technology Center for Aging Research, Italian National Research Center of Aging (IRCCS INRCA), IRCCS INRCA, Ancona, Italy.
| | - Fabiola Olivieri
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy.
- Clinic of Laboratory and Precision Medicine, Italian National Research Center of Aging (IRCCS INRCA), Ancona, Italy.
| | | | | | - Silvia Marino
- IRCCS Centro Neurolesi "Bonino-Pulejo”, Messina, Italy.
| | | | - Leonardo Biscetti
- Section of Neurology, Italian National Research Center on Aging (IRCCS INRCA), Ancona, Italy.
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Choza JI, Virani M, Kuhn NC, Adams M, Kochmanski J, Bernstein AI. Parkinson's disease-associated shifts between DNA methylation and DNA hydroxymethylation in human brain in PD-related genes, including PARK19 (DNAJC6) and PTPRN2 (IA-2β). RESEARCH SQUARE 2024:rs.3.rs-4572401. [PMID: 39070644 PMCID: PMC11275970 DOI: 10.21203/rs.3.rs-4572401/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Background The majority of Parkinson's disease (PD) cases are due to a complex interaction between aging, genetics, and environmental factors; epigenetic mechanisms are thought to act as important mediators of these risk factors. While multiple studies to date have explored the role of DNA modifications in PD, few focus on 5-hydroxymethylcytosine (5hmC). Because 5hmC occurs at its highest levels in the brain and is thought to be particularly important in the central nervous system, particularly in the response to neurotoxicants, it is important to explore the potential role of 5hmC in PD. This study expands on our previously published epigenome-wide association study (EWAS) performed on DNA isolated from neuron-enriched nuclei from human postmortem parietal cortex from the Banner Sun Health Research Institute Brain Bank. The study aimed to identify paired changes in 5hmC and 5mC in PD in enriched neuronal nuclei isolated from PD post-mortem parietal cortex and age- and sex-matched controls. We performed oxidative bisulfite (oxBS) conversion and paired it with our previously published bisulfite (BS)-based EWAS on the same samples to identify cytosines with significant shifts between these two related epigenetic marks. Interaction differentially modified cytosines (iDMCs) were identified using our recently published mixed-effects model for co-analyzing βmC and βhmC data. Results We identified 1,030 iDMCs with paired changes in 5mC and 5hmC (FDR < 0.05) that map to 695 genes, including PARK19 (DNAJC6), a familial PD gene, and PTPRN2 (IA-2), which has been previously implicated in PD in both epigenetic and mechanistic studies. The majority of iDMC-containing genes have not previously been implicated in PD and were not identified in our previous BS-based EWAS. Conclusions These data potentially link epigenetic regulation of the PARK19 and PTPRN2 loci in the pathogenesis of idiopathic PD. In addition, iDMC-containing genes have known functions in synaptic formation and function, cell cycle and senescence, neuroinflammation, and epigenetic regulation. These data suggest that there are significant shifts between 5mC and 5hmC associated with PD in genes relevant to PD pathogenesis that are not captured by analyzing BS-based data alone or by analyzing each mark as a distinct dataset.
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Mishra T, Singh S, Singh TG. Therapeutic Implications and Regulations of Protein Post-translational Modifications in Parkinsons Disease. Cell Mol Neurobiol 2024; 44:53. [PMID: 38960968 PMCID: PMC11222187 DOI: 10.1007/s10571-024-01471-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/16/2024] [Indexed: 07/05/2024]
Abstract
Parkinsons disease (PD) is a neurodegenerative disorder characterized by dopaminergic neuron loss and alpha-synuclein aggregation. This comprehensive review examines the intricate role of post-translational modifications (PTMs) in PD pathogenesis, focusing on DNA methylation, histone modifications, phosphorylation, SUMOylation, and ubiquitination. Targeted PTM modulation, particularly in key proteins like Parkin, DJ1, and PINK1, emerges as a promising therapeutic strategy for mitigating dopaminergic degeneration in PD. Dysregulated PTMs significantly contribute to the accumulation of toxic protein aggregates and dopaminergic neuronal dysfunction observed in PD. Targeting PTMs, including epigenetic strategies, addressing aberrant phosphorylation events, and modulating SUMOylation processes, provides potential avenues for intervention. The ubiquitin-proteasome system, governed by enzymes like Parkin and Nedd4, offers potential targets for clearing misfolded proteins and developing disease-modifying interventions. Compounds like ginkgolic acid, SUMO E1 enzyme inhibitors, and natural compounds like Indole-3-carbinol illustrate the feasibility of modulating PTMs for therapeutic purposes in PD. This review underscores the therapeutic potential of PTM-targeted interventions in modulating PD-related pathways, emphasizing the need for further research in this promising area of Parkinsons disease therapeutics.
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Affiliation(s)
- Twinkle Mishra
- Chitkara College of Pharmacy, Chitkara University, Punjab, 140401, India
| | - Shareen Singh
- Chitkara College of Pharmacy, Chitkara University, Punjab, 140401, India
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Müller T, Riederer P. The vicious circle between homocysteine, methyl group-donating vitamins and chronic levodopa intake in Parkinson's disease. J Neural Transm (Vienna) 2024; 131:631-638. [PMID: 37329350 DOI: 10.1007/s00702-023-02666-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023]
Abstract
A biomarker for declined methylation capacity is elevation of homocysteine levels. They increase the risk for onset of vascular disease and contribute to progression of chronic neurodegeneration and aging. This narrative review discusses associations between homocysteine, consumption of methyl group-donating vitamins and impact on disease-generating mechanisms in levodopa-treated patients with Parkinson's disease. We conclude to recommend levodopa-treated patients to substitute themselves with methyl group-donating vitamins. This is harmless in terms of application of folic acid, methylcobalamin or hydroxocobalamin. Moreover, we suggest a crucial discussion on the value of the various popular hypotheses on Parkinson's disease-generating mechanisms. Findings from studies with acute levodopa exposure describe oxidative stress generation and impaired methylation capacity, which causes gene dysfunction. Their repeated occurrences contribute to onset of mitochondrial dysfunction, iron enrichment and pathologic protein accumulation in the long term. Current research underestimates these epigenetic, metabolic consequences of chronic levodopa application. Supplementary treatment strategies are recommended to avoid levodopa-related side effects.
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Affiliation(s)
- Thomas Müller
- Department of Neurology, St. Joseph Hospital Berlin-Weissensee, Gartenstr. 1, 13088, Berlin, Germany.
| | - Peter Riederer
- Center of Mental Health, Department of Psychiatry, Psychosomatics and Psychotherapy, University Hospital Würzburg, Margarete-Höppel Platz 1, 97080, Würzburg, Germany
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Zhang S, Kiarasi F. Therapeutic effects of resveratrol on epigenetic mechanisms in age-related diseases: A comprehensive review. Phytother Res 2024; 38:2347-2360. [PMID: 38421057 DOI: 10.1002/ptr.8176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/28/2024] [Accepted: 02/10/2024] [Indexed: 03/02/2024]
Abstract
Recently, various studies have shown that epigenetic changes are associated with aging and age-related diseases. Both animal and human models have revealed that epigenetic processes are involved in aging mechanisms. These processes happen at multiple levels and include histone modification, DNA methylation, and changes in noncoding RNA expression. Consequently, changes in the organization of chromatin and DNA accessibility lead to the regulation of gene expression. With increasing awareness of the pivotal function of epigenetics in the aging process, researchers' attention has been drawn to how these epigenetic changes can be modified to prevent, stop, or reverse aging, senescence, and age-related diseases. Among various agents that can affect epigenetic, polyphenols are well-known phytochemicals found in fruits, vegetables, and plants. Polyphenols are found to modify epigenetic-related mechanisms in various diseases and conditions, such as metabolic disorders, obesity, neurodegenerative diseases, cancer, and cardiovascular diseases. Resveratrol (RSV) is a member of the stilbene subgroup of polyphenols which is derived from various plants, such as grapes, apples, and blueberries. Therefore, herein, we aim to summarize how RSV affects different epigenetic processes to change aging-related mechanisms. Furthermore, we discuss its roles in age-related diseases, such as Alzheimer's, Parkinson's, osteoporosis, and cardiovascular diseases.
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Affiliation(s)
| | - Farzam Kiarasi
- Department of Medical Nanotechnology, Applied Biophotonics Research Center, Science and Research Branch, Islamic Azad University, Tehran, Iran
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Hamidpour SK, Amiri M, Ketabforoush AHME, Saeedi S, Angaji A, Tavakol S. Unraveling Dysregulated Cell Signaling Pathways, Genetic and Epigenetic Mysteries of Parkinson's Disease. Mol Neurobiol 2024:10.1007/s12035-024-04128-1. [PMID: 38573414 DOI: 10.1007/s12035-024-04128-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/19/2024] [Indexed: 04/05/2024]
Abstract
Parkinson's disease (PD) is a prevalent and burdensome neurodegenerative disorder that has been extensively researched to understand its complex etiology, diagnosis, and treatment. The interplay between genetic and environmental factors in PD makes its pathophysiology difficult to comprehend, emphasizing the need for further investigation into genetic and epigenetic markers involved in the disease. Early diagnosis is crucial for optimal management of the disease, and the development of novel diagnostic biomarkers is ongoing. Although many efforts have been made in the field of recognition and interpretation of the mechanisms involved in the pathophysiology of the disease, the current knowledge about PD is just the tip of the iceberg. By scrutinizing genetic and epigenetic patterns underlying PD, new avenues can be opened for dissecting the pathology of the disorder, leading to more precise and efficient diagnostic and therapeutic approaches. This review emphasizes the importance of studying dysregulated cell signaling pathways and molecular processes associated with genes and epigenetic alterations in understanding PD, paving the way for the development of novel therapeutic strategies to combat this devastating disease.
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Affiliation(s)
- Shayesteh Kokabi Hamidpour
- Department of Cell and Molecular Biology, Faculty of Biological Science, Kharazmi University, Tehran, Iran
| | - Mobina Amiri
- Department of Cell and Molecular Biology, Faculty of Biological Science, Kharazmi University, Tehran, Iran
| | | | - Saeedeh Saeedi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Abdolhamid Angaji
- Department of Cell and Molecular Biology, Faculty of Biological Science, Kharazmi University, Tehran, Iran
| | - Shima Tavakol
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, 1449614535, Iran.
- Department of Research and Development, Tavakol BioMimetic Technologies Company, Tehran, Iran.
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8
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Gionco JT, Bernstein AI. Emerging Role of Environmental Epitranscriptomics and RNA Modifications in Parkinson's Disease. JOURNAL OF PARKINSON'S DISEASE 2024; 14:643-656. [PMID: 38578904 PMCID: PMC11191529 DOI: 10.3233/jpd-230457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/10/2024] [Indexed: 04/07/2024]
Abstract
Environmental risk factors and gene-environment interactions play a critical role in Parkinson's disease (PD). However, the relatively large contribution of environmental risk factors in the overwhelming majority of PD cases has been widely neglected in the field. A "PD prevention agenda" proposed in this journal laid out a set of research priorities focused on preventing PD through modification of environmental risk factors. This agenda includes a call for preclinical studies to employ new high-throughput methods for analyzing transcriptomics and epigenomics to provide a deeper understanding of the effects of exposures linked to PD. Here, we focus on epitranscriptomics as a novel area of research with the potential to add to our understanding of the interplay between genes and environmental exposures in PD. Both epigenetics and epitranscriptomics have been recognized as potential mediators of the complex relationship between genes, environment, and disease. Multiple studies have identified epigenetic alterations, such as DNA methylation, associated with PD and PD-related exposures in human studies and preclinical models. In addition, recent technological advancements have made it possible to study epitranscriptomic RNA modifications, such as RNA N6-methyladenosine (m6A), and a handful of recent studies have begun to explore epitranscriptomics in PD-relevant exposure models. Continued exploration of epitranscriptomic mechanisms in environmentally relevant PD models offers the opportunity to identify biomarkers, pre-degenerative changes that precede symptom onset, and potential mitigation strategies for disease prevention and treatment.
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Affiliation(s)
- John T. Gionco
- Graduate Program in Cell and Developmental Biology, Rutgers University, Piscataway, NJ, USA
| | - Alison I. Bernstein
- Department of Pharmacology and Toxicology, Rutgers University, Piscataway, NJ, USA
- Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, NJ, USA
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9
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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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10
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Kreutz A, Hu G, Tokar E. Pluripotent Stem Cell-derived Dopaminergic Neurons for Studying Developmental Neurotoxicity. Stem Cell Rev Rep 2023; 19:2120-2130. [PMID: 37273171 PMCID: PMC10579108 DOI: 10.1007/s12015-023-10555-9] [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] [Accepted: 05/08/2023] [Indexed: 06/06/2023]
Abstract
With the vast number of chemicals in commerce, higher throughput strategies are needed to inform risk assessment. The field of toxicology is therefore moving away from traditional in vivo guideline studies towards in vitro new approach methodologies. There has been a great push for such a shift in the field of developmental neurotoxicity, where there is a particular lack of data. A battery of in vitro new approach methodologies has thus been developed to help fill this gap. Included in this battery are assays for numerous processes critical to neurodevelopment, such as proliferation, migration, and synaptogenesis. The current battery of developmental neurotoxicity new approach methodologies still lacks recapitulation of several critical neurodevelopmental processes, including development of neuronal subtypes. With their pluripotency, alongside other advantages, pluripotent stem cells (PSCs) are uniquely suited to address questions of developmental neurotoxicity, as they can recapitulate the different stages of human in vivo neurodevelopment. Among the various neuronal subtypes, development of dopaminergic neurons (DA) is perhaps the best understood and several approaches exist to differentiate PSCs into DA. Herein we review these approaches and propose utilizing PSCs for screening of the impact of environmental chemicals on development of DA. Related techniques and gaps in knowledge are also addressed.
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Affiliation(s)
- Anna Kreutz
- Mechanistic Toxicology Branch, Division of Translational Toxicology, NIEHS, Research Triangle Park, Durham, NC, 27709, USA.
- Epigenetics and Stem Cell Biology Laboratory, Division of Intramural Research, NIEHS, Research Triangle Park, Durham, NC, 27709, USA.
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, Division of Intramural Research, NIEHS, Research Triangle Park, Durham, NC, 27709, USA
| | - Erik Tokar
- Mechanistic Toxicology Branch, Division of Translational Toxicology, NIEHS, Research Triangle Park, Durham, NC, 27709, USA
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11
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Lomeli-Lepe AK, Castañeda-Cabral JL, López-Pérez SJ. Synucleinopathies: Intrinsic and Extrinsic Factors. Cell Biochem Biophys 2023; 81:427-442. [PMID: 37526884 DOI: 10.1007/s12013-023-01154-z] [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: 05/05/2023] [Accepted: 07/23/2023] [Indexed: 08/02/2023]
Abstract
α-Synucleinopathies are a group of neurodegenerative disorders characterized by alterations in α-synuclein (α-syn), a protein associated with membrane phospholipids, whose precise function in normal cells is still unknown. These kinds of diseases are caused by multiple factors, but the regulation of the α-syn gene is believed to play a central role in the pathology of these disorders; therefore, the α-syn gene is one of the most studied genes. α-Synucleinopathies are complex disorders that derive from the interaction between genetic and environmental factors. Here, we offer an update on the landscape of the epigenetic regulation of α-syn gene expression that has been linked with α-synucleinopathies. We also delve into the reciprocal influence between epigenetic modifications and other factors related to these disorders, such as posttranslational modifications, microbiota participation, interactions with lipids, neuroinflammation and oxidative stress, to promote α-syn aggregation by acting on the transcription and/or translation of the α-syn gene.
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Affiliation(s)
- Alma Karen Lomeli-Lepe
- Departamento de Biología Celular y Molecular, CUCBA, Universidad de Guadalajara, Guadalajara, JAL, México
| | - Jose Luis Castañeda-Cabral
- Departamento de Biología Celular y Molecular, CUCBA, Universidad de Guadalajara, Guadalajara, JAL, México
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12
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Qu J, Liu N, Gao L, Hu J, Sun M, Yu D. Development of CRISPR Cas9, spin-off technologies and their application in model construction and potential therapeutic methods of Parkinson's disease. Front Neurosci 2023; 17:1223747. [PMID: 37483347 PMCID: PMC10359996 DOI: 10.3389/fnins.2023.1223747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/22/2023] [Indexed: 07/25/2023] Open
Abstract
Parkinson's disease (PD) is one of the most common degenerative diseases. It is most typically characterized by neuronal death following the accumulation of Lewis inclusions in dopaminergic neurons in the substantia nigra region, with clinical symptoms such as motor retardation, autonomic dysfunction, and dystonia spasms. The exact molecular mechanism of its pathogenesis has not been revealed up to now. And there is a lack of effective treatments for PD, which places a burden on patients, families, and society. CRISPR Cas9 is a powerful technology to modify target genomic sequence with rapid development. More and more scientists utilized this technique to perform research associated neurodegenerative disease including PD. However, the complexity involved makes it urgent to organize and summarize the existing findings to facilitate a clearer understanding. In this review, we described the development of CRISPR Cas9 technology and the latest spin-off gene editing systems. Then we focused on the application of CRISPR Cas9 technology in PD research, summarizing the construction of the novel PD-related medical models including cellular models, small animal models, large mammal models. We also discussed new directions and target molecules related to the use of CRISPR Cas9 for PD treatment from the above models. Finally, we proposed the view about the directions for the development and optimization of the CRISPR Cas9 technology system, and its application to PD and gene therapy in the future. All these results provided a valuable reference and enhanced in understanding for studying PD.
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Affiliation(s)
- Jiangbo Qu
- Center for Medical Genetics and Prenatal Diagnosis, Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong, China
| | - Na Liu
- Center for Medical Genetics and Prenatal Diagnosis, Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong, China
| | - Lu Gao
- Center for Medical Genetics and Prenatal Diagnosis, Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong, China
| | - Jia Hu
- School of Life Science and Technology, Weifang Medical University, Weifang, Shandong, China
| | - Miao Sun
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Dongyi Yu
- Center for Medical Genetics and Prenatal Diagnosis, Key Laboratory of Birth Defect Prevention and Genetic Medicine of Shandong Health Commission, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, Shandong, China
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13
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Wüllner U, Borghammer P, Choe CU, Csoti I, Falkenburger B, Gasser T, Lingor P, Riederer P. The heterogeneity of Parkinson's disease. J Neural Transm (Vienna) 2023; 130:827-838. [PMID: 37169935 PMCID: PMC10174621 DOI: 10.1007/s00702-023-02635-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 04/12/2023] [Indexed: 05/13/2023]
Abstract
The heterogeneity of Parkinson's disease (PD), i.e. the various clinical phenotypes, pathological findings, genetic predispositions and probably also the various implicated pathophysiological pathways pose a major challenge for future research projects and therapeutic trail design. We outline several pathophysiological concepts, pathways and mechanisms, including the presumed roles of α-synuclein misfolding and aggregation, Lewy bodies, oxidative stress, iron and melanin, deficient autophagy processes, insulin and incretin signaling, T-cell autoimmunity, the gut-brain axis and the evidence that microbial (viral) agents may induce molecular hallmarks of neurodegeneration. The hypothesis is discussed, whether PD might indeed be triggered by exogenous (infectious) agents in susceptible individuals upon entry via the olfactory bulb (brain first) or the gut (body-first), which would support the idea that disease mechanisms may change over time. The unresolved heterogeneity of PD may have contributed to the failure of past clinical trials, which attempted to slow the course of PD. We thus conclude that PD patients need personalized therapeutic approaches tailored to specific phenomenological and etiologic subtypes of disease.
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Affiliation(s)
- Ullrich Wüllner
- Department of Neurology, University Clinic Bonn and German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Per Borghammer
- Department of Nuclear Medicine and PET, Aarhus University Hospital, Aarhus, Denmark
| | - Chi-un Choe
- Department of Neurology, Klinikum Itzehoe, Robert-Koch-Straße 2, 25524 Itzehoe, Germany
| | - Ilona Csoti
- Fachklinik Für Parkinson, Gertrudis Klinik Biskirchen, Karl-Ferdinand-Broll-Straße 2-4, 35638 Leun-Biskirchen, Germany
| | - Björn Falkenburger
- Department of Neurology, University Hospital Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Thomas Gasser
- Department of Neurology, Hertie-Institute for Clinical Brain Research, University of Tübingen and German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Paul Lingor
- Department of Neurology, School of Medicine, Klinikum Rechts Der Isar, Technical University of Munich, Munich, Germany
- Department of Neurology and German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Peter Riederer
- University Hospital Wuerzburg, Clinic and Policlinic for Psychiatry, Psychosomatics and Psychotherapy, Margarete-Höppel-Platz 1, 97080 Würzburg, Germany
- Department of Psychiatry, University of Southern Denmark Odense, J.B. Winslows Vey 18, 5000 Odense, Denmark
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14
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Wang R, Tong S, Wang M, Zou J, Wang N, Sun F, Zhou X, Chen J, Wang H. CREB5 hypermethylation involved in the ganglioside GM1 therapy of Parkinson's disease. Front Aging Neurosci 2023; 15:1122647. [PMID: 37323142 PMCID: PMC10264581 DOI: 10.3389/fnagi.2023.1122647] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/05/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction The treatment with monosialotetrahexosylganglioside (GM1) improves the symptoms of Parkinson's disease (PD). The alteration of DNA methylation in the blood was examined to investigate epigenetic modification by GM1 treatment. Methods After a 28-day continuous intravenous infusion of GM1 (100mg), the motor and non-motor symptoms were evaluated by UPDRS III, Mini-mental state examination (MMSE) scores, FS-14, SCOPA-AUT, and PDQ-8. Moreover, blood samples were collected and PBMC was isolated. Genome-wide DNA methylation was performed by an 850K BeadChip. RNA levels and apoptosis were examined by RT-PCR and flow cytometry in rotenone-based cell models. The CREB5 plasmid was transfected by electroporation into SH-SY5Y cells. We also identified 235 methylation variable positions achieving genome-wide significance in 717558 differentially methylated positions (DMPs) (P = 0.0003) in comparison of pre-treatment with post-treatment measurements (statistical analysis paired-samples t-test). Results By searching the Gene Expression Omnibus (GEO) dataset and GWAS, 23 methylation variable positions were screened. Moreover, there are 7 hypomethylated methylation variable positions correlated with the scores of motor symptoms (UPDRS III scale). According to KEGG pathways enrichment analysis, the methylated genes CACNA1B (hypomethylated), CREB5 (hypermethylated), GNB4 (hypomethylated), and PPP2R5A (hypomethylated) were enriched in the dopaminergic synapse pathway. Pretreated with GM1 (80 μM) for 1 h, cell apoptosis and impaired neurite outgrowth were inhibited in rotenone-induced PD cell models. The RNA expression of CREB5 was increased in rotenone-treated SH-SY5Y cells. GM1 treatment decreased rotenone-induced CREB5 gene expression. The enhancement of CREB5 gene expression suppressed the protective role of GM1 in rotenone-induced cell apoptosis. Discussion The application of GM1 improves the motor and non-motor symptoms of PD associated with the decreased CREB5 expression and the hypermethylation of CREB5. Clinical trial registration https://www.chictr.org.cn/showproj.html?proj=120582t, identifier ChiCTR2100042537.
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Affiliation(s)
- Rui Wang
- Department of Neurology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Shanshan Tong
- Department of Neurology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Mengdi Wang
- Department of Neurology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Junjie Zou
- Department of Neurology, Penglai People’s Hospital, Yantai, China
| | - Nan Wang
- Medical Research Center, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Fengjiao Sun
- Medical Research Center, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Xiaosheng Zhou
- Department of Neurology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Jinbo Chen
- Department of Neurology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Hongcai Wang
- Department of Neurology, Binzhou Medical University Hospital, Binzhou, Shandong, China
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15
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Zobdeh F, Eremenko II, Akan MA, Tarasov VV, Chubarev VN, Schiöth HB, Mwinyi J. The Epigenetics of Migraine. Int J Mol Sci 2023; 24:ijms24119127. [PMID: 37298078 DOI: 10.3390/ijms24119127] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 06/12/2023] Open
Abstract
Migraine is a complex neurological disorder and a major cause of disability. A wide range of different drug classes such as triptans, antidepressants, anticonvulsants, analgesics, and beta-blockers are used in acute and preventive migraine therapy. Despite a considerable progress in the development of novel and targeted therapeutic interventions during recent years, e.g., drugs that inhibit the calcitonin gene-related peptide (CGRP) pathway, therapy success rates are still unsatisfactory. The diversity of drug classes used in migraine therapy partly reflects the limited perception of migraine pathophysiology. Genetics seems to explain only to a minor extent the susceptibility and pathophysiological aspects of migraine. While the role of genetics in migraine has been extensively studied in the past, the interest in studying the role of gene regulatory mechanisms in migraine pathophysiology is recently evolving. A better understanding of the causes and consequences of migraine-associated epigenetic changes could help to better understand migraine risk, pathogenesis, development, course, diagnosis, and prognosis. Additionally, it could be a promising avenue to discover new therapeutic targets for migraine treatment and monitoring. In this review, we summarize the state of the art regarding epigenetic findings in relation to migraine pathogenesis and potential therapeutic targets, with a focus on DNA methylation, histone acetylation, and microRNA-dependent regulation. Several genes and their methylation patterns such as CALCA (migraine symptoms and age of migraine onset), RAMP1, NPTX2, and SH2D5 (migraine chronification) and microRNA molecules such as miR-34a-5p and miR-382-5p (treatment response) seem especially worthy of further study regarding their role in migraine pathogenesis, course, and therapy. Additionally, changes in genes including COMT, GIT2, ZNF234, and SOCS1 have been linked to migraine progression to medication overuse headache (MOH), and several microRNA molecules such as let-7a-5p, let-7b-5p, let-7f-5p, miR-155, miR-126, let-7g, hsa-miR-34a-5p, hsa-miR-375, miR-181a, let-7b, miR-22, and miR-155-5p have been implicated with migraine pathophysiology. Epigenetic changes could be a potential tool for a better understanding of migraine pathophysiology and the identification of new therapeutic possibilities. However, further studies with larger sample sizes are needed to verify these early findings and to be able to establish epigenetic targets as disease predictors or therapeutic targets.
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Affiliation(s)
- Farzin Zobdeh
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Husargatan 3, P.O. Box 593, 75124 Uppsala, Sweden
| | - Ivan I Eremenko
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Husargatan 3, P.O. Box 593, 75124 Uppsala, Sweden
- Advanced Molecular Technology, LLC, 354340 Moscow, Russia
| | - Mikail A Akan
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Husargatan 3, P.O. Box 593, 75124 Uppsala, Sweden
- Advanced Molecular Technology, LLC, 354340 Moscow, Russia
| | | | | | - Helgi B Schiöth
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Husargatan 3, P.O. Box 593, 75124 Uppsala, Sweden
| | - Jessica Mwinyi
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Husargatan 3, P.O. Box 593, 75124 Uppsala, Sweden
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Sugeno N, Hasegawa T. Unraveling the Complex Interplay between Alpha-Synuclein and Epigenetic Modification. Int J Mol Sci 2023; 24:ijms24076645. [PMID: 37047616 PMCID: PMC10094812 DOI: 10.3390/ijms24076645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/21/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
Alpha-synuclein (αS) is a small, presynaptic neuronal protein encoded by the SNCA gene. Point mutations and gene multiplication of SNCA cause rare familial forms of Parkinson’s disease (PD). Misfolded αS is cytotoxic and is a component of Lewy bodies, which are a pathological hallmark of PD. Because SNCA multiplication is sufficient to cause full-blown PD, gene dosage likely has a strong impact on pathogenesis. In sporadic PD, increased SNCA expression resulting from a minor genetic background and various environmental factors may contribute to pathogenesis in a complementary manner. With respect to genetic background, several risk loci neighboring the SNCA gene have been identified, and epigenetic alterations, such as CpG methylation and regulatory histone marks, are considered important factors. These alterations synergistically upregulate αS expression and some post-translational modifications of αS facilitate its translocation to the nucleus. Nuclear αS interacts with DNA, histones, and their modifiers to alter epigenetic status; thereby, influencing the stability of neuronal function. Epigenetic changes do not affect the gene itself but can provide an appropriate transcriptional response for neuronal survival through DNA methylation or histone modifications. As a new approach, publicly available RNA sequencing datasets from human midbrain-like organoids may be used to compare transcriptional responses through epigenetic alterations. This informatic approach combined with the vast amount of transcriptomics data will lead to the discovery of novel pathways for the development of disease-modifying therapies for PD.
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Affiliation(s)
- Naoto Sugeno
- Division of Neurology, Department of Neuroscience & Sensory Organs, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Takafumi Hasegawa
- Division of Neurology, Department of Neuroscience & Sensory Organs, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
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17
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Surguchov A. α-Synuclein and Mechanisms of Epigenetic Regulation. Brain Sci 2023; 13:brainsci13010150. [PMID: 36672131 PMCID: PMC9857298 DOI: 10.3390/brainsci13010150] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Synucleinopathies are a group of neurodegenerative diseases with common pathological lesions associated with the excessive accumulation and abnormal intracellular deposition of toxic species of α-synuclein. The shared clinical features are chronic progressive decline of motor, cognitive, and behavioral functions. These disorders include Parkinson's disease, dementia with Lewy body, and multiple system atrophy. Vigorous research in the mechanisms of pathology of these illnesses is currently under way to find disease-modifying treatment and molecular markers for early diagnosis. α-Synuclein is a prone-to-aggregate, small amyloidogenic protein with multiple roles in synaptic vesicle trafficking, neurotransmitter release, and intracellular signaling events. Its expression is controlled by several mechanisms, one of which is epigenetic regulation. When transmitted to the nucleus, α-synuclein binds to DNA and histones and participates in epigenetic regulatory functions controlling specific gene transcription. Here, we discuss the various aspects of α-synuclein involvement in epigenetic regulation in health and diseases.
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Affiliation(s)
- Andrei Surguchov
- Department of Neurology, Kansas University Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
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18
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Wang JY, Cui L, Shi HY, Chen LH, Jin RW, Jiang XX, Chen ZL, Zhu JH, Zhang X. Gene-wide significant association analyses of DNMT1 genetic variants with Parkinson's disease. Front Genet 2023; 14:1112388. [PMID: 36950137 PMCID: PMC10025298 DOI: 10.3389/fgene.2023.1112388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/24/2023] [Indexed: 03/08/2023] Open
Abstract
Background: DNA methylation plays an important role in Parkinson's disease (PD) pathogenesis. DNA methyltransferase 1 (DNMT1) is critical for maintaining DNA methylation in mammals. The link between DNMT1 polymorphisms and PD remains elusive. Methods: The DNMT1 gene contained a total of 28 single nucleotide polymorphisms (SNPs). Four representing tag-SNPs (rs16999593, rs2162560, rs11880553, and rs9305012) were identified and genotyped in a Han Chinese population comprising 712 PD patients and 696 controls. Association analyses were performed at gene-wide significance (p < 1.8 × 10-3). Results: Rs9305012, but not the other 3 tag-SNPs, was gene-wide significantly associated with PD risk (p = 0.8 × 10-3). The rs9305012/C was a protective allele against PD (p = 1.5 × 10-3, OR 0.786, 95% CI 0.677-0.912). No significant association was observed in individual genders or PD subtypes. Haplotypes of the 4 tag-SNPs showed a significant overall distribution difference between PD patients and controls (p < 1 × 10-4). The 3-allele ACC module in the order of rs2162560, rs11880553, and rs9305012 was the highest-risk haplotype associated with PD (p < 1 × 10-4, OR 2.439, 95% CI 1.563-3.704). Rs9305012 displayed certain probability to affect transcription factor binding and target gene expression based on functional annotation analyses. Conclusion: The DNMT1 variant rs9305012 together with its haplotypes may gene-wide significantly modulate PD susceptibility. Our results support a role of DNMT1 in PD pathogenesis and provide novel insights into the genetic connection in between.
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Affiliation(s)
- Jian-Yong Wang
- Department of Neurology, Institute of Geriatric Neurology, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lei Cui
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Hong-Yi Shi
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ling-Hao Chen
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ren-Wei Jin
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiao-Xia Jiang
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhu-Ling Chen
- Department of Neurology, Institute of Geriatric Neurology, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jian-Hong Zhu
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, Zhejiang, China
- *Correspondence: Jian-Hong Zhu, ; Xiong Zhang,
| | - Xiong Zhang
- Department of Neurology, Institute of Geriatric Neurology, The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, Zhejiang, China
- *Correspondence: Jian-Hong Zhu, ; Xiong Zhang,
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19
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Kretzschmar GC, Targa ADS, Soares-Lima SC, dos Santos PI, Rodrigues LS, Macedo DA, Ribeiro Pinto LF, Lima MMS, Boldt ABW. Folic Acid and Vitamin B12 Prevent Deleterious Effects of Rotenone on Object Novelty Recognition Memory and Kynu Expression in an Animal Model of Parkinson's Disease. Genes (Basel) 2022; 13:genes13122397. [PMID: 36553663 PMCID: PMC9778036 DOI: 10.3390/genes13122397] [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: 10/24/2022] [Revised: 12/10/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Parkinson's disease (PD) is characterized by a range of motor signs, but cognitive dysfunction is also observed. Supplementation with folic acid and vitamin B12 is expected to prevent cognitive impairment. To test this in PD, we promoted a lesion within the substantia nigra pars compacta of rats using the neurotoxin rotenone. In the sequence, the animals were supplemented with folic acid and vitamin B12 for 14 consecutive days and subjected to the object recognition test. We observed an impairment in object recognition memory after rotenone administration, which was prevented by supplementation (p < 0.01). Supplementation may adjust gene expression through efficient DNA methylation. To verify this, we measured the expression and methylation of the kynureninase gene (Kynu), whose product metabolizes neurotoxic metabolites often accumulated in PD as kynurenine. Supplementation prevented the decrease in Kynu expression induced by rotenone in the substantia nigra (p < 0.05), corroborating the behavioral data. No differences were observed concerning the methylation analysis of two CpG sites in the Kynu promoter. Instead, we suggest that folic acid and vitamin B12 increased global DNA methylation, reduced the expression of Kynu inhibitors, maintained Kynu-dependent pathway homeostasis, and prevented the memory impairment induced by rotenone. Our study raises the possibility of adjuvant therapy for PD with folic acid and vitamin B12.
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Affiliation(s)
- Gabriela Canalli Kretzschmar
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Adriano D. S. Targa
- Laboratory of Neurophysiology, Department of Physiology, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Sheila Coelho Soares-Lima
- Molecular Carcinogenesis Program, National Cancer Institute, Research Coordination, Rio de Janeiro 20231-050, RJ, Brazil
| | - Priscila Ianzen dos Santos
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Lais S. Rodrigues
- Laboratory of Neurophysiology, Department of Physiology, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Daniel A. Macedo
- Laboratory of Neurophysiology, Department of Physiology, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Luis Felipe Ribeiro Pinto
- Molecular Carcinogenesis Program, National Cancer Institute, Research Coordination, Rio de Janeiro 20231-050, RJ, Brazil
| | - Marcelo M. S. Lima
- Laboratory of Neurophysiology, Department of Physiology, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Angelica Beate Winter Boldt
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
- Correspondence: ; Tel.: +55-(41)-3361-1553
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20
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Parkinson's disease-associated, sex-specific changes in DNA methylation at PARK7 (DJ-1), SLC17A6 (VGLUT2), PTPRN2 (IA-2β), and NR4A2 (NURR1) in cortical neurons. NPJ Parkinsons Dis 2022; 8:120. [PMID: 36151217 PMCID: PMC9508164 DOI: 10.1038/s41531-022-00355-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 06/24/2022] [Indexed: 12/04/2022] Open
Abstract
Evidence for epigenetic regulation playing a role in Parkinson's disease (PD) is growing, particularly for DNA methylation. Approximately 90% of PD cases are due to a complex interaction between age, genes, and environmental factors, and epigenetic marks are thought to mediate the relationship between aging, genetics, the environment, and disease risk. To date, there are a small number of published genome-wide studies of DNA methylation in PD, but none accounted for cell type or sex in their analyses. Given the heterogeneity of bulk brain tissue samples and known sex differences in PD risk, progression, and severity, these are critical variables to account for. In this genome-wide analysis of DNA methylation in an enriched neuronal population from PD postmortem parietal cortex, we report sex-specific PD-associated methylation changes in PARK7 (DJ-1), SLC17A6 (VGLUT2), PTPRN2 (IA-2β), NR4A2 (NURR1), and other genes involved in developmental pathways, neurotransmitter packaging and release, and axon and neuron projection guidance.
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21
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Avolio E, Olivito I, Rosina E, Romano L, Angelone T, Bartolo Anna D, Scimeca M, Bellizzi D, D'Aquila P, Passarino G, Alò R, Maria Facciolo R, Bagni C, De Lorenzo A, Canonaco M. Modifications of behavior and inflammation in mice following transplant with fecal microbiota from children with autism. Neuroscience 2022; 498:174-189. [DOI: 10.1016/j.neuroscience.2022.06.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 10/17/2022]
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22
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Min S, Xu Q, Qin L, Li Y, Li Z, Chen C, Wu H, Han J, Zhu X, Jin P, Tang B. Altered hydroxymethylome in the substantia nigra of Parkinson's disease. Hum Mol Genet 2022; 31:3494-3503. [PMID: 35661211 PMCID: PMC9558850 DOI: 10.1093/hmg/ddac122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/05/2022] [Accepted: 05/21/2022] [Indexed: 01/26/2023] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder, and aging and genetic and environmental exposure can contribute to its pathogenesis. DNA methylation has been suggested to play a pivotal role in neurodevelopment and neurodegenerative diseases. 5-hydroxymethylcytosine (5hmC) is generated through 5-methylcytosine (5mC) oxidization by ten-eleven translocation proteins and is particularly enriched in the brain. Although 5hmC has been linked to multiple neurological disorders, little is known about 5hmC alterations in the substantia nigra of patients with PD. To determine the specific alterations in DNA methylation and hydroxymethylation in PD brain samples, we examined the genome-wide profiles of 5mC and 5hmC in the substantia nigra of patients with PD and Alzheimer's disease (ad). We identified 4119 differentially hydroxymethylated regions (DhMRs) and no differentially methylated regions (DMRs) in the postmortem brains of patients with PD compared with those of controls. These DhMRs were PD-specific when compared with the results of AD. Gene ontology analysis revealed that several signaling pathways, such as neurogenesis and neuronal differentiation, were significantly enriched in PD DhMRs. KEGG enrichment analysis revealed substantial alterations in multiple signaling pathways, including phospholipase D (PLD), cAMP and Rap1. In addition, using a PD Drosophila model, we found that one of the 5hmC-modulated genes, PLD1, modulated α-synuclein toxicity. Our analysis suggested that 5hmC may act as an independent epigenetic marker and contribute to the pathogenesis of PD.
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Affiliation(s)
| | | | | | - Yujing Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ziyi Li
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA 30322, USA
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA 30322, USA
| | - Junhai Han
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu 210096, China
| | - Xiongwei Zhu
- To whom correspondence should be addressed at: Department of Neurology, Xiangya Hospital, Central South University, #87 Xiangya Road, Changsha, Hunan 410008, China. Tel: +86-731-84327398; ; Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA. Tel: +1 404-727-3729; ; Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA. Tel: +1-216-368-5903,
| | - Peng Jin
- To whom correspondence should be addressed at: Department of Neurology, Xiangya Hospital, Central South University, #87 Xiangya Road, Changsha, Hunan 410008, China. Tel: +86-731-84327398; ; Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA. Tel: +1 404-727-3729; ; Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA. Tel: +1-216-368-5903,
| | - Beisha Tang
- To whom correspondence should be addressed at: Department of Neurology, Xiangya Hospital, Central South University, #87 Xiangya Road, Changsha, Hunan 410008, China. Tel: +86-731-84327398; ; Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA. Tel: +1 404-727-3729; ; Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA. Tel: +1-216-368-5903,
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Iakovenko EV, Abramycheva NY, Fedotova EY, Illarioshkin SN. Methylation of MAPT Gene in Neurodegenerative Synucleinopathies. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422050118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Perez GA, Villarraso JC. An Entropy Approach to Multiple Sclerosis Identification. J Pers Med 2022; 12:jpm12030398. [PMID: 35330398 PMCID: PMC8948909 DOI: 10.3390/jpm12030398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 11/16/2022] Open
Abstract
Multiple sclerosis (MS) is a relatively common neurodegenerative illness that frequently causes a large level of disability in patients. While its cause is not fully understood, it is likely due to a combination of genetic and environmental factors. Diagnosis of multiple sclerosis through a simple clinical examination might be challenging as the evolution of the illness varies significantly from patient to patient, with some patients experiencing long periods of remission. In this regard, having a quick and inexpensive tool to help identify the illness, such as DNA CpG (cytosine-phosphate-guanine) methylation, might be useful. In this paper, a technique is presented, based on the concept of Shannon Entropy, to select CpGs as inputs for non-linear classification algorithms. It will be shown that this approach generates accurate classifications that are a statistically significant improvement over using all the data available or randomly selecting the same number of CpGs. The analysis controlled for factors such as age, gender and smoking status of the patient. This approach managed to reduce the number of CpGs used while at the same time significantly increasing the accuracy.
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Affiliation(s)
- Gerardo Alfonso Perez
- Department of Biochemistry and Molecular Biology, University of Cordoba, 14071 Cordoba, Spain;
- Correspondence:
| | - Javier Caballero Villarraso
- Department of Biochemistry and Molecular Biology, University of Cordoba, 14071 Cordoba, Spain;
- Biochemical Laboratory, Reina Sofia University Hospital, 14004 Cordoba, Spain
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25
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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: 20] [Impact Index Per Article: 10.0] [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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26
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Martínez-Iglesias O, Naidoo V, Cacabelos N, Cacabelos R. Epigenetic Biomarkers as Diagnostic Tools for Neurodegenerative Disorders. Int J Mol Sci 2021; 23:13. [PMID: 35008438 PMCID: PMC8745005 DOI: 10.3390/ijms23010013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/03/2021] [Accepted: 12/17/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetics is the study of heritable changes in gene expression that occur without alterations to the DNA sequence, linking the genome to its surroundings. The accumulation of epigenetic alterations over the lifespan may contribute to neurodegeneration. The aim of the present study was to identify epigenetic biomarkers for improving diagnostic efficacy in patients with neurodegenerative diseases. We analyzed global DNA methylation, chromatin remodeling/histone modifications, sirtuin (SIRT) expression and activity, and the expression of several important neurodegeneration-related genes. DNA methylation, SIRT expression and activity and neuregulin 1 (NRG1), microtubule-associated protein tau (MAPT) and brain-derived neurotrophic factor (BDNF) expression were reduced in buffy coat samples from patients with neurodegenerative disorders. Our data suggest that these epigenetic biomarkers may be useful in clinical practical for the diagnosis, surveillance, and prognosis of disease activity in patients with neurodegenerative diseases.
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Affiliation(s)
- Olaia Martínez-Iglesias
- EuroEspes Biomedical Research Center, International Center of Neuroscience and Genomic Medicine, Bergondo, 15165 Corunna, Spain; (V.N.); (N.C.); (R.C.)
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27
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CRISPR-Cas9-Mediated Gene Therapy in Neurological Disorders. Mol Neurobiol 2021; 59:968-982. [PMID: 34813019 DOI: 10.1007/s12035-021-02638-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/03/2021] [Indexed: 12/20/2022]
Abstract
Neurological disorders are primarily diseases with sophisticated etiology that are always refractory and recrudescent. The major obstruction to effective therapies for neurological disorders is the poor understanding of their pathogenic mechanisms. CRISPR-Cas9 technology, which allows precise and effective gene editing in almost any cell type and organism, is accelerating the pace of basic biological research. An increasing number of groups are focusing on uncovering the molecular mechanisms of neurological disorders and developing novel therapies using the CRISPR-Cas9 system. This review highlights the application of CRISPR-Cas9 technology in the treatment of neurological disorders, including Alzheimer's disease, amyotrophic lateral sclerosis and/or frontotemporal dementia, Duchenne muscular dystrophy, Dravet syndrome, epilepsy, Huntington's disease, and Parkinson's disease. Hopefully, it will improve our understanding of neurological disorders and give insights into future treatments for neurological disorders.
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28
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Meng J, Wang F, Ji L, Liang Y, Nian W, Song L, Zhu A. Comprehensive methylation profile of CSF cfDNA revealed pathogenesis and diagnostic markers for early-onset Parkinson's disease. Epigenomics 2021; 13:1637-1651. [PMID: 34664993 DOI: 10.2217/epi-2021-0176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Background: Early-onset Parkinson's disease (EOPD) is one uncommon Parkinson's disease subtype with characteristic clinicopathological features. The full epigenomic profile of EOPD is largely unknown. Methods: We performed the first study to investigate the EOPD full methylation profile of cerebrospinal fluid (CSF) cell-free DNA (cfDNA) from 26 EOPD patients and 10 control patients. Results: 2220 differentially methylated genes were identified in EOPD. Hypermethylation far outweighed hypomethylation in gene numbers. Clustering and enrichment analyses identified aberrant neuronal function and immune response. Weighted correlation network analysis demonstrated significant correlation between methylation signatures and clock drawing test (CDT), mini-mental state examination (MMSE), education, working status, alcohol drinking history and Hamilton anxiety scale (HAMA). Several key networking genes in EOPD aberrant methylation were also identified. Conclusions: The methylation profile and signatures of CSF cfDNA were revealed for the first time in EOPD. Aberrant methylation signatures were correlated with education, working status, alcohol drinking history, CDT, MMSE and HAMA.
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Affiliation(s)
- Jie Meng
- Institution of Geriatric, Qinghai Provincial People's Hospital, Xining, 810007, PR China.,Department of Neurology & State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, & Collaborative Innovation Center for Biotherapy, Chengdu, 610041, PR China
| | - Fenglin Wang
- Department of genetics and cell biology, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Lei Ji
- Institution of Geriatric, Qinghai Provincial People's Hospital, Xining, 810007, PR China
| | - Yuhua Liang
- Institution of Geriatric, Qinghai Provincial People's Hospital, Xining, 810007, PR China
| | - Wei Nian
- Institution of Geriatric, Qinghai Provincial People's Hospital, Xining, 810007, PR China
| | - Lele Song
- Institution of Geriatric, Qinghai Provincial People's Hospital, Xining, 810007, PR China.,Department of Radiotherapy, The Eighth Medical Center of the Chinese PLA General Hospital, Beijing, 100091, PR China
| | - Aiqin Zhu
- Institution of Geriatric, Qinghai Provincial People's Hospital, Xining, 810007, PR China
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29
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Stahl F, Denner P, Piston D, Evert BO, de Boni L, Schmitt I, Breuer P, Wüllner U. Activators of alpha synuclein expression identified by reporter cell line-based high throughput drug screen. Sci Rep 2021; 11:19857. [PMID: 34615900 PMCID: PMC8494889 DOI: 10.1038/s41598-021-98841-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/08/2021] [Indexed: 11/29/2022] Open
Abstract
Multiplications, mutations and dysregulation of the alpha synuclein gene (SNCA) are associated with the demise of dopaminergic neurons and are considered to play important roles in the pathogenesis of familial and sporadic forms of Parkinson's disease. Regulation of SNCA expression might thus be an appropriate target for treatment. We aimed to identify specific modulators of SNCA transcription, generated CRISPR/Cas9 modified SNCA-GFP-luciferase (LUC) genomic fusion- and control cell lines and screened a library of 1649 bioactive compounds, including the FDA approved drugs. We found no inhibitors but three selective activators which increased SNCA mRNA and protein levels.
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Affiliation(s)
- Fabian Stahl
- DZNE, German Center for Neurodegenerative Diseases, Venusberg-Campus 1/99, 53127, Bonn, Germany
- Department of Neurology, University Hospital Bonn, 53127, Bonn, Germany
| | - Philip Denner
- DZNE, German Center for Neurodegenerative Diseases, Venusberg-Campus 1/99, 53127, Bonn, Germany
| | - Dominik Piston
- DZNE, German Center for Neurodegenerative Diseases, Venusberg-Campus 1/99, 53127, Bonn, Germany
| | - Bernd O Evert
- Department of Neurology, University Hospital Bonn, 53127, Bonn, Germany
| | - Laura de Boni
- Department of Neurology, University Hospital Bonn, 53127, Bonn, Germany
| | - Ina Schmitt
- Department of Neurology, University Hospital Bonn, 53127, Bonn, Germany
| | - Peter Breuer
- Department of Neurology, University Hospital Bonn, 53127, Bonn, Germany.
| | - Ullrich Wüllner
- DZNE, German Center for Neurodegenerative Diseases, Venusberg-Campus 1/99, 53127, Bonn, Germany.
- Department of Neurology, University Hospital Bonn, 53127, Bonn, Germany.
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30
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Chen Z, Rasheed M, Deng Y. The epigenetic mechanisms involved in mitochondrial dysfunction: Implication for Parkinson's disease. Brain Pathol 2021; 32:e13012. [PMID: 34414627 PMCID: PMC9048811 DOI: 10.1111/bpa.13012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 06/21/2021] [Accepted: 07/27/2021] [Indexed: 12/18/2022] Open
Abstract
Mitochondrial dysfunction is one of the crucial factors involved in PD’s pathogenicity, which emerges from a combination of genetic and environmental factors. These factors cause differential molecular expression in neurons, such as varied transcriptional regulation of genes, elevated oxidative stress, α‐synuclein aggregation and endogenous neurotoxins release, which induces epigenetic modifications and triggers energy crisis by damaging mitochondria of the dopaminergic neurons (DN). So far, these events establish a complicated relationship with underlying mechanisms of mitochondrial anomalies in PD, which has remained unclear for years and made PD diagnosis and treatment extremely difficult. Therefore, in this review, we endeavored to discuss the complex association of epigenetic modifications and other associated vital factors in mitochondrial dysfunction. We propose a hypothesis that describes a vicious cycle in which mitochondrial dysfunction and oxidative stress act as a hub for regulating DA neuron's fate in PD. Oxidative stress triggers the release of endogenous neurotoxins (CTIQs) that lead to mitochondrial dysfunction along with abnormal α‐synuclein aggregation and epigenetic modifications. These disturbances further intensify oxidative stress and mitochondrial damage, amplifying the synthesis of CTIQs and works vice versa. This vicious cycle may result in the degeneration of DN to hallmark Parkinsonism. Furthermore, we have also highlighted various endogenous compounds and epigenetic marks (neurotoxic and neuroprotective), which may help for devising future diagnostic biomarkers and target specific drugs using novel PD management strategies.
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Affiliation(s)
- Zixuan Chen
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Madiha Rasheed
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yulin Deng
- School of Life Science, Beijing Institute of Technology, Beijing, China
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31
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Wu TT, Liu T, Li X, Chen YJ, Chen TJ, Zhu XY, Chen JL, Li Q, Liu Y, Feng Y, Wu YC. TET2-mediated Cdkn2A DNA hydroxymethylation in midbrain dopaminergic neuron injury of Parkinson's disease. Hum Mol Genet 2021; 29:1239-1252. [PMID: 32037456 DOI: 10.1093/hmg/ddaa022] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/03/2020] [Accepted: 02/03/2020] [Indexed: 12/31/2022] Open
Abstract
It has been reported that abnormal epigenetic modification is associated with the occurrence of Parkinson's disease (PD). Here, we found that a ten-eleven translocation 2 (TET2), a staff of the DNA hydroxylases family, was increased in dopaminergic neurons in vitro and in vivo. Genome-wide mapping of DNA 5-hydroxymethylcytosine (5-hmC)-sequencing has revealed an aberrant epigenome 5-hmC landscape in 1-methyl-4-phenylpyridinium iodide (MPP+)-induced SH-SY5Y cells. The TET family of DNA hydroxylases could reverse DNA methylation by oxidization of 5-methylcytosine (5-mC) to 5-hmC. However, the relationship between modification of DNA hydroxymethylation and the pathogenesis of PD is not clear. According to the results of 5-hmC-sequencing studies, 5-hmC was associated with gene-rich regions in the genomes related to cell cycle, especially gene-cyclin-dependent kinase inhibitor 2A (Cdkn2A). Downregulation of TET2 expression could significantly rescue MPP+-stimulated SH-SY5Y cell damage and cell cycle arrest. Meanwhile, knockdown of Tet2 expression in the substantia nigra pars compacta of MPTP-induced PD mice resulted in attenuated MPTP-induced motor deficits and dopaminergic neuronal injury via p16 suppression. In this study, we demonstrated a critical function of TET2 in PD development via the CDKN2A activity-dependent epigenetic pathway, suggesting a potential new strategy for epigenetic therapy.
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Affiliation(s)
- Ting-Ting Wu
- Department of Neurology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Te Liu
- Shanghai Geriatric Institute of Chinese Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200031, P.R. China
| | - Xuan Li
- Department of Neurology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Ya-Jing Chen
- Department of Neurology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Tian-Jiao Chen
- Department of Neurology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Xiao-Ying Zhu
- Department of Neurology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Jiu-Lin Chen
- Shanghai Geriatric Institute of Chinese Medicine, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200031, P.R. China
| | - Qing Li
- The State Key Laboratory of Medical Neurobiology, The Institutes of Brain Science and the Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Ye Liu
- Department of Neurology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Ya Feng
- Department of Neurology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Yun-Cheng Wu
- Department of Neurology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
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Sharma A, Müller J, Schuetze K, Rolfes V, Bissinger R, Rosero N, Ahmad A, Franklin BS, Zur B, Fröhlich H, Lang F, Oldenburg J, Pötzsch B, Wüllner U. Comprehensive Profiling of Blood Coagulation and Fibrinolysis Marker Reveals Elevated Plasmin-Antiplasmin Complexes in Parkinson's Disease. BIOLOGY 2021; 10:716. [PMID: 34439949 PMCID: PMC8389253 DOI: 10.3390/biology10080716] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 01/22/2023]
Abstract
Parkinson's disease (PD) is the second most common age-related neurodegenerative disease. Accumulating evidence demonstrates that alpha-synuclein (α-Syn), an apparently predominant neuronal protein, is a major contributor to PD pathology. As α-Syn is also highly abundant in blood, particularly in red blood cells (RBCs) and platelets, this in turn raises the question on the function of presumably dysfunctional α-Syn in "peripheral" cells and its putative effect on the other enclosed constituents. Herein, we detected the internal variance in erythrocytes of PD patients by Raman spectroscopy, but no measurable amount of erythrocytic behavioural change (eryptosis) or any haemoglobin variation was noticed. An elevated level of plasmin-antiplasmin complexes (PAP) was observed in the plasma of PD patients, indicating activation of the fibrinolytic system, but platelet activation after thrombin stimulation was not altered. Sex-specific patterns were noticed for blood coagulation factor XIII and factor XII activity in PD patients. Additionally, the alterations in homocysteine levels which have often been observed in PD patients were found to be independent from L-DOPA usage and PAP levels. Furthermore, a selective gene expression analysis identified subsets of genes related to different blood-associated compartments (RBCs, platelets, coagulation-fibrinolysis) also involved in PD-related pathways.
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Affiliation(s)
- Amit Sharma
- Department of Neurology, University Hospital Bonn, 53127 Bonn, Germany;
| | - Jens Müller
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, 53127 Bonn, Germany; (J.M.); (J.O.); (B.P.)
| | | | - Verena Rolfes
- Institute of Innate Immunity, University Hospital Bonn, 53127 Bonn, Germany; (V.R.); (N.R.); (B.S.F.)
| | - Rosi Bissinger
- Department of Internal Medicine IV, Eberhard Karl University, 72076 Tuebingen, Germany;
| | - Nathalia Rosero
- Institute of Innate Immunity, University Hospital Bonn, 53127 Bonn, Germany; (V.R.); (N.R.); (B.S.F.)
| | - Ashar Ahmad
- Bonn-Aachen International Center for IT (B-IT), University Hospital Bonn, 53115 Bonn, Germany; (A.A.); (H.F.)
| | - Bernardo S Franklin
- Institute of Innate Immunity, University Hospital Bonn, 53127 Bonn, Germany; (V.R.); (N.R.); (B.S.F.)
| | - Berndt Zur
- Central Laboratory of the Rheinland Klinikum Neuss, 41464 Neuss, Germany;
| | - Holger Fröhlich
- Bonn-Aachen International Center for IT (B-IT), University Hospital Bonn, 53115 Bonn, Germany; (A.A.); (H.F.)
| | - Florian Lang
- Department of Physiology, Eberhard Karls University, 72076 Tuebingen, Germany;
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, 53127 Bonn, Germany; (J.M.); (J.O.); (B.P.)
| | - Bernd Pötzsch
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, 53127 Bonn, Germany; (J.M.); (J.O.); (B.P.)
| | - Ullrich Wüllner
- Department of Neurology, University Hospital Bonn, 53127 Bonn, Germany;
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
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Ravel-Godreuil C, Massiani-Beaudoin O, Mailly P, Prochiantz A, Joshi RL, Fuchs J. Perturbed DNA methylation by Gadd45b induces chromatin disorganization, DNA strand breaks and dopaminergic neuron death. iScience 2021; 24:102756. [PMID: 34278264 PMCID: PMC8264156 DOI: 10.1016/j.isci.2021.102756] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/14/2021] [Accepted: 06/17/2021] [Indexed: 12/13/2022] Open
Abstract
Age is a major risk factor for neurodegenerative diseases like Parkinson's disease, but few studies have explored the contribution of key hallmarks of aging, namely DNA methylation changes and heterochromatin destructuration, in the neurodegenerative process. Here, we investigated the consequences of viral overexpression of Gadd45b, a multifactorial protein involved in DNA demethylation, in the mouse midbrain. Gadd45b overexpression induced global and stable changes in DNA methylation, particularly in introns of genes related to neuronal functions, as well as on LINE-1 transposable elements. This was paralleled by disorganized heterochromatin, increased DNA damage, and vulnerability to oxidative stress. LINE-1 de-repression, a potential source of DNA damage, preceded Gadd45b-induced neurodegeneration, whereas prolonged Gadd45b expression deregulated expression of genes related to heterochromatin maintenance, DNA methylation, or Parkinson's disease. Our data indicates that aging-related alterations contribute to dopaminergic neuron degeneration with potential implications for Parkinson's disease.
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Affiliation(s)
- Camille Ravel-Godreuil
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Olivia Massiani-Beaudoin
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Philippe Mailly
- Orion Imaging Facility, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Labex Memolife, Université PSL, Paris, France
| | - Alain Prochiantz
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Rajiv L. Joshi
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Julia Fuchs
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
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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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Zhang HQ, Wang JY, Li ZF, Cui L, Huang SS, Zhu LB, Sun Y, Yang R, Fan HH, Zhang X, Zhu JH. DNA Methyltransferase 1 Is Dysregulated in Parkinson's Disease via Mediation of miR-17. Mol Neurobiol 2021; 58:2620-2633. [PMID: 33483902 DOI: 10.1007/s12035-021-02298-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/14/2021] [Indexed: 12/12/2022]
Abstract
Aberrant DNA methylation is closely associated with the pathogenesis of Parkinson's disease (PD). DNA methyltransferases (DNMTs) are the enzymes for establishment and maintenance of DNA methylation patterns. It has not been clearly defined how DNMTs respond in PD and what mechanisms are associated. Models of PD were established by treatment of five different neurotoxins in cells and intraperitoneal injection of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine in mice. Plasma samples of PD patients were also used. Western blot, real-time PCR, immunostaining, and/or luciferase reporter were employed. DNA methylation was analyzed by the bisulfite sequencing analysis. Protein expression of DNMT1, but not of DNMT3A and DNMT3B, was reduced in the cellular and mouse models of PD. Paradoxically, mRNA levels of DNMT1 were increased in these models. After ruling out the possibility of protein degradation, we screened a set of miRNAs that potentially targeted DNMT1 3'-UTR by luciferase reporters and expression abundancies. miR-17 was identified for further investigation with miR-19a of low expression as a parallel comparison. Although exogenous transfection of either miR-17 or miR-19a mimics could inhibit DNMT1 expression, results of miRNA inhibitors showed that miR-17, but not miR-19a, endogenously regulated DNMT1 and the subsequent DNA methylation. Furthermore, levels of miR-17 were elevated in the neurotoxin-induced PD models and the plasma of PD patients. This study demonstrates that the miR-17-mediated DNMT1 downregulation underlies the aberrant DNA methylation in PD. Our results provide a link bridging environmental insults and epigenetic changes and implicate miR-17 in therapeutical modulation of DNA methylation in PD.
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Affiliation(s)
- Hong-Qiu Zhang
- Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- Department of Geriatrics and Neurology, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Jian-Yong Wang
- Department of Geriatrics and Neurology, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Zhao-Feng Li
- Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Lei Cui
- Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Shi-Shi Huang
- Department of Geriatrics and Neurology, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Lan-Bing Zhu
- Department of Geriatrics and Neurology, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Yue Sun
- Department of Geriatrics and Neurology, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Rui Yang
- Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- Nelson Institute of Environmental Medicine, New York University School of Medicine, 341 East 25th Street, New York, NY, 10010, USA
| | - Hui-Hui Fan
- Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Xiong Zhang
- Department of Geriatrics and Neurology, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China.
| | - Jian-Hong Zhu
- Department of Preventive Medicine, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Department of Geriatrics and Neurology, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China.
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36
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Epigenetic Modulation of Microglia Function and Phenotypes in Neurodegenerative Diseases. Neural Plast 2021; 2021:9912686. [PMID: 34194489 PMCID: PMC8181095 DOI: 10.1155/2021/9912686] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/14/2021] [Indexed: 12/14/2022] Open
Abstract
Microglia-mediated neuroinflammation is one of the most remarkable hallmarks of neurodegenerative diseases (NDDs), including AD, PD, and ALS. Accumulating evidence indicates that microglia play both neuroprotective and detrimental roles in the onset and progression of NDDs. Yet, the specific mechanisms of action surrounding microglia are not clear. Modulation of microglia function and phenotypes appears to be a potential strategy to reverse NDDs. Until recently, research into the epigenetic mechanisms of diseases has been gradually developed, making it possible to elucidate the molecular mechanisms underlying the epigenetic regulation of microglia in NDDs. This review highlights the function and phenotypes of microglia, elucidates the relationship between microglia, epigenetic modifications, and NDDs, as well as the possible mechanisms underlying the epigenetic modulation of microglia in NDDs with a focus on potential intervention strategies.
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37
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Rasheed M, Liang J, Wang C, Deng Y, Chen Z. Epigenetic Regulation of Neuroinflammation in Parkinson's Disease. Int J Mol Sci 2021; 22:4956. [PMID: 34066949 PMCID: PMC8125491 DOI: 10.3390/ijms22094956] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/27/2021] [Accepted: 04/29/2021] [Indexed: 02/08/2023] Open
Abstract
Neuroinflammation is one of the most significant factors involved in the initiation and progression of Parkinson's disease. PD is a neurodegenerative disorder with a motor disability linked with various complex and diversified risk factors. These factors trigger myriads of cellular and molecular processes, such as misfolding defective proteins, oxidative stress, mitochondrial dysfunction, and neurotoxic substances that induce selective neurodegeneration of dopamine neurons. This neuronal damage activates the neuronal immune system, including glial cells and inflammatory cytokines, to trigger neuroinflammation. The transition of acute to chronic neuroinflammation enhances the susceptibility of inflammation-induced dopaminergic neuron damage, forming a vicious cycle and prompting an individual to PD development. Epigenetic mechanisms recently have been at the forefront of the regulation of neuroinflammatory factors in PD, proposing a new dawn for breaking this vicious cycle. This review examined the core epigenetic mechanisms involved in the activation and phenotypic transformation of glial cells mediated neuroinflammation in PD. We found that epigenetic mechanisms do not work independently, despite being coordinated with each other to activate neuroinflammatory pathways. In this regard, we attempted to find the synergic correlation and contribution of these epigenetic modifications with various neuroinflammatory pathways to broaden the canvas of underlying pathological mechanisms involved in PD development. Moreover, this study highlighted the dual characteristics (neuroprotective/neurotoxic) of these epigenetic marks, which may counteract PD pathogenesis and make them potential candidates for devising future PD diagnosis and treatment.
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Affiliation(s)
| | | | | | | | - Zixuan Chen
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (M.R.); (J.L.); (C.W.); (Y.D.)
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38
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Li B, Zhao G, Zhou Q, Xie Y, Wang Z, Fang Z, Lu B, Qin L, Zhao Y, Zhang R, Jiang L, Pan H, He Y, Wang X, Luo T, Zhang Y, Wang Y, Chen Q, Liu Z, Guo J, Tang B, Li J. Gene4PD: A Comprehensive Genetic Database of Parkinson's Disease. Front Neurosci 2021; 15:679568. [PMID: 33981200 PMCID: PMC8107430 DOI: 10.3389/fnins.2021.679568] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 04/07/2021] [Indexed: 01/02/2023] Open
Abstract
Parkinson’s disease (PD) is a complex neurodegenerative disorder with a strong genetic component. A growing number of variants and genes have been reported to be associated with PD; however, there is no database that integrate different type of genetic data, and support analyzing of PD-associated genes (PAGs). By systematic review and curation of multiple lines of public studies, we integrate multiple layers of genetic data (rare variants and copy-number variants identified from patients with PD, associated variants identified from genome-wide association studies, differentially expressed genes, and differential DNA methylation genes) and age at onset in PD. We integrated five layers of genetic data (8302 terms) with different levels of evidences from more than 3,000 studies and prioritized 124 PAGs with strong or suggestive evidences. These PAGs were identified to be significantly interacted with each other and formed an interconnected functional network enriched in several functional pathways involved in PD, suggesting these genes may contribute to the pathogenesis of PD. Furthermore, we identified 10 genes were associated with a juvenile-onset (age ≤ 30 years), 11 genes were associated with an early-onset (age of 30–50 years), whereas another 10 genes were associated with a late-onset (age > 50 years). Notably, the AAOs of patients with loss of function variants in five genes were significantly lower than that of patients with deleterious missense variants, while patients with VPS13C (P = 0.01) was opposite. Finally, we developed an online database named Gene4PD (http://genemed.tech/gene4pd) which integrated published genetic data in PD, the PAGs, and 63 popular genomic data sources, as well as an online pipeline for prioritize risk variants in PD. In conclusion, Gene4PD provides researchers and clinicians comprehensive genetic knowledge and analytic platform for PD, and would also improve the understanding of pathogenesis in PD.
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Affiliation(s)
- Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Mobile Health Ministry of Education-China Mobile Joint Laboratory, Xiangya Hospital, Central South University, Changsha, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qiao Zhou
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Yali Xie
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Zhenghuan Fang
- Center for Medical Genetics, Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Bin Lu
- Department of Pathogen Biology, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Lixia Qin
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuwen Zhao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Rui Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Li Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongxu Pan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yan He
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaomeng Wang
- Center for Medical Genetics, Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Tengfei Luo
- Center for Medical Genetics, Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Yi Zhang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Yijing Wang
- Center for Medical Genetics, Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
| | - Qian Chen
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Zhenhua Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Beisha Tang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics, Hunan Key Laboratory, School of Life Sciences, Central South University, Changsha, China
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39
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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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40
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Tafani X, Pascale E, Fattapposta F, Pucci M, D'Addario C, Adriani W. Cross-correlations between motifs in the 5'-UTR of DAT1 gene: Findings from Parkinson's disease. Adv Biol Regul 2020; 78:100753. [PMID: 33022465 DOI: 10.1016/j.jbior.2020.100753] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/28/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
Parkinson's disease (PD) is a neuro-degenerative disorder affecting the striatal motor system, caused by the loss of neuronal cells in the mid-brain, where reduced amounts of dopamine do cause involuntary movements and others symptoms. Alterations of methylome have been reported in PD epigenomic studies, and also human dopamine transporter gene (DAT1, SLC6A3) is considered as a candidate risk factor for PD. Since the DNA methylation on DAT promoter may well have a role in the development of this disease, we aimed to further assess the epigenetic control, by focusing on specific CpG sites located in the 5'-untranslated region (5'-UTR) of the DAT1 gene. Significant changes in DAT 5'-UTR methylation were already found in peripheral blood mononuclear cells (PBMCs) of PD subjects (Rubino et al., 2020). Of note, methylation values at the CpG 5 were increased. We run on same data a novel statistical approach: cross-correlation between pairs of loci. CpG 5 was the only always-differing variable but, alternatively, CpGs 2 and 6 or CpGs 1 and 3 were also significantly correlated with CpG 5. Interestingly, this picture emerged for those patients whose M2xM6 index was above-median; loci were rather independent for below-median patients. Present data may shed light into dynamics occurring at 5'-UTR of DAT1, a gene involved in PD but also in many psycho-physiological pathologies.
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Affiliation(s)
- Xhensina Tafani
- Faculty of Psychology - UTIU Università Telematica Internazionale "Uninettuno", Rome, Italy
| | - Esterina Pascale
- Department of Medical-Surgical Sciences and Biotechnologies, Sapienza University, Rome, Italy
| | | | - Mariangela Pucci
- Faculty of Bioscience & Technology for Food, for Agriculture and for Environment - University of Teramo, Teramo, Italy
| | - Claudio D'Addario
- Faculty of Bioscience & Technology for Food, for Agriculture and for Environment - University of Teramo, Teramo, Italy
| | - Walter Adriani
- Faculty of Psychology - UTIU Università Telematica Internazionale "Uninettuno", Rome, Italy; Reference Center for Behavioral Science and Mental Health - Istituto Superiore di Sanità, Rome, Italy.
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41
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Zhan Y, Guo Z, Zheng F, Zhang Z, Li K, Wang Q, Wang L, Cai Z, Chen N, Wu S, Li H. Reactive oxygen species regulate miR-17-5p expression via DNA methylation in paraquat-induced nerve cell damage. ENVIRONMENTAL TOXICOLOGY 2020; 35:1364-1373. [PMID: 32691990 DOI: 10.1002/tox.23001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 06/04/2020] [Accepted: 06/28/2020] [Indexed: 06/11/2023]
Abstract
There is emerging evidence suggesting that oxidative stress and DNA methylation can alter miRNA expression. However, little is known on the mechanism of miR-17-5p expression changes in paraquat (PQ)-induced nerve cell damage. In the present study, neuro-2a cells were pretreated with antioxidant N-acetylcysteine (NAC) or DNA methylation inhibitor decitabine (DAC), then exposed to different concentrations of PQ, while the expression levels of miR-17-5p were detected by qRT-PCR. Here, it is showed that PQ downregulated the expression of miR-17-5p dose-dependently in neuro-2a cells. The DNA methylation level was upregulated after PQ exposure, while downregulated with the pretreatment of NAC in the above content, detected by 5-mC immunofluorescence technique. The interaction effect of NAC and PQ in alternating DNA methylation level was further confirmed by flow cytometry. NAC and DAC individually had an interaction effect in PQ-induced nerve cell damage. After using NAC, PQ-induced ROS elevation and DNA methylation are reduced, thereby preventing the proapoptotic effect of miR-17-5p. Above all, PQ can induce DNA methylation variations through ROS production, leading to the downregulation of miR-17-5p expression in PQ-induced nerve cell damage.
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Affiliation(s)
- Yanting Zhan
- Department of Health Management, Fujian Health College, Fuzhou, China
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Zhenkun Guo
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
- Key Laboratory of Environment and Health, Universities and Colleges in Fujian, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Fuli Zheng
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
- Key Laboratory of Environment and Health, Universities and Colleges in Fujian, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Zhipeng Zhang
- Fujian Provincial Center for Adverse Drug Reaction Monitoring, Fujian Provincial Food and Drug Administration, Fuzhou, China
| | - Ke Li
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Qingqing Wang
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Lijin Wang
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Zhipeng Cai
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Nengzhou Chen
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Siying Wu
- Key Laboratory of Environment and Health, Universities and Colleges in Fujian, School of Public Health, Fujian Medical University, Fuzhou, China
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Huangyuan Li
- Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fuzhou, China
- Key Laboratory of Environment and Health, Universities and Colleges in Fujian, School of Public Health, Fujian Medical University, Fuzhou, China
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42
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Wang C, Chen L, Zhang M, Yang Y, Wong G. PDmethDB: A curated Parkinson's disease associated methylation information database. Comput Struct Biotechnol J 2020; 18:3745-3749. [PMID: 33304468 PMCID: PMC7714663 DOI: 10.1016/j.csbj.2020.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 11/10/2020] [Accepted: 11/10/2020] [Indexed: 01/12/2023] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease, of which the histopathological hallmark is the formation of Lewy bodies consisting of α-synuclein as the major component. α-Synuclein can sequester DNA Methyltransferase 1 (DNMT1), the maintenance DNA methylation enzyme, from the nucleus and into the cytoplasm, leading to global DNA hypomethylation in human brain. As DNA methylation is a major epigenetic modification that regulates gene expression and there is no specific database storing PD associated methylation information, PDmethDB (Parkinson's Disease Methylation Database) aims to curate PD associated methylation information from literature to facilitate the study of the relationship between PD and methylation. Currently, PDmethDB contains 97,077 PD methylation associated entries among 12,308 molecules, 37,944 CpG sites, 31 tissues and 3 species through a review of about 1600 published papers. This includes information concerning the gene/molecule name, CpG site, methylation alteration, expression alteration, tissue, PMID, experimental method, and a brief description about the entry. PDmethDB provides a user-friendly interface to search, browse, download and submit data. PDmethDB supports browsing by molecule, species, tissue, gene region, methylation alteration and experimental methods. PDmethDB also shows the entry gene interaction network including protein-protein interactions and miRNA-targets interactions with a highlight of PD associated genes from DisGeNET database. PDmethDB aims to facilitate the understanding of the relationship between PD and methylation. Database URL: https://ageing.shinyapps.io/pdmethdb/.
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Affiliation(s)
- Changliang Wang
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau S.A.R., China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Liang Chen
- Department of Computer Science, College of Engineering, Shantou University, Shantou, China
- Key Laboratory of Intelligent Manufacturing Technology of Ministry of Education, Shantou University, Shantou, China
| | - Menglei Zhang
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau S.A.R., China
| | - Yang Yang
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau S.A.R., China
| | - Garry Wong
- Cancer Centre, Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau S.A.R., China
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43
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Yan Y, Yan Q, Qian L, Jiang Y, Chen X, Zeng S, Xu Z, Gong Z. S-adenosylmethionine administration inhibits levodopa-induced vascular endothelial growth factor-A expression. Aging (Albany NY) 2020; 12:21290-21307. [PMID: 33170152 PMCID: PMC7695432 DOI: 10.18632/aging.103863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/17/2020] [Indexed: 02/06/2023]
Abstract
Background: Studies have demonstrated that S-adenosylmethionine could effectively affect the clinical wearing-off phenomena of levodopa, an antiparkinsonian agent; however, the detailed mechanisms for this effect need to be further clarified. Results: S-adenosylmethionine and levodopa had opposite effects on the protein stability of vascular endothelial growth factor-A. The analysis of tube formation and cell viability also showed the nonconforming functions of S-adenosylmethionine and levodopa on cell angiogenesis and proliferation. Meanwhile, S-adenosylmethionine could significantly abolish the increased angiogenesis and cell viability induced by levodopa. S-adenosylmethionine resulted in G1/S phase arrest, with decreased cyclin dependent kinase 4/6 and increased p16, a specific cyclin dependent kinase inhibitor. Mechanically, the different effects of levodopa and S-adenosylmethionine were dependent on the phosphorylation and activation of extracellular signal-regulated kinase. S-adenosylmethionine could be fitted into the predicted docking pocket in the crystal structure of vascular endothelial growth factor-A, enhancing its acetylation level and reducing half-life. Conclusions: These observations suggested that methyl donor S-adenosylmethionine could act as a potential agent against vascular endothelial growth factor-A-related diseases induced by levodopa treatment. Methods: We performed in vitro cytological analyses to assess whether S-adenosylmethionine intake could influence levodopa-induced vascular endothelial growth factor-A expression in human umbilical vein endothelial cells.
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Affiliation(s)
- Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Hunan, China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, China
| | - Qijia Yan
- Department of Pathology, Xiangya Hospital, Central South University, Hunan, China
| | - Long Qian
- Department of Pharmacy, Xiangya Hospital, Central South University, Hunan, China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, China
| | - Yueping Jiang
- Department of Pharmacy, Xiangya Hospital, Central South University, Hunan, China
| | - Xi Chen
- Department of Pharmacy, Xiangya Hospital, Central South University, Hunan, China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, China
| | - Shuangshuang Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Hunan, China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Hunan, China
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South University, Hunan, China.,Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Hunan, China
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44
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LC-MS/MS Determination of Modified Nucleosides in The Urine of Parkinson's Disease and Parkinsonian Syndromes Patients. Molecules 2020; 25:molecules25214959. [PMID: 33120888 PMCID: PMC7663364 DOI: 10.3390/molecules25214959] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 12/20/2022] Open
Abstract
Epigenetic modifications play a key role in gene regulation and expression and are involved in numerous cellular processes. Due to the limited research on nucleosides in Parkinson's disease (PD), it is very important to consider epigenetic factors and their role in the development of PD. The aim of this study was to investigate and compare the levels of modified nucleosides, such as O-methylguanosine, N6-methyl-2'-deoxyadenosine, 1-methyladenosine, 1-methylguanine, 7-methylguanine, 3-methyladenine and 7-methylguanosine in the urine of Parkinson's disease (PD) patients and the control group, and to verify that the results obtained differ in a subgroup of patients with parkinsonian syndromes. The study group comprised 18 patients with diagnosed idiopathic Parkinson's disease and four parkinsonian syndromes. The control group consisted of 30 age- and sex-matched neurological patients without confirmation by neuroimaging brain damage and extrapyramidal symptoms. The levels of nucleosides were determined by validated liquid chromatography coupled with the mass spectrometry (LC-MS/MS) method using the multiple reaction monitoring (MRM) mode. Lower levels of O-methylguanosine, 3-methyladenine, 1-methylguanine, N6-methyl-2'-deoxyadenosine and a higher level of 7-methylguanine in the urine of 22 PD patients were observed. Moreover, elevated levels of 1-methyladenosine, 7-methylguanine, and O-methylguanosine were observed in the parkinsonian syndrome subgroup. These preliminary results may indicate that modified nucleosides describe metabolic disturbances in the metabolism of purine, which was the most severely affected pathway that mediated the detrimental effects of neuroinflammation on PD.
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45
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Rubino A, D'Addario C, Di Bartolomeo M, Michele Salamone E, Locuratolo N, Fattapposta F, Vanacore N, Pascale E. DNA methylation of the 5'-UTR DAT 1 gene in Parkinson's disease patients. Acta Neurol Scand 2020; 142:275-280. [PMID: 32415851 DOI: 10.1111/ane.13279] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/30/2020] [Accepted: 05/11/2020] [Indexed: 12/27/2022]
Abstract
OBJECTIVES The involvement of epigenetics mechanisms in the transcriptional regulation of key genes has been investigated in the initiation and progression of neurodegenerative disorders, including Parkinson's disease (PD). Among others, we, here, focused the attention on the dopamine transporter (DAT) gene playing a critical role in maintaining the integrity of dopaminergic neurons. MATERIALS AND METHODS We performed bisulfite pyrosequencing to examine DNA methylation levels of six CpG sites in the 5'-UTR of DAT1 gene in human peripheral blood mononuclear cells (PBMCs) obtained from 101 sporadic PD patients and 59 healthy controls. RESULTS We selectively report for CpG5 an increase in DNA methylation levels in PD subjects respect to controls, that almost reaches statistical significance (30.06 ± 12.4 vs 26.58 ± 7.6, P = .052). Of interest, a significantly higher methylation at specific CpG sites (ANOVA: P = .029) was observed in PD subjects with advanced stage of illness. Namely, a multivariate regression analysis showed that a higher methylation level at specific CpG sites in the group of PD patients was associated with increased methylation at CpG2, CpG3, and with H&Y stage but not with age and gender. This regression model explains the 38% of the variance of methylation at CpG5. CONCLUSION Our results do seem to suggest that the methylation level of CpG5 is different between PD patients and controls. Moreover, this methylation level for CpG5 may be associated also with the stage of disease.
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Affiliation(s)
- Alfonso Rubino
- Department of Human NeurosciencesSapienza University Rome Italy
| | - Claudio D'Addario
- Faculty of Bioscience and Technology for Food, Agriculture and EnvironmentUniversity of Teramo Teramo Italy
- Department of Clinical NeuroscienceKarolinska Institute Stockholm Stockholm Sweden
| | - Martina Di Bartolomeo
- Faculty of Bioscience and Technology for Food, Agriculture and EnvironmentUniversity of Teramo Teramo Italy
| | | | | | | | - Nicola Vanacore
- National Centre for Disease Prevention and Health PromotionNational Institute of Health Rome Italy
| | - Esterina Pascale
- Department of Medical‐Surgical Sciences and BiotechnologiesSapienza University Rome Italy
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46
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Epigenetics in Lewy Body Diseases: Impact on Gene Expression, Utility as a Biomarker, and Possibilities for Therapy. Int J Mol Sci 2020; 21:ijms21134718. [PMID: 32630630 PMCID: PMC7369933 DOI: 10.3390/ijms21134718] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 02/07/2023] Open
Abstract
Lewy body disorders (LBD) include Parkinson's disease (PD) and dementia with Lewy bodies (DLB). They are synucleinopathies with a heterogeneous clinical manifestation. As a cause of neuropathological overlap with other neurodegenerative diseases, the establishment of a correct clinical diagnosis is still challenging, and clinical management may be difficult. The combination of genetic variation and epigenetic changes comprising gene expression-modulating DNA methylation and histone alterations modifies the phenotype, disease course, and susceptibility to disease. In this review, we summarize the results achieved in the deciphering of the LBD epigenome. To provide an appropriate context, first LBD genetics is briefly outlined. Afterwards, a detailed review of epigenetic modifications identified for LBD in human cells, postmortem, and peripheral tissues is provided. We also focus on the difficulty of identifying epigenome-related biomarker candidates and discuss the results obtained so far. Additionally, epigenetic changes as therapeutic targets, as well as different epigenome-based treatments, are revised. The number of studies focusing on PD is relatively limited and practically inexistent for DLB. There is a lack of replication studies, and some results are even contradictory, probably due to differences in sample collection and analytical techniques. In summary, we show the current achievements and directions for future research.
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47
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Phanus-Umporn C, Prachayasittikul V, Nantasenamat C, Prachayasittikul S, Prachayasittikul V. QSAR-driven rational design of novel DNA methyltransferase 1 inhibitors. EXCLI JOURNAL 2020; 19:458-475. [PMID: 32398970 PMCID: PMC7214779 DOI: 10.17179/excli2020-1096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/24/2020] [Indexed: 01/30/2023]
Abstract
DNA methylation, an epigenetic modification, is mediated by DNA methyltransferases (DNMTs), a family of enzymes. Inhibitions of these enzymes are considered a promising strategy for the treatment of several diseases. In this study, a quantitative structure-activity relationship (QSAR) modeling was employed to understand the structure-activity relationship (SAR) of currently available non-nucleoside DNMT1 inhibitors (i.e., indole and oxazoline/1,2-oxazole scaffolds). Two QSAR models were successfully constructed using multiple linear regression (MLR) and provided good predictive performance (R2Tr = 0.850-0.988 and R2CV = 0.672-0.869). Bond information content index (BIC1) and electronegativity (R6e+) are the most influential descriptors governing the activity of compounds. The constructed QSAR models were further applied for guiding a rational design of novel inhibitors. A novel set of 153 structurally modified compounds were designed in silico according to the important descriptors deduced from the QSAR finding, and their DNMT1 inhibitory activities were predicted. This result demonstrated that 86 newly designed inhibitors were predicted to elicit enhanced DNMT1 inhibitory activity when compared to their parent compounds. Finally, a set of promising compounds as potent DNMT1 inhibitors were highlighted to be further developed. The key SAR findings may also be beneficial for structural optimization to improve properties of the known inhibitors.
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Affiliation(s)
- Chuleeporn Phanus-Umporn
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Veda Prachayasittikul
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Chanin Nantasenamat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Supaluk Prachayasittikul
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Virapong Prachayasittikul
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
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48
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Thompson C, Otero P, Srinageshwar B, Petersen RB, Dunbar GL, Rossignol J. Possible roles of epigenetics in stem cell therapy for Parkinson's disease. Epigenomics 2020; 12:647-656. [PMID: 32396465 DOI: 10.2217/epi-2019-0347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disease with loss of dopaminergic neurons. PD has genetic and epigenetic influences that determine specific changes in the brain. Epigenetic changes result in defective methylation of genes leading to differential gene-expression causing PD. This review provides an overview of stem cell transplantations as potential therapies for PD, with a focus on the epigenetic changes, prior or following transplantation. To date, no reports have addressed epigenetic alterations following stem cell transplantation into the PD brain. Given the potential for affecting the efficacy of stem cell therapy, increased attention needs to be given to the epigenetic processes that occur during stem cell culture and transplantation to maximize the therapeutic potential of stem cells to PD.
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Affiliation(s)
- Cassandra Thompson
- Field Neurosciences Institute laboratory for Restorative Neurology, Central Michigan University, Mt. Pleasant, MI 48859, USA.,Program in Neuroscience, Central Michigan University, Mt. Pleasant, MI 48859, USA
| | - Paulina Otero
- Field Neurosciences Institute laboratory for Restorative Neurology, Central Michigan University, Mt. Pleasant, MI 48859, USA.,Program in Neuroscience, Central Michigan University, Mt. Pleasant, MI 48859, USA
| | - Bhairavi Srinageshwar
- Field Neurosciences Institute laboratory for Restorative Neurology, Central Michigan University, Mt. Pleasant, MI 48859, USA.,Program in Neuroscience, Central Michigan University, Mt. Pleasant, MI 48859, USA.,College of Medicine, Central Michigan University, Mt. Pleasant, MI 48859, USA
| | - Robert B Petersen
- College of Medicine, Central Michigan University, Mt. Pleasant, MI 48859, USA
| | - Gary L Dunbar
- Field Neurosciences Institute laboratory for Restorative Neurology, Central Michigan University, Mt. Pleasant, MI 48859, USA.,Program in Neuroscience, Central Michigan University, Mt. Pleasant, MI 48859, USA.,College of Medicine, Central Michigan University, Mt. Pleasant, MI 48859, USA.,Department of Psychology, Central Michigan University, Mt. Pleasant, MI 48859, USA.,Field Neurosciences Institute, St. Mary's of Michigan, Saginaw, MI 48604, USA
| | - Julien Rossignol
- Field Neurosciences Institute laboratory for Restorative Neurology, Central Michigan University, Mt. Pleasant, MI 48859, USA.,Program in Neuroscience, Central Michigan University, Mt. Pleasant, MI 48859, USA.,College of Medicine, Central Michigan University, Mt. Pleasant, MI 48859, USA
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49
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Ohnmacht J, May P, Sinkkonen L, Krüger R. Missing heritability in Parkinson's disease: the emerging role of non-coding genetic variation. J Neural Transm (Vienna) 2020; 127:729-748. [PMID: 32248367 PMCID: PMC7242266 DOI: 10.1007/s00702-020-02184-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/24/2020] [Indexed: 02/01/2023]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder caused by a complex interplay of genetic and environmental factors. For the stratification of PD patients and the development of advanced clinical trials, including causative treatments, a better understanding of the underlying genetic architecture of PD is required. Despite substantial efforts, genome-wide association studies have not been able to explain most of the observed heritability. The majority of PD-associated genetic variants are located in non-coding regions of the genome. A systematic assessment of their functional role is hampered by our incomplete understanding of genotype-phenotype correlations, for example through differential regulation of gene expression. Here, the recent progress and remaining challenges for the elucidation of the role of non-coding genetic variants is reviewed with a focus on PD as a complex disease with multifactorial origins. The function of gene regulatory elements and the impact of non-coding variants on them, and the means to map these elements on a genome-wide level, will be delineated. Moreover, examples of how the integration of functional genomic annotations can serve to identify disease-associated pathways and to prioritize disease- and cell type-specific regulatory variants will be given. Finally, strategies for functional validation and considerations for suitable model systems are outlined. Together this emphasizes the contribution of rare and common genetic variants to the complex pathogenesis of PD and points to remaining challenges for the dissection of genetic complexity that may allow for better stratification, improved diagnostics and more targeted treatments for PD in the future.
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Affiliation(s)
- Jochen Ohnmacht
- LCSB, University of Luxembourg, Belvaux, Luxembourg
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Patrick May
- LCSB, University of Luxembourg, Belvaux, Luxembourg
| | - Lasse Sinkkonen
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Rejko Krüger
- LCSB, University of Luxembourg, Belvaux, Luxembourg.
- Luxembourg Institute of Health (LIH), Transversal Translational Medicine, Strassen, Luxembourg.
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg.
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50
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Iakovenko EV, Abramycheva NY, Fedotova EY, Illarioshkin SN. The SNCA-Rep1 Polymorphic Locus: Association with the Risk of Parkinson's Disease and SNCA Gene Methylation. Acta Naturae 2020; 12:105-110. [PMID: 32742734 PMCID: PMC7385090 DOI: 10.32607/actanaturae.10956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Neurodegeneration in Parkinson’s disease is characterized by the
accumulation of alpha-synuclein, a protein encoded by the SNCA
gene, in neurons. In addition to mutations, many polymorphisms have
been identified in this gene, and one of these is a dinucleotide
microsatellite: SNCA-Rep1. The mechanisms by
which specific configurations of SNCA-Rep1 may contribute to
the development of this disease have yet to be clarified. In our study, a
relationship between long SNCA-Rep1 alleles and
Parkinson’s was confirmed in the Russian population. Long allelic
variants of SNCA-Rep1 were shown to be associated with the
hypomethylation of the CpG-sites in intron 1 of the SNCA gene.
Long variants of SNCA-Rep1 are supposed to exert their effect
through the hypomethylation of a transcriptionally significant region of this
gene. Hypomethylation is usually associated with increased expression, which,
in turn, contributes to alpha-synuclein accumulation in neuronal cytoplasm,
with the latter being the main molecular marker of Parkinson’s disease.
Further studies are needed to establish a relationship between our finding and
SNCA gene expression.
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