1
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Isik FB, Knight HM, Rajkumar AP. Extracellular vesicle microRNA-mediated transcriptional regulation may contribute to dementia with Lewy bodies molecular pathology. Acta Neuropsychiatr 2024; 36:29-38. [PMID: 37339939 DOI: 10.1017/neu.2023.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
OBJECTIVE Dementia with Lewy bodies (DLB) is the second most common dementia. Advancing our limited understanding of its molecular pathogenesis is essential for identifying novel biomarkers and therapeutic targets for DLB. DLB is an α-synucleinopathy, and small extracellular vesicles (SEV) from people with DLB can transmit α-synuclein oligomerisation between cells. Post-mortem DLB brains and serum SEV from those with DLB share common miRNA signatures, and their functional implications are uncertain. Hence, we aimed to investigate potential targets of DLB-associated SEV miRNA and to analyse their functional implications. METHODS We identified potential targets of six previously reported differentially expressed miRNA genes in serum SEV of people with DLB (MIR26A1, MIR320C2, MIR320D2, MIR548BA, MIR556, and MIR4722) using miRBase and miRDB databases. We analysed functional implications of these targets using EnrichR gene set enrichment analysis and analysed their protein interactions using Reactome pathway analysis. RESULTS These SEV miRNA may regulate 4278 genes that were significantly enriched among the genes involved in neuronal development, cell-to-cell communication, vesicle-mediated transport, apoptosis, regulation of cell cycle, post-translational protein modifications, and autophagy lysosomal pathway, after Benjamini-Hochberg false discovery rate correction at 5%. The miRNA target genes and their protein interactions were significantly associated with several neuropsychiatric disorders and with multiple signal transduction, transcriptional regulation, and cytokine signalling pathways. CONCLUSION Our findings provide in-silico evidence that potential targets of DLB-associated SEV miRNAs may contribute to Lewy pathology by transcriptional regulation. Experimental validation of these dysfunctional pathways is warranted and could lead to novel therapeutic avenues for DLB.
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Affiliation(s)
- Fatma Busra Isik
- School of Life Science, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Helen Miranda Knight
- School of Life Science, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Anto P Rajkumar
- Institute of Mental Health, Mental Health and Clinical Neurosciences Academic Unit, University of Nottingham, Nottingham, UK
- Mental Health Services for Older People, Nottinghamshire Healthcare NHS Foundation Trust, Nottingham, UK
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2
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Armstrong MJ, Barnes LL. Under-Diagnosis of Dementia with Lewy Bodies in Individuals Racialized as Black: Hypotheses Regarding Potential Contributors. J Alzheimers Dis 2024; 97:1571-1580. [PMID: 38277299 PMCID: PMC10894581 DOI: 10.3233/jad-231177] [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: 12/07/2023] [Indexed: 01/28/2024]
Abstract
Dementia with Lewy bodies (DLB) is one of the most common degenerative dementias after Alzheimer's disease (AD) dementia. DLB is under-diagnosed across populations but may be particularly missed in older Black adults. The object of this review was to examine key features of DLB and potential associations with race in order to hypothesize why DLB may be under-diagnosed in Black adults in the U.S. In terms of dementia, symptoms associated with high rates of co-pathology (e.g., AD, vascular disease) in older Black adults may obscure the clinical picture that might suggest Lewy body pathology. Research also suggests that clinicians may be predisposed to give AD dementia diagnoses to Black adults, potentially missing contributions of Lewy body pathology. Hallucinations in Black adults may be misattributed to AD or primary psychiatric disease rather than Lewy body pathology. Research on the prevalence of REM sleep behavior in diverse populations is lacking, but REM sleep behavior disorder could be under-diagnosed in Black adults due to sleep patterns or reporting by caregivers who are not bed partners. Recognition of parkinsonism could be reduced in Black adults due to clinician biases, cultural effects on self-report, and potentially underlying differences in the frequency of parkinsonism. These considerations are superimposed on structural and systemic contributions to health (e.g., socioeconomic status, education, structural racism) and individual-level social exposures (e.g., social interactions, discrimination). Improving DLB recognition in Black adults will require research to investigate reasons for diagnostic disparities and education to increase identification of core symptoms in this population.
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Affiliation(s)
- Melissa J. Armstrong
- Department of Neurology, University of Florida College of Medicine, Gainesville, FL, USA
- 1Florida Alzheimer Disease Research Center, Gainesville, FL, USA
| | - Lisa L. Barnes
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
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3
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Zhang D, Zhang J, Wang Y, Wang G, Tang P, Liu Y, Zhang Y, Ouyang L. Targeting epigenetic modifications in Parkinson's disease therapy. Med Res Rev 2023; 43:1748-1777. [PMID: 37119043 DOI: 10.1002/med.21962] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 01/10/2023] [Accepted: 04/12/2023] [Indexed: 04/30/2023]
Abstract
Parkinson's disease (PD) is a multifactorial disease due to a complex interplay between genetic and epigenetic factors. Recent efforts shed new light on the epigenetic mechanisms involved in regulating pathways related to the development of PD, including DNA methylation, posttranslational modifications of histones, and the presence of microRNA (miRNA or miR). Epigenetic regulators are potential therapeutic targets for neurodegenerative disorders. In the review, we aim to summarize mechanisms of epigenetic regulation in PD, and describe how the DNA methyltransferases, histone deacetylases, and histone acetyltransferases that mediate the key processes of PD are attractive therapeutic targets. We discuss the use of inhibitors and/or activators of these regulators in PD models or patients, and how these small molecule epigenetic modulators elicit neuroprotective effects. Further more, given the importance of miRNAs in PD, their contributions to the underlying mechanisms of PD will be discussed as well, together with miRNA-based therapies.
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Affiliation(s)
- Dan Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Jifa Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Yuxi Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Guan Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Pan Tang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Yun Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Yiwen Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Liang Ouyang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
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4
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Rajan S, Tryphena KP, Khan S, Vora L, Srivastava S, Singh SB, Khatri DK. Understanding the involvement of innate immunity and the Nrf2-NLRP3 axis on mitochondrial health in Parkinson's disease. Ageing Res Rev 2023; 87:101915. [PMID: 36963313 DOI: 10.1016/j.arr.2023.101915] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/01/2023] [Accepted: 03/19/2023] [Indexed: 03/26/2023]
Abstract
Parkinson's disease (PD), a multifactorial movement disorder, is interlinked with numerous molecular pathways, including neuroinflammation, which is a critical factor in the development and progression of PD. Microglia play a central role in driving neuroinflammation through activation and overexpression of the M1 phenotype, which has a significant impact on mitochondria. Multiple regulators converge together, and among these, the NOD-like receptor family pyrin domain-containing 3 (NLRP3) inflammasomes have been implicated in transmitting inflammatory and deleterious components to the mitochondria. Nuclear factor erythroid 2-related factor 2 (Nrf2) regulates the NLRP3 inflammasome and acts as the saviour of the mitochondria. Together, the NLRP3-Nrf2 axis functions in regulating mitochondrial function in the case of PD. It regulates fundamental processes such as oxidative stress, mitochondrial respiratory function, and mitochondrial dynamics. In this review, we discuss the contributions that a variety of miRNAs make to the regulation of the NLRP3 inflammasome and Nrf2, which can be used to target this important axis and contribute to the preservation of mitochondrial integrity. This axis may prove to be a crucial target for extending the lives of Parkinson's patients by deferring neuroinflammatory damage to mitochondria.
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Affiliation(s)
- Shruti Rajan
- Molecular and Cellular Neuroscience Lab, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Telangana 500037, India
| | - Kamatham Pushpa Tryphena
- Molecular and Cellular Neuroscience Lab, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Telangana 500037, India
| | - Sabiya Khan
- Molecular and Cellular Neuroscience Lab, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Telangana 500037, India
| | - Lalitkumar Vora
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK.
| | - Saurabh Srivastava
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Telangana 500037, India.
| | - Shashi Bala Singh
- Molecular and Cellular Neuroscience Lab, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Telangana 500037, India
| | - Dharmendra Kumar Khatri
- Molecular and Cellular Neuroscience Lab, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Telangana 500037, India.
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5
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Xylaki M, Paiva I, Al-Azzani M, Gerhardt E, Jain G, Islam MR, Vasili E, Wassouf Z, Schulze-Hentrich JM, Fischer A, Outeiro TF. miR-101a-3p Impairs Synaptic Plasticity and Contributes to Synucleinopathy. JOURNAL OF PARKINSON'S DISEASE 2023; 13:179-196. [PMID: 36744345 PMCID: PMC10041420 DOI: 10.3233/jpd-225055] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Synucleinopathies are disorders characterized by the abnormal accumulation of α-synuclein (aSyn). Synaptic compromise is observed in synucleinopathies parallel to aSyn aggregation and is accompanied by transcript deregulation. OBJECTIVE We sought to identify microRNAs associated with synaptic processes that may contribute to synaptic dysfunction and degeneration in synucleinopathies. METHODS We performed small RNA-sequencing of midbrain from 6-month-old transgenic mice expressing A30P mutant aSyn, followed by comparative expression analysis. We then used real-time quantitative polymerase chain reaction (qPCR) for validation. Functional analysis was performed in primary neurons by biochemical assays and imaging. RESULTS We found several deregulated biological processes linked to the synapse. miR-101a-3p was validated as a synaptic miRNA upregulated in aSyn Tg mice and in the cortex of dementia with Lewy bodies patients. Mice and primary cultured neurons overexpressing miR-101a-3p showed downregulation of postsynaptic proteins GABA Ab2 and SAPAP3 and altered dendritic morphology resembling synaptic plasticity impairments and/or synaptic damage. Interestingly, primary cultured neuron exposure to recombinant wild-type aSyn species efficiently increased miR-101a-3p levels. Finally, a dynamic role of miR-101a-3p in synapse plasticity was shown by identifying downregulation of miR-101a-3p in a condition of enhanced synaptic plasticity modelled in Wt animals housed in enriched environment. CONCLUSION To conclude, we correlated pathologic aSyn with high levels of miR-101a-3p and a novel dynamic role of the miRNA in synaptic plasticity.
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Affiliation(s)
- Mary Xylaki
- Department of Experimental Neurodegeneration, Centre for Biostructural Imaging of Neurodegeneration, University Medical Centre Göttingen, Göttingen, Germany
| | - Isabel Paiva
- Department of Experimental Neurodegeneration, Centre for Biostructural Imaging of Neurodegeneration, University Medical Centre Göttingen, Göttingen, Germany
- Present address: Laboratory of Cognitive and Adaptive Neuroscience, UMR 7364 (CNRS/ Strasbourg University), Strasbourg, France
| | - Mohammed Al-Azzani
- Department of Experimental Neurodegeneration, Centre for Biostructural Imaging of Neurodegeneration, University Medical Centre Göttingen, Göttingen, Germany
| | - Ellen Gerhardt
- Department of Experimental Neurodegeneration, Centre for Biostructural Imaging of Neurodegeneration, University Medical Centre Göttingen, Göttingen, Germany
| | - Gaurav Jain
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Centre for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Md Rezaul Islam
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Centre for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Eftychia Vasili
- Department of Experimental Neurodegeneration, Centre for Biostructural Imaging of Neurodegeneration, University Medical Centre Göttingen, Göttingen, Germany
| | - Zinah Wassouf
- Department of Experimental Neurodegeneration, Centre for Biostructural Imaging of Neurodegeneration, University Medical Centre Göttingen, Göttingen, Germany
| | | | - André Fischer
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Centre for Neurodegenerative Diseases (DZNE), Göttingen, Germany
- Department of Psychiatry and Psychotherapy, University Medical Centre, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Tiago Fleming Outeiro
- Department of Experimental Neurodegeneration, Centre for Biostructural Imaging of Neurodegeneration, University Medical Centre Göttingen, Göttingen, Germany
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, UK
- Scientific employee with an honorary contract at German Centre for Neurodegenerative Diseases (DZNE), Göttingen, Germany
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6
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Shao X, Vishweswaraiah S, Čuperlović-Culf M, Yilmaz A, Greenwood CMT, Surendra A, McGuinness B, Passmore P, Kehoe PG, Maddens ME, Bennett SAL, Green BD, Radhakrishna U, Graham SF. Dementia with Lewy bodies post-mortem brains reveal differentially methylated CpG sites with biomarker potential. Commun Biol 2022; 5:1279. [PMID: 36418427 PMCID: PMC9684551 DOI: 10.1038/s42003-022-03965-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 09/08/2022] [Indexed: 11/25/2022] Open
Abstract
Dementia with Lewy bodies (DLB) is a common form of dementia with known genetic and environmental interactions. However, the underlying epigenetic mechanisms which reflect these gene-environment interactions are poorly studied. Herein, we measure genome-wide DNA methylation profiles of post-mortem brain tissue (Broadmann area 7) from 15 pathologically confirmed DLB brains and compare them with 16 cognitively normal controls using Illumina MethylationEPIC arrays. We identify 17 significantly differentially methylated CpGs (DMCs) and 17 differentially methylated regions (DMRs) between the groups. The DMCs are mainly located at the CpG islands, promoter and first exon regions. Genes associated with the DMCs are linked to "Parkinson's disease" and "metabolic pathway", as well as the diseases of "severe intellectual disability" and "mood disorders". Overall, our study highlights previously unreported DMCs offering insights into DLB pathogenesis with the possibility that some of these could be used as biomarkers of DLB in the future.
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Affiliation(s)
- Xiaojian Shao
- grid.24433.320000 0004 0449 7958National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Canada
| | - Sangeetha Vishweswaraiah
- grid.261277.70000 0001 2219 916XOakland University-William Beaumont School of Medicine, Rochester, MI 48309 USA
| | - Miroslava Čuperlović-Culf
- grid.24433.320000 0004 0449 7958National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Canada ,grid.28046.380000 0001 2182 2255Ottawa Institute of Systems Biology, Ottawa, Ontario Canada ,grid.28046.380000 0001 2182 2255Department of Biochemistry, Microbiology, sand Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario Canada
| | - Ali Yilmaz
- grid.261277.70000 0001 2219 916XOakland University-William Beaumont School of Medicine, Rochester, MI 48309 USA ,Beaumont Research Institute, Royal Oak, MI 48073 USA
| | - Celia M. T. Greenwood
- grid.414980.00000 0000 9401 2774Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Canada ,grid.14709.3b0000 0004 1936 8649Gerald Bronfman Department of Oncology, McGill University, Montréal, Canada
| | - Anuradha Surendra
- grid.24433.320000 0004 0449 7958National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Canada
| | - Bernadette McGuinness
- grid.4777.30000 0004 0374 7521Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK
| | - Peter Passmore
- grid.4777.30000 0004 0374 7521Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK
| | - Patrick G. Kehoe
- grid.5337.20000 0004 1936 7603Dementia Research Group, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Michael E. Maddens
- grid.261277.70000 0001 2219 916XOakland University-William Beaumont School of Medicine, Rochester, MI 48309 USA ,Beaumont Research Institute, Royal Oak, MI 48073 USA
| | - Steffany A. L. Bennett
- grid.28046.380000 0001 2182 2255Ottawa Institute of Systems Biology, Ottawa, Ontario Canada ,grid.28046.380000 0001 2182 2255Department of Biochemistry, Microbiology, sand Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario Canada
| | - Brian D. Green
- grid.4777.30000 0004 0374 7521Institute for Global Food Security, School of Biological Sciences, Faculty of Medicine, Health and Life Sciences, Queen’s University Belfast, Northern Ireland, UK
| | - Uppala Radhakrishna
- grid.261277.70000 0001 2219 916XOakland University-William Beaumont School of Medicine, Rochester, MI 48309 USA ,Beaumont Research Institute, Royal Oak, MI 48073 USA
| | - Stewart F. Graham
- grid.261277.70000 0001 2219 916XOakland University-William Beaumont School of Medicine, Rochester, MI 48309 USA ,Beaumont Research Institute, Royal Oak, MI 48073 USA
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7
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Azari A, Goodarzi A, Jafarkhani B, Eghbali M, Karimi Z, Hosseini Balef SS, Irannejad H. Novel molecular targets and mechanisms for neuroprotective modulation in neurodegenerative disorders. Cent Nerv Syst Agents Med Chem 2022; 22:88-107. [PMID: 35713146 DOI: 10.2174/1871524922666220616092132] [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: 03/02/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Neuronal death underlies the symptoms of several human neurological disorders, including Alzheimer's, Parkinson's and Huntington's diseases, and amyotrophic lateral sclerosis that their precise pathophysiology have not yet been elucidated. According to various studies the prohibition is the best therapy with neuroprotective approaches which are advanced and safe methods. METHODS This review summarizes some of the already-known and newly emerged neuroprotective targets and strategies that their experimental effects have been reported. Accordingly, literature was studied from 2000 to 2021 and appropriate articles were searched in Google Scholar and Scopus with the keywords given in the Keywords section of the current review. RESULTS Lewy bodies are the histopathologic characteristics of neurodegenerative disorders and are protein-rich intracellular deposits in which Alpha-Synuclein is its major protein. Alpha-Synuclein's toxic potential provides a compelling rationale for therapeutic strategies aimed at decreasing its burden in neuronal cells through numerous pathways including ubiquitin-proteasome system and autophagy-lysosome Pathway, proteolytic breakdown via cathepsin D, kallikrein-6 (neurosin), calpain-1 or MMP9, heat shock proteins, and proteolysis targeting chimera which consists of a target protein ligand and an E3 ubiquitin ligase (E3) followed by target protein ubiquitination (PROTACs). Other targets that have been noticed recently are the mutant huntingtin, tau proteins and glycogen synthase kinase 3β that their accumulation proceeds extensive neuronal damage and up to the minute approach such as Proteolysis Targeting Chimera promotes its degradation in cells. As various studies demonstrated that Mendelian gene mutations can result into the neurodegenerative diseases, additional target that has gained much interest is epigenetics such as mutation, phosphodiesterase, RNA binding proteins and Nuclear respiratory factor 1. CONCLUSION The novel molecular targets and new strategies compiled and introduced here can be used by scientists to design and discover more efficient small molecule drugs against the neurodegenerative diseases. And also the genes in which their mutations can lead to the α-synuclein aggregation or accumulation are discussed and considered a valuable information of epigenetics in dementia.
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Affiliation(s)
- Aala Azari
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Amin Goodarzi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Behrouz Jafarkhani
- Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohammad Eghbali
- Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Zohreh Karimi
- Department of Obstetrics & Gynecology, Imam Khomeini hospital, Mazandaran University of Medical Sciences, Sari, Iran
| | - Seyed Sajad Hosseini Balef
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Hamid Irannejad
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
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8
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Sarkar S, Feany MB. Precision Medicine on the Fly: Using Drosophila to Decipher Gene-Environment Interactions in Parkinson's Disease. Toxicol Sci 2021; 182:159-167. [PMID: 34076689 DOI: 10.1093/toxsci/kfab060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Big data approaches have profoundly influenced state-of-the-art in many fields of research, with toxicology being no exception. Here, we use Parkinson's disease as a window through which to explore the challenges of a dual explosion of metabolomic data addressing the myriad environmental exposures individuals experience and genetic analyses implicating many different loci as risk factors for disease. We argue that new experimental approaches are needed to convert the growing body of omics data into molecular mechanisms of disease that can be therapeutically targeted in specific patients. We outline one attractive strategy, which capitalizes on the rapid generation time and advanced molecular tools available in the fruit fly, Drosophila, to provide a platform for mechanistic dissection and drug discovery.
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Affiliation(s)
- Souvarish Sarkar
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mel B Feany
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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9
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Murthy M, Cheng YY, Holton JL, Bettencourt C. Neurodegenerative movement disorders: An epigenetics perspective and promise for the future. Neuropathol Appl Neurobiol 2021; 47:897-909. [PMID: 34318515 PMCID: PMC9291277 DOI: 10.1111/nan.12757] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/12/2021] [Indexed: 02/02/2023]
Abstract
Neurodegenerative movement disorders (NMDs) are age‐dependent disorders that are characterised by the degeneration and loss of neurons, typically accompanied by pathological accumulation of different protein aggregates in the brain, which lead to motor symptoms. NMDs include Parkinson's disease, multiple system atrophy, progressive supranuclear palsy, and Huntington's disease, among others. Epigenetic modifications are responsible for functional gene regulation during development, adult life and ageing and have progressively been implicated in complex diseases such as cancer and more recently in neurodegenerative diseases, such as NMDs. DNA methylation is by far the most widely studied epigenetic modification and consists of the reversible addition of a methyl group to the DNA without changing the DNA sequence. Although this research field is still in its infancy in relation to NMDs, an increasing number of studies point towards a role for DNA methylation in disease processes. This review addresses recent advances in epigenetic and epigenomic research in NMDs, with a focus on human brain DNA methylation studies. We discuss the current understanding of the DNA methylation changes underlying these disorders, the potential for use of these DNA modifications in peripheral tissues as biomarkers in early disease detection, classification and progression as well as a promising role in future disease management and therapy.
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Affiliation(s)
- Megha Murthy
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.,Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Yun Yung Cheng
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Janice L Holton
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.,Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Conceição Bettencourt
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.,Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
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10
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Kee TR, Espinoza Gonzalez P, Wehinger JL, Bukhari MZ, Ermekbaeva A, Sista A, Kotsiviras P, Liu T, Kang DE, Woo JAA. Mitochondrial CHCHD2: Disease-Associated Mutations, Physiological Functions, and Current Animal Models. Front Aging Neurosci 2021; 13:660843. [PMID: 33967741 PMCID: PMC8100248 DOI: 10.3389/fnagi.2021.660843] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/31/2021] [Indexed: 12/19/2022] Open
Abstract
Rare mutations in the mitochondrial protein coiled-coil-helix-coiled-coil-helix domain containing 2 (CHCHD2) are associated with Parkinson's disease (PD) and other Lewy body disorders. CHCHD2 is a bi-organellar mediator of oxidative phosphorylation, playing crucial roles in regulating electron flow in the mitochondrial electron transport chain and acting as a nuclear transcription factor for a cytochrome c oxidase subunit (COX4I2) and itself in response to hypoxic stress. CHCHD2 also regulates cell migration and differentiation, mitochondrial cristae structure, and apoptosis. In this review, we summarize the known disease-associated mutations of CHCHD2 in Asian and Caucasian populations, the physiological functions of CHCHD2, how CHCHD2 mutations contribute to α-synuclein pathology, and current animal models of CHCHD2. Further, we discuss the necessity of continued investigation into the divergent functions of CHCHD2 and CHCHD10 to determine how mutations in these similar mitochondrial proteins contribute to different neurodegenerative diseases.
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Affiliation(s)
- Teresa R Kee
- USF Health Byrd Alzheimer's Center and Research Institute, Tampa, FL, United States.,Department of Molecular Pharmacology and Physiology, USF Health Morsani College of Medicine, Tampa, FL, United States
| | | | - Jessica L Wehinger
- USF Health Byrd Alzheimer's Center and Research Institute, Tampa, FL, United States
| | - Mohammed Zaheen Bukhari
- USF Health Byrd Alzheimer's Center and Research Institute, Tampa, FL, United States.,Department of Molecular Medicine, USF Health Morsani College of Medicine, Tampa, FL, United States
| | - Aizara Ermekbaeva
- USF Health Byrd Alzheimer's Center and Research Institute, Tampa, FL, United States
| | - Apoorva Sista
- USF Health Byrd Alzheimer's Center and Research Institute, Tampa, FL, United States
| | - Peter Kotsiviras
- USF Health Byrd Alzheimer's Center and Research Institute, Tampa, FL, United States
| | - Tian Liu
- USF Health Byrd Alzheimer's Center and Research Institute, Tampa, FL, United States.,Department of Molecular Medicine, USF Health Morsani College of Medicine, Tampa, FL, United States
| | - David E Kang
- USF Health Byrd Alzheimer's Center and Research Institute, Tampa, FL, United States.,Department of Molecular Medicine, USF Health Morsani College of Medicine, Tampa, FL, United States.,James A. Haley Veterans Administration Hospital, Tampa, FL, United States
| | - Jung-A A Woo
- USF Health Byrd Alzheimer's Center and Research Institute, Tampa, FL, United States.,Department of Molecular Pharmacology and Physiology, USF Health Morsani College of Medicine, Tampa, FL, United States
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Phytochemicals as Regulators of Genes Involved in Synucleinopathies. Biomolecules 2021; 11:biom11050624. [PMID: 33922207 PMCID: PMC8145209 DOI: 10.3390/biom11050624] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 12/13/2022] Open
Abstract
Synucleinopathies are a group of neurodegenerative diseases characterized by the accumulation of α-synuclein aggregates in neurons, nerve fibers or glial cells. Three main types of diseases belong to the synucleinopathies: Parkinson’s disease, dementia with Lewy bodies, and multiple system atrophy. All of them develop as a result of an interplay of genetic and environmental factors. Emerging evidence suggests that epigenetic mechanisms play an essential role in the development of synucleinopathies. Since there is no disease-modifying treatment for these disorders at this time, interest is growing in plant-derived chemicals as a potential treatment option. Phytochemicals are substances of plant origin that possess biological activity, which might have effects on human health. Phytochemicals with neuroprotective activity target different elements in pathogenic pathways due to their antioxidants, anti-inflammatory, and antiapoptotic properties, and ability to reduce cellular stress. Multiple recent studies demonstrate that the beneficial effects of phytochemicals may be explained by their ability to modulate the expression of genes implicated in synucleinopathies and other diseases. These substances may regulate transcription directly via transcription factors (TFs) or play the role of epigenetic regulators through their effect on histone modification, DNA methylation, and RNA-based mechanisms. Here, we summarize new data about the impact of phytochemicals on the pathogenesis of synucleinopathies through regulation of gene expression.
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12
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Krokidis MG, Exarchos TP, Vlamos P. Data-driven biomarker analysis using computational omics approaches to assess neurodegenerative disease progression. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:1813-1832. [PMID: 33757212 DOI: 10.3934/mbe.2021094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The complexity of biological systems suggests that current definitions of molecular dysfunctions are essential distinctions of a complex phenotype. This is well seen in neurodegenerative diseases (ND), such as Alzheimer's disease (AD) and Parkinson's disease (PD), multi-factorial pathologies characterized by high heterogeneity. These challenges make it necessary to understand the effectiveness of candidate biomarkers for early diagnosis, as well as to obtain a comprehensive mapping of how selective treatment alters the progression of the disorder. A large number of computational methods have been developed to explain network-based approaches by integrating individual components for modeling a complex system. In this review, high-throughput omics methodologies are presented for the identification of potent biomarkers associated with AD and PD pathogenesis as well as for monitoring the response of dysfunctional molecular pathways incorporating multilevel clinical information. In addition, principles for efficient data analysis pipelines are being discussed that can help address current limitations during the experimental process by increasing the reproducibility of benchmarking studies.
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Affiliation(s)
- Marios G Krokidis
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Greece
| | - Themis P Exarchos
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Greece
| | - Panagiotis Vlamos
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Greece
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13
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Nasamran CA, Sachan ANS, Mott J, Kuras YI, Scherzer CR, Study HB, Ricciardelli E, Jepsen K, Edland SD, Fisch KM, Desplats P. Differential blood DNA methylation across Lewy body dementias. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2021; 13:e12156. [PMID: 33665346 PMCID: PMC7896631 DOI: 10.1002/dad2.12156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/29/2020] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Dementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD) are characterized by cognitive alterations, visual hallucinations, and motor impairment. Diagnosis is based on type and timing of clinical manifestations; however, determination of clinical subtypes is challenging. The utility of blood DNA methylation as a biomarker for Lewy body disorders (LBD) is mostly unexplored. METHODS We performed a cross-sectional analysis of blood methylation in 42 DLB and 50 PDD cases applying linear models to compare groups and logistic least absolute shrinkage and selection operator regression to explore the discriminant power of methylation signals. RESULTS DLB blood shows differential methylation compared to PDD. Some methylation changes associate with core features of LBD. Sets of probes show high predictive value to discriminate between variants. DISCUSSION Our study is the first to explore LBD blood methylation. Despite overlapping clinical presentation, we detected differential epigenetic signatures that, if confirmed in independent cohorts, could be developed into useful biomarkers.
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Affiliation(s)
- Chanond A. Nasamran
- Center for Computational Biology & BioinformaticsDepartment of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Anubhav Nikunj Singh Sachan
- Division of Biostatistics, Department of Family Medicine and Public HealthUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Jennifer Mott
- Department of Neurosciences, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Yuliya I. Kuras
- Center for Advanced Parkinson Research and Precision Neurology Program, Harvard Medical SchoolBrigham & Women's HospitalBostonMassachusettsUSA
| | - Clemens R. Scherzer
- Center for Advanced Parkinson Research and Precision Neurology Program, Harvard Medical SchoolBrigham & Women's HospitalBostonMassachusettsUSA
| | | | - Eugenia Ricciardelli
- Genomics CenterInstitute for Genomics MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Kristen Jepsen
- Genomics CenterInstitute for Genomics MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Steven D. Edland
- Department of Neurosciences, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of Family Medicine and Public HealthUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Kathleen M. Fisch
- Center for Computational Biology & BioinformaticsDepartment of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Paula Desplats
- Department of Neurosciences, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of Pathology, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
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14
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Systematic Analysis of the Lysine Crotonylome and Multiple Posttranslational Modification Analysis (Acetylation, Succinylation, and Crotonylation) in Candida albicans. mSystems 2021; 6:6/1/e01316-20. [PMID: 33500332 PMCID: PMC7842366 DOI: 10.1128/msystems.01316-20] [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] [Indexed: 12/16/2022] Open
Abstract
Candida albicans is an opportunistic pathogen that causes lethal fungal infections in immunocompromised patients. Lysine crotonylation is a newly discovered PTM (posttranslational modification) epigenetic type that may play a critical role in regulating gene expression. In this study, we used an antibody-enrichment approach along with LC-MS/MS to carry out a quantitative crotonylome analysis in C. albicans We found a total of 5,242 crotonylation sites and 1,584 crotonylated proteins among 9,038 proteins in this organism. Of these crotonylated proteins, a few unique crotonylated motifs are noted such as D and E in positions +1, +2, or +3 or K and R in positions +5 or +6, while A, E, F, G, P, W, and Y are in the -1 position or A, K, and R are found in positions -5, -6, -7, or -8. Functional analysis has shown that a majority of the crotonylated proteins are related to biosynthetic events and carbon metabolism. When combined with previously collected data on acetylation and succinylation, PPI (protein-protein interaction network) analysis reveals that proteins with functions in ribosomal biogenesis, oxidative phosphorylation, nucleus activity, and proteasome formation are heavily modified by these three PTM types. To the best of our knowledge, this is the first crotonylome study carried out in C. albicans and is an important step to a better understanding of the biological and pathogenic impact of PTM in C. albicans IMPORTANCE C. albicans is a kind of pathogen of fungal infections that is found worldwide. Lysine crotonylation of proteins as a recently discovered PTM (posttranslational modification) may have a critical role in regulating cells. We first carried out large-scale analysis of crotonylated proteome and multiple PTM analysis (acetylation, succinylation, and crotonylation), then drew a diagram to show multiple PTM sites on histones in C. albicans of our study. This study about crotonylome in human pathogenic fungi is a milestone that first and deeply investigates the functional analysis of crotonylated proteins in C. albicans, which marks an important start for further research.
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15
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Okechukwu C. Deciphering and manipulating the epigenome for the treatment of Parkinson’s and Alzheimer’s disease. MGM JOURNAL OF MEDICAL SCIENCES 2021. [DOI: 10.4103/mgmj.mgmj_90_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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