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Villa C, Combi R. Epigenetics in Alzheimer's Disease: A Critical Overview. Int J Mol Sci 2024; 25:5970. [PMID: 38892155 PMCID: PMC11173284 DOI: 10.3390/ijms25115970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Epigenetic modifications have been implicated in a number of complex diseases as well as being a hallmark of organismal aging. Several reports have indicated an involvement of these changes in Alzheimer's disease (AD) risk and progression, most likely contributing to the dysregulation of AD-related gene expression measured by DNA methylation studies. Given that DNA methylation is tissue-specific and that AD is a brain disorder, the limitation of these studies is the ability to identify clinically useful biomarkers in a proxy tissue, reflective of the tissue of interest, that would be less invasive, more cost-effective, and easily obtainable. The age-related DNA methylation changes have also been used to develop different generations of epigenetic clocks devoted to measuring the aging in different tissues that sometimes suggests an age acceleration in AD patients. This review critically discusses epigenetic changes and aging measures as potential biomarkers for AD detection, prognosis, and progression. Given that epigenetic alterations are chemically reversible, treatments aiming at reversing these modifications will be also discussed as promising therapeutic strategies for AD.
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Affiliation(s)
| | - Romina Combi
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy;
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Lozupone M, Dibello V, Sardone R, Castellana F, Zupo R, Lampignano L, Bortone I, Daniele A, Bellomo A, Solfrizzi V, Panza F. The Impact of Apolipoprotein E ( APOE) Epigenetics on Aging and Sporadic Alzheimer's Disease. BIOLOGY 2023; 12:1529. [PMID: 38132357 PMCID: PMC10740847 DOI: 10.3390/biology12121529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023]
Abstract
Sporadic Alzheimer's disease (AD) derives from an interplay among environmental factors and genetic variants, while epigenetic modifications have been expected to affect the onset and progression of its complex etiopathology. Carriers of one copy of the apolipoprotein E gene (APOE) ε4 allele have a 4-fold increased AD risk, while APOE ε4/ε4-carriers have a 12-fold increased risk of developing AD in comparison with the APOE ε3-carriers. The main longevity factor is the homozygous APOE ε3/ε3 genotype. In the present narrative review article, we summarized and described the role of APOE epigenetics in aging and AD pathophysiology. It is not fully understood how APOE variants may increase or decrease AD risk, but this gene may affect tau- and amyloid-mediated neurodegeneration directly or indirectly, also by affecting lipid metabolism and inflammation. For sporadic AD, epigenetic regulatory mechanisms may control and influence APOE expression in response to external insults. Diet, a major environmental factor, has been significantly associated with physical exercise, cognitive function, and the methylation level of several cytosine-phosphate-guanine (CpG) dinucleotide sites of APOE.
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Affiliation(s)
- Madia Lozupone
- Department of Translational Biomedicine and Neuroscience (DiBrain), University of Bari Aldo Moro, 70121 Bari, Italy;
| | - Vittorio Dibello
- Department of Orofacial Pain and Dysfunction, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
| | - Rodolfo Sardone
- Local Healthcare Authority of Taranto, 74121 Taranto, Italy;
| | - Fabio Castellana
- Department of Interdisciplinary Medicine, Clinica Medica e Geriatria “Cesare Frugoni”, University of Bari Aldo Moro, 70121 Bari, Italy; (F.C.); (R.Z.); (V.S.)
| | - Roberta Zupo
- Department of Interdisciplinary Medicine, Clinica Medica e Geriatria “Cesare Frugoni”, University of Bari Aldo Moro, 70121 Bari, Italy; (F.C.); (R.Z.); (V.S.)
| | - Luisa Lampignano
- Local Healthcare Authority of Bari, ASL Bari, 70132 Bari, Italy;
| | - Ilaria Bortone
- Department of Translational Biomedicine and Neuroscience (DiBrain), University of Bari Aldo Moro, 70121 Bari, Italy;
| | - Antonio Daniele
- Department of Neuroscience, Catholic University of Sacred Heart, 00168 Rome, Italy;
- Neurology Unit, IRCCS Fondazione Policlinico Universitario A. Gemelli, 00168 Rome, Italy
| | - Antonello Bellomo
- Psychiatric Unit, Department of Clinical & Experimental Medicine, University of Foggia, 71122 Foggia, Italy;
| | - Vincenzo Solfrizzi
- Department of Interdisciplinary Medicine, Clinica Medica e Geriatria “Cesare Frugoni”, University of Bari Aldo Moro, 70121 Bari, Italy; (F.C.); (R.Z.); (V.S.)
| | - Francesco Panza
- Department of Interdisciplinary Medicine, Clinica Medica e Geriatria “Cesare Frugoni”, University of Bari Aldo Moro, 70121 Bari, Italy; (F.C.); (R.Z.); (V.S.)
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Housini M, Zhou Z, Gutierrez J, Rao S, Jomaa R, Subasinghe K, Reid DM, Silzer T, Phillips N, O'Bryant S, Barber RC. Top Alzheimer's disease risk allele frequencies differ in HABS-HD Mexican- versus Non-Hispanic White Americans. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2023; 15:e12518. [PMID: 38155914 PMCID: PMC10752755 DOI: 10.1002/dad2.12518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/13/2023] [Accepted: 11/25/2023] [Indexed: 12/30/2023]
Abstract
INTRODUCTION: Here we evaluate frequencies of the top 10 Alzheimer's disease (AD) risk alleles for late-onset AD in Mexican American (MA) and non-Hispanic White (NHW) American participants enrolled in the Health and Aging Brain Study-Health Disparities Study cohort. METHODS: Using DNA extracted from this community-based diverse population, we calculated the genotype frequencies in each population to determine whether a significant difference is detected between the different ethnicities. DNA genotyping was performed per manufacturers' protocols. RESULTS: Allele and genotype frequencies for 9 of the 11 single nucleotide polymorphisms (two apolipoprotein E variants, CR1, BIN1, DRB1, NYAP1, PTK2B, FERMT2, and ABCA7) differed significantly between MAs and NHWs. DISCUSSION: The significant differences in frequencies of top AD risk alleles observed here across MAs and NHWs suggest that ethnicity-specific genetic risks for AD exist. Given our results, we are advancing additional projects to further elucidate ethnicity-specific differences in AD.
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Affiliation(s)
- Mohammad Housini
- Department of Pharmacology and NeuroscienceSchool of Biomedical SciencesUniversity of North Texas Health Science CenterFort WorthTexasUSA
- Department of Family Medicine & Manipulative MedicineTexas College of Osteopathic MedicineUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | - Zhengyang Zhou
- Department of Biostatistics and EpidemiologySchool of Public HealthUniversity of North Texas Health Science CenterFort WorthTexasUSA
- Institute for Translational ResearchUNT Health Science CenterFort WorthTexasUSA
| | - John Gutierrez
- Department of Internal MedicineTexas Institute for Graduate Medical Education and ResearchSan AntonioTexasUSA
| | - Sumedha Rao
- Department of Family Medicine & Manipulative MedicineTexas College of Osteopathic MedicineUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | - Rodwan Jomaa
- Department of Family Medicine & Manipulative MedicineTexas College of Osteopathic MedicineUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | - Kumudu Subasinghe
- Department of MicrobiologyImmunology and GeneticsSchool of Biomedical SciencesUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | - Danielle Marie Reid
- Department of MicrobiologyImmunology and GeneticsSchool of Biomedical SciencesUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | - Talisa Silzer
- Department of MicrobiologyImmunology and GeneticsSchool of Biomedical SciencesUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | - Nicole Phillips
- Institute for Translational ResearchUNT Health Science CenterFort WorthTexasUSA
- Department of MicrobiologyImmunology and GeneticsSchool of Biomedical SciencesUniversity of North Texas Health Science CenterFort WorthTexasUSA
| | - Sid O'Bryant
- Department of Family Medicine & Manipulative MedicineTexas College of Osteopathic MedicineUniversity of North Texas Health Science CenterFort WorthTexasUSA
- Institute for Translational ResearchUNT Health Science CenterFort WorthTexasUSA
| | - Robert Clinton Barber
- Department of Family Medicine & Manipulative MedicineTexas College of Osteopathic MedicineUniversity of North Texas Health Science CenterFort WorthTexasUSA
- Institute for Translational ResearchUNT Health Science CenterFort WorthTexasUSA
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Ereqat S, Cauchi S, Eweidat K, Elqadi M, Ghatass M, Sabarneh A, Nasereddin A. Association of DNA methylation and genetic variations of the APOE gene with the risk of diabetic dyslipidemia. Biomed Rep 2022; 17:61. [PMID: 35719839 PMCID: PMC9198989 DOI: 10.3892/br.2022.1544] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/05/2022] [Indexed: 11/06/2022] Open
Abstract
Apolipoprotein E (APOE) is a key regulator of lipoprotein metabolism, and consequently, affects the plasma and tissue lipid contents. The aim of the present study was to investigate the parallel effects of APOE genetic variants and promoter methylation levels of six CpGs on the risk of diabetic dyslipidemia. A total of 204 Palestinian type 2 diabetes (T2D) patients (mean age ± SD: 62.7±10.2) were enrolled in the present study (n=96 with dyslipidemia and n=108 without dyslipidemia). Next generation sequencing was performed to analyze five single nucleotide polymorphisms: Two variants rs7412 and rs429358 that determine APOE ε alleles, and three variants in the promoter region (rs769446, rs449647, and rs405509). For all subjects, the most common genotype was ε3/ε3 (79.4%). No statistical differences were observed in the APOE ε polymorphisms and the three promoter variants among T2D patients with and without dyslipidemia (P>0.05). A comparison of lipid parameters between ε3/ε3 subjects and ε4 carriers in both groups revealed no significant differences in the mean values of LDL-C, HDL-C, TG, and TC levels (P>0.05). Six CpG sites in the APOE promoter on chromosome 19:44905755-44906078 were identified, and differential DNA methylation in these CpGs were observed between the study groups. Logistic regression analysis revealed a significant association of DNA methylation level at the six CpGs with an increased risk of diabetic dyslipidemia (odds ratio, 1.038; 95% confidence interval, 1.012-1.064; P=0.004). In conclusion, the present study revealed that DNA methylation levels in six CpGs in the APOE promoter region was associated with the risk of diabetic dyslipidemia independently of the APOE ε4 variant which could be a potential therapeutic target to reverse the methylation of the APOE promoter.
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Affiliation(s)
- Suheir Ereqat
- Biochemistry and Molecular Biology Department, Faculty of Medicine, Al‑Quds University, Abu Dis P144, Palestine
| | - Stéphane Cauchi
- Centre National de la Recherche Scientfique (CNRS), Unité Mixte de Recherche UMR8204 Lille, France
| | - Khaled Eweidat
- Faculty of Medicine, Al‑Quds University, East Jerusalem, Abu Dis P144, Palestine
| | - Muawiyah Elqadi
- Faculty of Medicine, Al‑Quds University, East Jerusalem, Abu Dis P144, Palestine
| | - Manal Ghatass
- Biochemistry and Molecular Biology Department, Faculty of Medicine, Al‑Quds University, Abu Dis P144, Palestine
| | - Anas Sabarneh
- Palestine Medical Complex, Laboratories Division, Ramallah P606, Palestine
| | - Abedelmajeed Nasereddin
- Biochemistry and Molecular Biology Department, Faculty of Medicine, Al‑Quds University, Abu Dis P144, Palestine
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Wang K, Lu Y, Morrow DF, Xiao D, Xu C. Associations of ARHGAP26 Polymorphisms with Alzheimer's Disease and Cardiovascular Disease. J Mol Neurosci 2022; 72:1085-1097. [PMID: 35171450 DOI: 10.1007/s12031-022-01972-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/10/2022] [Indexed: 02/03/2023]
Abstract
The Rho GTPase activating protein 26 (ARHGAP26) gene has been reported to be associated with neuropsychiatric diseases and neurodegenerative diseases including Parkinson's disease. We examined whether the ARHGAP26 gene is associated with Alzheimer's disease (AD) and/or cardiovascular disease (CVD). Multivariable logistic regression model was used to examine the associations of 154 single nucleotide polymorphisms (SNPs) within the ARHGAP26 gene with AD and CVD using the Alzheimer's Disease Neuroimaging Initiative 1 (ADNI-1) cohort. Fourteen SNPs were associated with AD (top SNP rs3776362 with p = 3.43 × 10-3), while 37 SNPs revealed associations with CVD (top SNP rs415235 with p = 2.06 × 10-4). Interestingly, 13 SNPs were associated with both AD and CVD. SNP rs3776362 was associated with CVD, Functional Activities Questionnaire (FAQ), and Clinical Dementia Rating Sum of Boxes (CDR-SB). A replication study using a Caribbean Hispanics sample showed that 17 SNPs revealed associations with AD, and 12 SNPs were associated with CVD. The third sample using a family-based study design showed that 9 SNPs were associated with AD, and 3 SNPs were associated with CVD. SNP rs6836509 within the ARHGAP10 gene (an important paralogon of ARHGAP26) was associated with AD and cerebrospinal fluid total tau (t-tau) level in the ADNI sample. Several SNPs were functionally important using the RegulomeDB, while a number of SNPs were associated with significant expression quantitative trait loci (eQTLs) using Genotype-Tissue Expression (GTEx) databases. In conclusion, genetic variants within ARHGAP26 were associated with AD and CVD. These findings add important new insights into the potentially shared pathogenesis of AD and CVD.
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Affiliation(s)
- Kesheng Wang
- Department of Family and Community Health, School of Nursing, Health Sciences Center, West Virginia University, Post Office Box 9600 - Office 6419, Morgantown, WV, 26506, USA.
| | - Yongke Lu
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, 25755, USA
| | - Deana F Morrow
- School of Social Work, West Virginia University, Morgantown, WV, 26506, USA
| | - Danqing Xiao
- Department of STEM, School of Arts and Sciences, Regis College, Weston, MA, 02493, USA
- McLean Imaging Center, McLean Hospital, MA, 02478, Belmont, USA
| | - Chun Xu
- Department of Health and Biomedical Sciences, College of Health Professions, University of Texas Rio Grande Valley, TX, 78520, Brownsville, USA.
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Levels of Angiotensin-Converting Enzyme and Apolipoproteins Are Associated with Alzheimer’s Disease and Cardiovascular Diseases. Cells 2021; 11:cells11010029. [PMID: 35011591 PMCID: PMC8744784 DOI: 10.3390/cells11010029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/10/2021] [Accepted: 12/17/2021] [Indexed: 01/01/2023] Open
Abstract
Angiotensin-converting enzyme-1 (ACE1) and apolipoproteins (APOs) may play important roles in the development of Alzheimer’s disease (AD) and cardiovascular diseases (CVDs). This study aimed to examine the associations of AD, CVD, and endocrine-metabolic diseases (EMDs) with the levels of ACE1 and 9 APO proteins (ApoAI, ApoAII, ApoAIV, ApoB, ApoCI, ApoCIII, ApoD, ApoE, and ApoH). Non-Hispanic white individuals including 109 patients with AD, 356 mild cognitive impairment (MCI), 373 CVD, 198 EMD and controls were selected from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset. Multivariable general linear model (GLM) was used to examine the associations. ApoE ε4 allele was associated with AD, as well as ApoAIV, ApoB and ApoE proteins, but not associated with CVD and EMD. Both AD and CVD were associated with levels of ACE1, ApoB, and ApoH proteins. AD, MCI and EMD were associated with levels of ACE1, ApoAII, and ApoE proteins. This is the first study to report associations of ACE1 and several APO proteins with AD, MCI, CVD and EMD, respectively, including upregulated and downregulated protein levels. In conclusion, as specific or shared biomarkers, the levels of ACE1 and APO proteins are implicated for AD, CVD, EMD and ApoE ε4 allele. Further studies are required for validation to establish reliable biomarkers for these health conditions.
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Wang L, Liu K, Zhang X, Wang Y, Liu W, Wang T, Hao L, Ju M, Xiao R. The Effect and Mechanism of Cholesterol and Vitamin B 12 on Multi-Domain Cognitive Function: A Prospective Study on Chinese Middle-Aged and Older Adults. Front Aging Neurosci 2021; 13:707958. [PMID: 34512309 PMCID: PMC8430239 DOI: 10.3389/fnagi.2021.707958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Nutrients are associated with cognitive function, but limited research studies have systematically evaluated on multi-domain cognitive function. The aim of this study was to investigate the effect and mechanism of specific nutrient on multi-domain cognitive function, and provide nutrition guidance for improving cognitive function. Methods: Participants were selected based on a multicenter prospective study on middle-aged and older adults in China. Global cognitive function was evaluated by the Mini-Mental State Examination (MMSE). Nutrients intake was assessed according to food frequency questionnaire and China Food Composition Database, and principal component analysis was performed to extract nutrient patterns. Associations between specific nutrients and cognitive function were assessed using log-binomial regression. Restricted cubic spline was used to illustrate the dose-response relationship of nutrients with multi-domain cognitive function. Mediation analysis was used to determine the mechanism of nutrients in cognitive function. Results: Four nutrient patterns were identified (vitamin-mineral, protein-carbohydrate, fatty acid-vitamin E, and cholesterol-vitamin B12), and only a nutrient pattern rich in cholesterol and vitamin B12 was found associated with cognitive function (RR = 0.891, 95%CI = 0.794–0.999). In multi-domain cognitive function, dietary cholesterol and vitamin B12 were related to better performance of visual memory function (P = 0.034, P = 0.02). In dose-response relationship, it suggested a U-shaped association between vitamin B12 and MMSE (P = 0.02) within a certain range. Conclusions: Dietary intake rich in cholesterol and vitamin B12 was associated with better cognitive function, and vitamin B12 had a U-shaped dose-response relation with MMSE. Thus, ensuring moderate cholesterol and vitamin B12intake may be an advisable strategy to improve cognitive function in middle-aged and older adults. Clinical Trial Registration: EMCOA, ChiCTR-OOC-17011882, Registered 5th, July 2017-Retrospectively registered, http://www.medresman.org/uc/project/projectedit.aspx?proj=2610
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Affiliation(s)
- Lijing Wang
- School of Public Health, Capital Medical University, Beijing, China
| | - Kuo Liu
- School of Public Health, Capital Medical University, Beijing, China
| | - Xiaona Zhang
- School of Public Health, Capital Medical University, Beijing, China
| | - Yushan Wang
- School of Public Health, Capital Medical University, Beijing, China
| | - Wen Liu
- School of Public Health, Capital Medical University, Beijing, China
| | - Tao Wang
- School of Public Health, Capital Medical University, Beijing, China
| | - Ling Hao
- School of Public Health, Capital Medical University, Beijing, China
| | - Mengwei Ju
- School of Public Health, Capital Medical University, Beijing, China
| | - Rong Xiao
- School of Public Health, Capital Medical University, Beijing, China
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Abstract
PURPOSE OF REVIEW The functions, genetic variations and impact of apolipoprotein E on lipoprotein metabolism in general are placed in the context of clinical practice dealing with moderate dyslipidaemia as well as dysbetalipoproteinemia, a highly atherogenic disorder and lipoprotein glomerulopathy. RECENT FINDINGS Additional variants of apolipoprotein E and participation of apolipoprotein E in inflammation are of interest. The mostly favourable effects of apolipoprotein E2 as well as the atherogenic nature of apolipoproteinE4, which has an association with cognitive impairment, are confirmed. The contribution of remnant lipoproteins of triglyceride-rich lipoproteins, of which dysbetalipoproteinemia represents an extreme, is explored in atherosclerosis. Mimetic peptides may present new therapeutic approaches. Apolipoprotein E is an important determinant of the lipid profile and cardiovascular health in the population at large and can precipitate dysbetalipoproteinemia and glomerulopathy. Awareness of apolipoprotein E polymorphisms should improve medical care.
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Nikolac Perkovic M, Videtic Paska A, Konjevod M, Kouter K, Svob Strac D, Nedic Erjavec G, Pivac N. Epigenetics of Alzheimer's Disease. Biomolecules 2021; 11:biom11020195. [PMID: 33573255 PMCID: PMC7911414 DOI: 10.3390/biom11020195] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/19/2021] [Accepted: 01/26/2021] [Indexed: 02/07/2023] Open
Abstract
There are currently no validated biomarkers which can be used to accurately diagnose Alzheimer’s disease (AD) or to distinguish it from other dementia-causing neuropathologies. Moreover, to date, only symptomatic treatments exist for this progressive neurodegenerative disorder. In the search for new, more reliable biomarkers and potential therapeutic options, epigenetic modifications have emerged as important players in the pathogenesis of AD. The aim of the article was to provide a brief overview of the current knowledge regarding the role of epigenetics (including mitoepigenetics) in AD, and the possibility of applying these advances for future AD therapy. Extensive research has suggested an important role of DNA methylation and hydroxymethylation, histone posttranslational modifications, and non-coding RNA regulation (with the emphasis on microRNAs) in the course and development of AD. Recent studies also indicated mitochondrial DNA (mtDNA) as an interesting biomarker of AD, since dysfunctions in the mitochondria and lower mtDNA copy number have been associated with AD pathophysiology. The current evidence suggests that epigenetic changes can be successfully detected, not only in the central nervous system, but also in the cerebrospinal fluid and on the periphery, contributing further to their potential as both biomarkers and therapeutic targets in AD.
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Affiliation(s)
- Matea Nikolac Perkovic
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Ruder Boskovic Institute, HR-10000 Zagreb, Croatia; (M.N.P.); (M.K.); (D.S.S.); (G.N.E.)
| | - Alja Videtic Paska
- Medical Center for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (A.V.P.); (K.K.)
| | - Marcela Konjevod
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Ruder Boskovic Institute, HR-10000 Zagreb, Croatia; (M.N.P.); (M.K.); (D.S.S.); (G.N.E.)
| | - Katarina Kouter
- Medical Center for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (A.V.P.); (K.K.)
| | - Dubravka Svob Strac
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Ruder Boskovic Institute, HR-10000 Zagreb, Croatia; (M.N.P.); (M.K.); (D.S.S.); (G.N.E.)
| | - Gordana Nedic Erjavec
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Ruder Boskovic Institute, HR-10000 Zagreb, Croatia; (M.N.P.); (M.K.); (D.S.S.); (G.N.E.)
| | - Nela Pivac
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Ruder Boskovic Institute, HR-10000 Zagreb, Croatia; (M.N.P.); (M.K.); (D.S.S.); (G.N.E.)
- Correspondence: ; Tel.: +38-514-571-207
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Walker RM, Vaher K, Bermingham ML, Morris SW, Bretherick AD, Zeng Y, Rawlik K, Amador C, Campbell A, Haley CS, Hayward C, Porteous DJ, McIntosh AM, Marioni RE, Evans KL. Identification of epigenome-wide DNA methylation differences between carriers of APOE ε4 and APOE ε2 alleles. Genome Med 2021; 13:1. [PMID: 33397400 PMCID: PMC7784364 DOI: 10.1186/s13073-020-00808-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 11/12/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The apolipoprotein E (APOE) ε4 allele is the strongest genetic risk factor for late onset Alzheimer's disease, whilst the ε2 allele confers protection. Previous studies report differential DNA methylation of APOE between ε4 and ε2 carriers, but associations with epigenome-wide methylation have not previously been characterised. METHODS Using the EPIC array, we investigated epigenome-wide differences in whole blood DNA methylation patterns between Alzheimer's disease-free APOE ε4 (n = 2469) and ε2 (n = 1118) carriers from the two largest single-cohort DNA methylation samples profiled to date. Using a discovery, replication and meta-analysis study design, methylation differences were identified using epigenome-wide association analysis and differentially methylated region (DMR) approaches. Results were explored using pathway and methylation quantitative trait loci (meQTL) analyses. RESULTS We obtained replicated evidence for DNA methylation differences in a ~ 169 kb region, which encompasses part of APOE and several upstream genes. Meta-analytic approaches identified DNA methylation differences outside of APOE: differentially methylated positions were identified in DHCR24, LDLR and ABCG1 (2.59 × 10-100 ≤ P ≤ 2.44 × 10-8) and DMRs were identified in SREBF2 and LDLR (1.63 × 10-4 ≤ P ≤ 3.01 × 10-2). Pathway and meQTL analyses implicated lipid-related processes and high-density lipoprotein cholesterol was identified as a partial mediator of the methylation differences in ABCG1 and DHCR24. CONCLUSIONS APOE ε4 vs. ε2 carrier status is associated with epigenome-wide methylation differences in the blood. The loci identified are located in trans as well as cis to APOE and implicate genes involved in lipid homeostasis.
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Affiliation(s)
- Rosie M. Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
- Present Address: Centre for Clinical Brain Sciences, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - Kadi Vaher
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
- Present Address: MRC Centre for Reproductive Health, The Queen’s Medical Research Institute, Edinburgh BioQuarter, 47 Little France Crescent, Edinburgh, EH16 4TJ UK
| | - Mairead L. Bermingham
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Stewart W. Morris
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Andrew D. Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Yanni Zeng
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
- Present address: Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080 China
| | - Konrad Rawlik
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Roslin, UK
| | - Carmen Amador
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Archie Campbell
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Chris S. Haley
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - David J. Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Andrew M. McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, EH10 5HF UK
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Kathryn L. Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
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