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Milicic L, Porter T, Vacher M, Laws SM. Utility of DNA Methylation as a Biomarker in Aging and Alzheimer's Disease. J Alzheimers Dis Rep 2023; 7:475-503. [PMID: 37313495 PMCID: PMC10259073 DOI: 10.3233/adr-220109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/23/2023] [Indexed: 06/15/2023] Open
Abstract
Epigenetic mechanisms such as DNA methylation have been implicated in a number of diseases including cancer, heart disease, autoimmune disorders, and neurodegenerative diseases. While it is recognized that DNA methylation is tissue-specific, a limitation for many studies is the ability to sample the tissue of interest, which is why there is a need for a proxy tissue such as blood, that is reflective of the methylation state of the target tissue. In the last decade, DNA methylation has been utilized in the design of epigenetic clocks, which aim to predict an individual's biological age based on an algorithmically defined set of CpGs. A number of studies have found associations between disease and/or disease risk with increased biological age, adding weight to the theory of increased biological age being linked with disease processes. Hence, this review takes a closer look at the utility of DNA methylation as a biomarker in aging and disease, with a particular focus on Alzheimer's disease.
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Affiliation(s)
- Lidija Milicic
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Tenielle Porter
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
| | - Michael Vacher
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- CSIRO Health and Biosecurity, Australian e-Health Research Centre, Floreat, Western Australia
| | - Simon M. Laws
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
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2
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Peng X, Zhang W, Cui W, Ding B, Lyu Q, Wang J. ADmeth: A Manually Curated Database for the Differential Methylation in Alzheimer's Disease. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:843-851. [PMID: 35617175 DOI: 10.1109/tcbb.2022.3178087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease. More and more evidence show that DNA methylation is closely related to the pathological mechanism of AD. Many AD-associated differentially methylated genes, regions and CpG sites have been identified in recent researches, which may have great potential in clinical research. However, there is no dedicated database to collect AD-related differential methylation up to now. To provide a reference to researchers, we design a database named ADmeth by manually curating relevant articles, which contains a total of 16,709 AD-related differentially methylated items identified from different brain regions and different cell types in the blood, involving 209 genes, 2,229 regions and 14,271 CpG sites. The ADmeth database provides user-friendly pages to search, submit and download data. We hope that the ADmeth database can facilitate researchers to select candidate AD-associated methylation markers in revealing the pathological mechanism of AD and promote the cell-free DNA based non-invasive diagnosis of AD. The ADmeth database is available at http://www.biobdlab.cn/ADmeth.
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3
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Hao SW, Li TR, Han C, Han Y, Cai YN. Associations Between Levels of Peripheral NCAPH2 Promoter Methylation and Different Stages of Alzheimer's Disease: A Cross-Sectional Study. J Alzheimers Dis 2023; 92:899-909. [PMID: 36806511 DOI: 10.3233/jad-221211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
BACKGROUND Several studies have examined NCAPH2 methylation in amnestic mild cognitive impairment (aMCI) and Alzheimer's disease (AD), but little is known of NCAPH2 methylation in subjective cognitive decline (SCD). OBJECTIVE To examine whether methylation of peripheral NCAPH2 are differentially changed at various phases of AD, and whether it could serve as a diagnostic biomarker for SCD. METHODS A total of 40 AD patients, 52 aMCI patients, 148 SCD patients, and 193 cognitively normal controls (NCs) were recruited in the current case-control study. Besides, 54 cognitively normal individuals have received amyloid positron emission tomography (amyloid PET) scans. Using bisulfite pyrosequencing method, we measured blood DNA methylation in the NCAPH2 gene promoter. RESULTS The main outcomes were: 1) For SCD, there was no significant difference between SCD and NC regarding NCAPH2 methylation; 2) For aMCI, NCAPH2 methylation at CpG2 were significantly lower in aMCI compared with NC and SCD in the entire population and male subgroup; 3) For AD, NCAPH2 methylation at CpG1 were significantly lower in AD compared with NC among females; 4) A relationship with apolipoprotein E (APOE) ɛ4 status was shown. Receiver operating characteristic (ROC) analysis by combining NCAPH2 methylation, age, education, and APOEɛ4 status could distinguish between patients with aMCI (area under the curve (AUC): 0.742) and AD (AUC: 0.873) from NCs. CONCLUSION NCAPH2 methylation levels were altered at the aMCI and AD stage and may be convenient and cost-effective biomarkers of AD and aMCI.
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Affiliation(s)
- Shu-Wen Hao
- Department of Neurobiology, Xuanwu Hospital, Capital Medical University, Beijing, China.,Department of Neurology, The First Hospital of Hebei Medical University, Shijiazhuang, China.,Department of Neurology, Hebei Hospital of Xuanwu Hospital Capital Medical University, Shijiazhuang, China
| | - Tao-Ran Li
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China.,Department of Neurology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Chao Han
- National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Ying Han
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China.,National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Yan-Ning Cai
- Department of Neurobiology, Xuanwu Hospital, Capital Medical University, Beijing, China.,Department of Biobank, Xuanwu Hospital, Capital Medical University, Beijing, China
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4
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Common Genetic Factors and Pathways in Alzheimer's Disease and Ischemic Stroke: Evidences from GWAS. Genes (Basel) 2023; 14:genes14020353. [PMID: 36833280 PMCID: PMC9957001 DOI: 10.3390/genes14020353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/19/2023] [Accepted: 01/27/2023] [Indexed: 02/03/2023] Open
Abstract
Alzheimer's disease (AD) and ischemic stroke (IS) are common neurological disorders, and the comorbidity of these two brain diseases is often seen. Although AD and IS were regarded as two distinct disease entities, in terms of different etiologies and clinical presentation, recent genome-wide association studies (GWASs) revealed that there were common risk genes between AD and IS, indicating common molecular pathways and their common pathophysiology. In this review, we summarize AD and IS risk single nucleotide polymorphisms (SNPs) and their representative genes from the GWAS Catalog database, and find thirteen common risk genes, but no common risk SNPs. Furthermore, the common molecular pathways associated with these risk gene products are summarized from the GeneCards database and clustered into inflammation and immunity, G protein-coupled receptor, and signal transduction. At least seven of these thirteen genes can be regulated by 23 microRNAs identified from the TargetScan database. Taken together, the imbalance of these molecular pathways may give rise to these two common brain disorders. This review sheds light on the pathogenesis of comorbidity of AD and IS, and provides molecular targets for disease prevention, manipulation, and brain health maintenance.
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Ortiz-Rodríguez MA, Martínez-Salazar MF, Antunez-Bautista PK, Jiménez-Osorio AS. Strategies for the study of neuroepigenetics and aging with a translational approach. AGING AND HEALTH RESEARCH 2023. [DOI: 10.1016/j.ahr.2023.100122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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6
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Migliore L, Coppedè F. Gene-environment interactions in Alzheimer disease: the emerging role of epigenetics. Nat Rev Neurol 2022; 18:643-660. [PMID: 36180553 DOI: 10.1038/s41582-022-00714-w] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2022] [Indexed: 12/15/2022]
Abstract
With the exception of a few monogenic forms, Alzheimer disease (AD) has a complex aetiology that is likely to involve multiple susceptibility genes and environmental factors. The role of environmental factors is difficult to determine and, until a few years ago, the molecular mechanisms underlying gene-environment (G × E) interactions in AD were largely unknown. Here, we review evidence that has emerged over the past two decades to explain how environmental factors, such as diet, lifestyle, alcohol, smoking and pollutants, might interact with the human genome. In particular, we discuss how various environmental AD risk factors can induce epigenetic modifications of key AD-related genes and pathways and consider how epigenetic mechanisms could contribute to the effects of oxidative stress on AD onset. Studies on early-life exposures are helping to uncover critical time windows of sensitivity to epigenetic influences from environmental factors, thereby laying the foundations for future primary preventative approaches. We conclude that epigenetic modifications need to be considered when assessing G × E interactions in AD.
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Affiliation(s)
- Lucia Migliore
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy. .,Department of Laboratory Medicine, Pisa University Hospital, Pisa, Italy.
| | - Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
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7
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Jin Y, Allen EG, Jin P. Cell-free DNA methylation as a potential biomarker in brain disorders. Epigenomics 2022; 14:369-374. [PMID: 35034473 PMCID: PMC9066291 DOI: 10.2217/epi-2021-0416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Yulin Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Emily G Allen
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
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8
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Rabaneda-Bueno R, Mena-Montes B, Torres-Castro S, Torres-Carrillo N, Torres-Carrillo NM. Advances in Genetics and Epigenetic Alterations in Alzheimer's Disease: A Notion for Therapeutic Treatment. Genes (Basel) 2021; 12:1959. [PMID: 34946908 PMCID: PMC8700838 DOI: 10.3390/genes12121959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 12/18/2022] Open
Abstract
Alzheimer's disease (AD) is a disabling neurodegenerative disorder that leads to long-term functional and cognitive impairment and greatly reduces life expectancy. Early genetic studies focused on tracking variations in genome-wide DNA sequences discovered several polymorphisms and novel susceptibility genes associated with AD. However, despite the numerous risk factors already identified, there is still no fully satisfactory explanation for the mechanisms underlying the onset of the disease. Also, as with other complex human diseases, the causes of low heritability are unclear. Epigenetic mechanisms, in which changes in gene expression do not depend on changes in genotype, have attracted considerable attention in recent years and are key to understanding the processes that influence age-related changes and various neurological diseases. With the recent use of massive sequencing techniques, methods for studying epigenome variations in AD have also evolved tremendously, allowing the discovery of differentially expressed disease traits under different conditions and experimental settings. This is important for understanding disease development and for unlocking new potential AD therapies. In this work, we outline the genomic and epigenomic components involved in the initiation and development of AD and identify potentially effective therapeutic targets for disease control.
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Affiliation(s)
- Rubén Rabaneda-Bueno
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, 37005 České Budějovice, Czech Republic
- School of Biological Sciences, James Clerk Maxwell Building, The King’s Buildings Campus, University of Edinburgh, Edinburgh EH9 3FD, UK
| | - Beatriz Mena-Montes
- Laboratorio de Biología del Envejecimiento, Departamento de Investigación Básica, Instituto Nacional de Geriatría, Mexico City 10200, Mexico;
| | - Sara Torres-Castro
- Departamento de Epidemiología Demográfica y Determinantes Sociales, Instituto Nacional de Geriatría, Mexico City 10200, Mexico;
| | - Norma Torres-Carrillo
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico; (N.T.-C.); (N.M.T.-C.)
| | - Nora Magdalena Torres-Carrillo
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico; (N.T.-C.); (N.M.T.-C.)
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9
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Pasyukova EG, Symonenko AV, Rybina OY, Vaiserman AM. Epigenetic enzymes: A role in aging and prospects for pharmacological targeting. Ageing Res Rev 2021; 67:101312. [PMID: 33657446 DOI: 10.1016/j.arr.2021.101312] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/05/2021] [Accepted: 02/25/2021] [Indexed: 02/06/2023]
Abstract
The development of interventions aimed at improving healthspan is one of the priority tasks for the academic and public health authorities. It is also the main objective of a novel branch in biogerontological research, geroscience. According to the geroscience concept, targeting aging is an effective way to combat age-related disorders. Since aging is an exceptionally complex process, system-oriented integrated approaches seem most appropriate for such an interventional strategy. Given the high plasticity and adaptability of the epigenome, epigenome-targeted interventions appear highly promising in geroscience research. Pharmaceuticals targeted at mechanisms involved in epigenetic control of gene activity are actively developed and implemented to prevent and treat various aging-related conditions such as cardiometabolic, neurodegenerative, inflammatory disorders, and cancer. In this review, we describe the roles of epigenetic mechanisms in aging; characterize enzymes contributing to the regulation of epigenetic processes; particularly focus on epigenetic drugs, such as inhibitors of DNA methyltransferases and histone deacetylases that may potentially affect aging-associated diseases and longevity; and discuss possible caveats associated with the use of epigenetic drugs.
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Affiliation(s)
- Elena G Pasyukova
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Kurchatov Sq. 2, Moscow, 123182, Russia
| | - Alexander V Symonenko
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Kurchatov Sq. 2, Moscow, 123182, Russia
| | - Olga Y Rybina
- Institute of Molecular Genetics of National Research Centre "Kurchatov Institute", Kurchatov Sq. 2, Moscow, 123182, Russia; Federal State Budgetary Educational Institution of Higher Education «Moscow Pedagogical State University», M. Pirogovskaya Str. 1/1, Moscow, 119991, Russia
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10
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Fransquet PD, Lacaze P, Saffery R, Phung J, Parker E, Shah RC, Murray A, Woods RL, Ryan J. DNA methylation analysis of candidate genes associated with dementia in peripheral blood. Epigenomics 2020; 12:2109-2123. [PMID: 33300824 DOI: 10.2217/epi-2020-0236] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aim: To investigate whether genes implicated in dementia pathogenesis are differently methylated in peripheral blood. Materials & methods: Participants included 160 cognitively healthy individuals aged 70+ years: 73 who were subsequently diagnosed with dementia and 87 controls matched on age, gender, education, smoking and baseline cognition. A total of 49 participants also provided blood samples at diagnosis. Blood DNA methylation of APOE, APP, BDNF, PIN1, SNCA and TOMM40 was examined. Results: A total of 56 of 299 probes were differentially methylated in dementia compared with controls and 39 probes prior to diagnosis. The greatest effect size was in APP (cg19423170, Δ-8.32%, adjusted p = 0.009 at diagnosis; cg19933173, Δ-4.18%, adjusted p < 0.0001 prediagnosis). Conclusion: Genes implicated in dementia pathogenesis show differential blood methylation in dementia, even prior to diagnosis.
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Affiliation(s)
- Peter D Fransquet
- School of Public Health & Preventive Medicine, Monash University, Melbourne, 3004 Victoria, Australia
| | - Paul Lacaze
- School of Public Health & Preventive Medicine, Monash University, Melbourne, 3004 Victoria, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute & Department of Paediatrics, The University of Melbourne, Parkville, 3052 Victoria, Australia
| | - James Phung
- School of Public Health & Preventive Medicine, Monash University, Melbourne, 3004 Victoria, Australia
| | - Emily Parker
- School of Public Health & Preventive Medicine, Monash University, Melbourne, 3004 Victoria, Australia
| | - Raj C Shah
- Department of Family Medicine & Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Anne Murray
- Berman Center for Outcomes & Clinical Research, Hennepin Healthcare Research Institute, Hennepin Healthcare; Division of Geriatrics, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Robyn L Woods
- School of Public Health & Preventive Medicine, Monash University, Melbourne, 3004 Victoria, Australia
| | - Joanne Ryan
- School of Public Health & Preventive Medicine, Monash University, Melbourne, 3004 Victoria, Australia.,PSNREC, University of Montpellier, INSERM, Montpellier, France
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11
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DNA methylation in Alzheimer’s disease: In brain and peripheral blood. Mech Ageing Dev 2020; 191:111319. [DOI: 10.1016/j.mad.2020.111319] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 12/30/2022]
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12
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Tecalco-Cruz AC, Ramírez-Jarquín JO, Alvarez-Sánchez ME, Zepeda-Cervantes J. Epigenetic basis of Alzheimer disease. World J Biol Chem 2020; 11:62-75. [PMID: 33024518 PMCID: PMC7520642 DOI: 10.4331/wjbc.v11.i2.62] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/30/2020] [Accepted: 09/10/2020] [Indexed: 02/05/2023] Open
Abstract
Alzheimer disease (AD) is the primary form of dementia that occurs spontaneously in older adults. Interestingly, the epigenetic profile of the cells forming the central nervous system changes during aging and may contribute to the progression of some neurodegenerative diseases such as AD. In this review, we present general insights into relevant epigenetic mechanisms and their relationship with aging and AD. The data suggest that some epigenetic changes during aging could be utilized as biomarkers and target molecules for the prevention and control of AD.
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Affiliation(s)
- Angeles C Tecalco-Cruz
- Programa en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico 03100, Mexico
| | - Josué O Ramírez-Jarquín
- División de neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico 04510, Mexico
| | | | - Jesus Zepeda-Cervantes
- Biología celular y de desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico 04510, Mexico
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Saffari A, Arno M, Nasser E, Ronald A, Wong CCY, Schalkwyk LC, Mill J, Dudbridge F, Meaburn EL. RNA sequencing of identical twins discordant for autism reveals blood-based signatures implicating immune and transcriptional dysregulation. Mol Autism 2019; 10:38. [PMID: 31719968 PMCID: PMC6839145 DOI: 10.1186/s13229-019-0285-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/01/2019] [Indexed: 11/13/2022] Open
Abstract
Background A gap exists in our mechanistic understanding of how genetic and environmental risk factors converge at the molecular level to result in the emergence of autism symptoms. We compared blood-based gene expression signatures in identical twins concordant and discordant for autism spectrum condition (ASC) to differentiate genetic and environmentally driven transcription differences, and establish convergent evidence for biological mechanisms involved in ASC. Methods Genome-wide gene expression data were generated using RNA-seq on whole blood samples taken from 16 pairs of monozygotic (MZ) twins and seven twin pair members (39 individuals in total), who had been assessed for ASC and autism traits at age 12. Differential expression (DE) analyses were performed between (a) affected and unaffected subjects (N = 36) and (b) within discordant ASC MZ twin pairs (total N = 11) to identify environmental-driven DE. Gene set enrichment and pathway testing was performed on DE gene lists. Finally, an integrative analysis using DNA methylation data aimed to identify genes with consistent evidence for altered regulation in cis. Results In the discordant twin analysis, three genes showed evidence for DE at FDR < 10%: IGHG4, EVI2A and SNORD15B. In the case-control analysis, four DE genes were identified at FDR < 10% including IGHG4, PRR13P5, DEPDC1B, and ZNF501. We find enrichment for DE of genes curated in the SFARI human gene database. Pathways showing evidence of enrichment included those related to immune cell signalling and immune response, transcriptional control and cell cycle/proliferation. Integrative methylomic and transcriptomic analysis identified a number of genes showing suggestive evidence for cis dysregulation. Limitations Identical twins stably discordant for ASC are rare, and as such the sample size was limited and constrained to the use of peripheral blood tissue for transcriptomic and methylomic profiling. Given these primary limitations, we focused on transcript-level analysis. Conclusions Using a cohort of ASC discordant and concordant MZ twins, we add to the growing body of transcriptomic-based evidence for an immune-based component in the molecular aetiology of ASC. Whilst the sample size was limited, the study demonstrates the utility of the discordant MZ twin design combined with multi-omics integration for maximising the potential to identify disease-associated molecular signals.
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Affiliation(s)
- Ayden Saffari
- 1Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
- 2Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck, University of London, London, UK
| | - Matt Arno
- 3Edinburgh Genomics, University of Edinburgh, Edinburgh, Scotland UK
- 4King's Genomics Centre, King's College London, London, UK
| | - Eric Nasser
- 4King's Genomics Centre, King's College London, London, UK
| | - Angelica Ronald
- 2Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck, University of London, London, UK
| | - Chloe C Y Wong
- 5Social Genetic and Developmental Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | | | - Jonathan Mill
- 7University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Frank Dudbridge
- 1Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
- 8Department of Health Sciences, University of Leicester, Leicester, UK
| | - Emma L Meaburn
- 2Centre for Brain and Cognitive Development, Department of Psychological Sciences, Birkbeck, University of London, London, UK
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14
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D'Addario C, Bellia F, Benatti B, Grancini B, Vismara M, Pucci M, De Carlo V, Viganò C, Galimberti D, Fenoglio C, Scarpini E, Maccarrone M, Dell'Osso B. Exploring the role of BDNF DNA methylation and hydroxymethylation in patients with obsessive compulsive disorder. J Psychiatr Res 2019; 114:17-23. [PMID: 31004918 DOI: 10.1016/j.jpsychires.2019.04.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/20/2019] [Accepted: 04/05/2019] [Indexed: 01/12/2023]
Abstract
Obsessive-compulsive disorder (OCD) is a clinically heterogeneous neuropsychiatric condition associated with profound disability, whose susceptibility, stemming from genetic and environmental factors that intersect with each other, is still under investigation. In this perspective, we sought to explore the transcriptional regulation of Brain Derived Neurotrophic Factor (BDNF), a promising candidate biomarker in both development and etiology of different neuropsychiatric conditions, in peripheral blood mononuclear cells from OCD patients and healthy controls. In particular, we focused on BDNF gene expression and interrogated in depth DNA methylation and hydroxymethylation at gene promoters (exons I, IV and IX) in a sample of OCD patients attending a tertiary OCD Clinic to receive guidelines-recommended treatment, and matched controls. Our preliminary data showed a significant increase in BDNF gene expression and a significant correlation with changes in the two epigenetic modifications selectively at promoter exon I, with no changes in the other promoters under study. We can conclude that transcriptional regulation of BDNF in OCD engages epigenetic mechanisms, and can suggest that this is likely evoked by the long-term pharmacotherapy. It is important to underline that many different factors need to be taken into account (i.e. age, sex, duration of illness, treatment), and thus further studies are mandatory to investigate their role in the epigenetic regulation of BDNF gene. Of note, we provide unprecedented evidence for the importance of analyzing 5-hydroxymethylcytosine levels to correctly evaluate 5-methylcytosine changes.
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Affiliation(s)
- Claudio D'Addario
- University of Teramo, Bioscience, Teramo, Italy; Karolinska Institutet, Department of Clinical Neuroscience, Stockholm, Sweden.
| | | | - Beatrice Benatti
- University of Milan, Department of Biomedical and Clinical Sciences Luigi Sacco, Milano, Italy
| | - Benedetta Grancini
- University of Milan, Department of Biomedical and Clinical Sciences Luigi Sacco, Milano, Italy
| | - Matteo Vismara
- University of Milan, Department of Biomedical and Clinical Sciences Luigi Sacco, Milano, Italy
| | | | - Vera De Carlo
- University of Milan, Department of Biomedical and Clinical Sciences Luigi Sacco, Milano, Italy
| | - Caterina Viganò
- University of Milan, Department of Biomedical and Clinical Sciences Luigi Sacco, Milano, Italy
| | - Daniela Galimberti
- University of Milan, Dino Ferrari Center, Milan, Italy; Fondazione IRCCS Ca' Granda, Ospedale Policlinico, Neurodegenerative Diseases Unit, Milan, Italy
| | - Chiara Fenoglio
- University of Milan, Dino Ferrari Center, Milan, Italy; Fondazione IRCCS Ca' Granda, Ospedale Policlinico, Neurodegenerative Diseases Unit, Milan, Italy
| | - Elio Scarpini
- University of Milan, Dino Ferrari Center, Milan, Italy; Fondazione IRCCS Ca' Granda, Ospedale Policlinico, Neurodegenerative Diseases Unit, Milan, Italy
| | - Mauro Maccarrone
- Department of Medicine, Campus Bio-Medico University of Rome, Rome, Italy; Fondazione IRCCS Santa Lucia, Unit of Lipid Neurochemistry, Rome, Italy
| | - Bernardo Dell'Osso
- University of Milan, Department of Biomedical and Clinical Sciences Luigi Sacco, Milano, Italy; CRC "Aldo Ravelli", University of Milan, Milano, Italy; Department of Psychiatry and Behavioral Sciences, Stanford University, CA, USA.
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15
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Mahady L, Nadeem M, Malek-Ahmadi M, Chen K, Perez SE, Mufson EJ. Frontal Cortex Epigenetic Dysregulation During the Progression of Alzheimer's Disease. J Alzheimers Dis 2019; 62:115-131. [PMID: 29439356 DOI: 10.3233/jad-171032] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although the frontal cortex plays an important role in cognitive function and undergoes neuronal dysfunction in Alzheimer's disease (AD), the factors driving these cellular alterations remain unknown. Recent studies suggest that alterations in epigenetic regulation play a pivotal role in this process in AD. We evaluated frontal cortex histone deacetylase (HDAC) and sirtuin (SIRT) levels in tissue obtained from subjects with a premortem diagnosis of no-cognitive impairment (NCI), mild cognitive impairment (MCI), mild to moderate AD (mAD), and severe AD (sAD) using quantitative western blotting. Immunoblots revealed significant increases in HDAC1 and HDAC3 in MCI and mAD, followed by a decrease in sAD compared to NCI. HDAC2 levels remained stable across clinical groups. HDAC4 was significantly increased in MCI and mAD, but not in sAD compared to NCI. HDAC6 significantly increased during disease progression, while SIRT1 decreased in MCI, mAD, and sAD compared to NCI. HDAC1 levels negatively correlated with perceptual speed, while SIRT1 positively correlated with perceptual speed, episodic memory, global cognitive score, and Mini-Mental State Examination. HDAC1 positively, while SIRT1 negatively correlated with cortical neurofibrillary tangle counts. These findings suggest that dysregulation of epigenetic proteins contribute to neuronal dysfunction and cognitive decline in the early stage of AD.
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Affiliation(s)
- Laura Mahady
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, USA.,Arizona State University Interdisciplinary Graduate Program in Neuroscience, Tempe, AZ, USA
| | - Muhammad Nadeem
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, USA
| | | | - Kewei Chen
- Banner Alzheimer's Institute, Phoenix, AZ, USA
| | - Sylvia E Perez
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Elliott J Mufson
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, USA
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16
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Grewal DS, Polascik BW, Hoffmeyer GC, Fekrat S. Assessment of Differences in Retinal Microvasculature Using OCT Angiography in Alzheimer's Disease: A Twin Discordance Report. Ophthalmic Surg Lasers Imaging Retina 2019; 49:440-444. [PMID: 29927472 DOI: 10.3928/23258160-20180601-09] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/04/2017] [Indexed: 01/02/2023]
Abstract
The authors report the optical coherence tomography angiography (OCTA)-based comparative assessment of the retinal microvasculature in a rare pair of 96-year-old female monozygotic twins discordant for Alzheimer's disease (AD). Using automated mapping of the superficial capillary plexus, the authors observed that the twin with advanced AD had a significantly reduced vessel density and a larger foveal avascular zone in the superficial capillary plexus as well as a thinner choroid compared to the twin who was cognitively normal. This unique twin discordance report adds to the evidence supporting the use of retinal microvasculature changes in the superficial capillary plexus on OCTA as a possible noninvasive biomarker for AD. [Ophthalmic Surg Lasers Imaging Retina. 2018;49:440-444.].
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17
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Liu X, Jiao B, Shen L. The Epigenetics of Alzheimer's Disease: Factors and Therapeutic Implications. Front Genet 2018; 9:579. [PMID: 30555513 PMCID: PMC6283895 DOI: 10.3389/fgene.2018.00579] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 11/08/2018] [Indexed: 02/05/2023] Open
Abstract
Alzheimer’s disease (AD) is a well-known neurodegenerative disorder that imposes a great burden on the world. The mechanisms of AD are not yet fully understood. Current insight into the role of epigenetics in the mechanism of AD focuses on DNA methylation, remodeling of chromatin, histone modifications and non-coding RNA regulation. This review summarizes the current state of knowledge regarding the role of epigenetics in AD and the possibilities for epigenetically based therapeutics. The general conclusion is that epigenetic mechanisms play a variety of crucial roles in the development of AD, and there are a number of viable possibilities for treatments based on modulating these effects, but significant advances in knowledge and technology will be needed to move these treatments from the bench to the bedside.
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Affiliation(s)
- Xiaolei Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,The Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Bin Jiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China
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18
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Epigenetic mechanisms in amyotrophic lateral sclerosis: A short review. Mech Ageing Dev 2018; 174:103-110. [DOI: 10.1016/j.mad.2018.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 03/08/2018] [Accepted: 03/11/2018] [Indexed: 12/13/2022]
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19
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Reynés B, Priego T, Cifre M, Oliver P, Palou A. Peripheral Blood Cells, a Transcriptomic Tool in Nutrigenomic and Obesity Studies: Current State of the Art. Compr Rev Food Sci Food Saf 2018; 17:1006-1020. [DOI: 10.1111/1541-4337.12363] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/13/2018] [Accepted: 04/14/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Bàrbara Reynés
- Laboratory of Molecular Biology, Nutrition and Biotechnology; Univ. de les Illes Balears; Palma Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN); Madrid Spain
- Inst. d'Investigació Sanitària Illes Balears (IdISBa); Palma Spain
| | - Teresa Priego
- Dept. of Physiology, Faculty of Medicine; Univ. Complutense de Madrid; Madrid Spain
| | - Margalida Cifre
- Laboratory of Molecular Biology, Nutrition and Biotechnology; Univ. de les Illes Balears; Palma Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN); Madrid Spain
| | - Paula Oliver
- Laboratory of Molecular Biology, Nutrition and Biotechnology; Univ. de les Illes Balears; Palma Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN); Madrid Spain
- Inst. d'Investigació Sanitària Illes Balears (IdISBa); Palma Spain
| | - Andreu Palou
- Laboratory of Molecular Biology, Nutrition and Biotechnology; Univ. de les Illes Balears; Palma Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN); Madrid Spain
- Inst. d'Investigació Sanitària Illes Balears (IdISBa); Palma Spain
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20
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PM20D1 is a quantitative trait locus associated with Alzheimer's disease. Nat Med 2018; 24:598-603. [PMID: 29736028 DOI: 10.1038/s41591-018-0013-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 02/12/2018] [Indexed: 11/09/2022]
Abstract
The chances to develop Alzheimer's disease (AD) result from a combination of genetic and non-genetic risk factors 1 , the latter likely being mediated by epigenetic mechanisms 2 . In the past, genome-wide association studies (GWAS) have identified an important number of risk loci associated with AD pathology 3 , but a causal relationship remains difficult to establish. In contrast, locus-specific or epigenome-wide association studies (EWAS) have revealed site-specific epigenetic alterations, which provide mechanistic insights for a particular risk gene but often lack the statistical power of GWAS 4 . Here, combining both approaches, we report a previously unidentified association of the peptidase M20-domain-containing protein 1 (PM20D1) with AD. We find that PM20D1 is a methylation and expression quantitative trait locus coupled to an AD-risk associated haplotype, which displays enhancer-like characteristics and contacts the PM20D1 promoter via a haplotype-dependent, CCCTC-binding-factor-mediated chromatin loop. Furthermore, PM20D1 is increased following AD-related neurotoxic insults at symptomatic stages in the APP/PS1 mouse model of AD and in human patients with AD who are carriers of the non-risk haplotype. In line, genetically increasing or decreasing the expression of PM20D1 reduces and aggravates AD-related pathologies, respectively. These findings suggest that in a particular genetic background, PM20D1 contributes to neuroprotection against AD.
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21
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Fransquet PD, Lacaze P, Saffery R, McNeil J, Woods R, Ryan J. Blood DNA methylation as a potential biomarker of dementia: A systematic review. Alzheimers Dement 2017; 14:81-103. [PMID: 29127806 DOI: 10.1016/j.jalz.2017.10.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/27/2017] [Accepted: 10/07/2017] [Indexed: 01/22/2023]
Abstract
Dementia is a major public health issue with rising prevalence rates, but many individuals remain undiagnosed. Accurate and timely diagnosis is key for the optimal targeting of interventions. A noninvasive, easily measurable peripheral biomarker would have greatest utility in population-wide diagnostic screening. Epigenetics, including DNA methylation, is implicated in dementia; however, it is unclear whether epigenetic changes can be detected in peripheral tissue. This study aimed to systematically review the evidence for an association between dementia and peripheral DNA methylation. Forty-eight studies that measured DNA methylation in peripheral blood were identified, and 67% reported significant associations with dementia. However, most studies were underpowered and limited by their case-control design. We emphasize the need for future longitudinal studies on large well-characterized populations, measuring epigenetic patterns in asymptomatic individuals. A biomarker detectable in the preclinical stages of the disease would have the greatest utility in future intervention and treatment trials.
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Affiliation(s)
- Peter D Fransquet
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia; Disease Epigenetics, Murdoch Children's Research Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Paul Lacaze
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Richard Saffery
- Disease Epigenetics, Murdoch Children's Research Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - John McNeil
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Robyn Woods
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Joanne Ryan
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia; Disease Epigenetics, Murdoch Children's Research Institute, The University of Melbourne, Parkville, Victoria, Australia; INSERM, Neuropsychiatry: Epidemiological and Clinical Research, University of Montpellier, Montpellier, France.
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