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Alves VC, Carro E, Figueiro-Silva J. Unveiling DNA methylation in Alzheimer's disease: a review of array-based human brain studies. Neural Regen Res 2024; 19:2365-2376. [PMID: 38526273 PMCID: PMC11090417 DOI: 10.4103/1673-5374.393106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 12/05/2023] [Indexed: 03/26/2024] Open
Abstract
The intricacies of Alzheimer's disease pathogenesis are being increasingly illuminated by the exploration of epigenetic mechanisms, particularly DNA methylation. This review comprehensively surveys recent human-centered studies that investigate whole genome DNA methylation in Alzheimer's disease neuropathology. The examination of various brain regions reveals distinctive DNA methylation patterns that associate with the Braak stage and Alzheimer's disease progression. The entorhinal cortex emerges as a focal point due to its early histological alterations and subsequent impact on downstream regions like the hippocampus. Notably, ANK1 hypermethylation, a protein implicated in neurofibrillary tangle formation, was recurrently identified in the entorhinal cortex. Further, the middle temporal gyrus and prefrontal cortex were shown to exhibit significant hypermethylation of genes like HOXA3, RHBDF2, and MCF2L, potentially influencing neuroinflammatory processes. The complex role of BIN1 in late-onset Alzheimer's disease is underscored by its association with altered methylation patterns. Despite the disparities across studies, these findings highlight the intricate interplay between epigenetic modifications and Alzheimer's disease pathology. Future research efforts should address methodological variations, incorporate diverse cohorts, and consider environmental factors to unravel the nuanced epigenetic landscape underlying Alzheimer's disease progression.
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Affiliation(s)
- Victoria Cunha Alves
- Neurodegenerative Diseases Group, Hospital Universitario 12 de Octubre Research Institute (imas12), Madrid, Spain
- Network Center for Biomedical Research, Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- PhD Program in Neuroscience, Autonoma de Madrid University, Madrid, Spain
- Neurotraumatology and Subarachnoid Hemorrhage Group, Hospital Universitario 12 de Octubre Research Institute (imas12), Madrid, Spain
| | - Eva Carro
- Network Center for Biomedical Research, Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- Neurobiology of Alzheimer's Disease Unit, Functional Unit for Research Into Chronic Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Joana Figueiro-Silva
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
- Department of Molecular Life Science, University of Zurich, Zurich, Switzerland
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2
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Cui M, Wang J, Deng M, Meng H, Fan Y, Ku C, Wang R, Wu B, Dai M, Ping Z. Longitudinal relationship between grip strength and cognitive function in a European population older than 50 years: A cross-lagged panel model. Arch Gerontol Geriatr 2024; 122:105396. [PMID: 38484671 DOI: 10.1016/j.archger.2024.105396] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/28/2024] [Accepted: 03/02/2024] [Indexed: 05/08/2024]
Abstract
OBJECTIVES The aim of this study was to investigate the dynamic longitudinal relationship between grip strength and cognitive function. METHODS 6175 participants aged ≥50 years were included in the study using three waves of follow-up data from the Survey of Health, Ageing, and Retirement in Europe in 2015 (T1), 2017 (T2) and 2019 (T3). Cognitive function was assessed using numeracy, verbal fluency, immediate recall, delayed recall and total. The cross-lagged panel model was used for analysis. RESULTS There was a correlation between grip strength and cognitive function. Standardized path coefficient from numeracy T1 to grip strength T2 was 0.017 (p = 0.003), and from numeracy T2 to grip strength T3 was 0.014 (p = 0.012). Standardized path coefficient from grip strength T1 to numeracy T2 was 0.096 (p < 0.001), and from grip strength T2 to numeracy T3 was 0.113 (p < 0.001). Other indicators of cognitive function had similar relationships with grip strength. CONCLUSIONS The study found a statistically significant longitudinal and bidirectional relationship between grip strength and cognitive function in a sample of people aged ≥50 years from several European countries.
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Affiliation(s)
- Man Cui
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Juan Wang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Miao Deng
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Hailan Meng
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yanshuai Fan
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Chaoyue Ku
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Ruizhe Wang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Binbin Wu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Man Dai
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Zhiguang Ping
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
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3
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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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4
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Davydova E, Perenkov A, Vedunova M. Building Minimized Epigenetic Clock by iPlex MassARRAY Platform. Genes (Basel) 2024; 15:425. [PMID: 38674360 PMCID: PMC11049545 DOI: 10.3390/genes15040425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Epigenetic clocks are valuable tools for estimating both chronological and biological age by assessing DNA methylation levels at specific CpG dinucleotides. While conventional epigenetic clocks rely on genome-wide methylation data, targeted approaches offer a more efficient alternative. In this study, we explored the feasibility of constructing a minimized epigenetic clock utilizing data acquired through the iPlex MassARRAY technology. The study enrolled a cohort of relatively healthy individuals, and their methylation levels of eight specific CpG dinucleotides in genes SLC12A5, LDB2, FIGN, ACSS3, FHL2, and EPHX3 were evaluated using the iPlex MassARRAY system and the Illumina EPIC array. The methylation level of five studied CpG sites demonstrated significant correlations with chronological age and an acceptable convergence of data obtained by the iPlex MassARRAY and Illumina EPIC array. At the same time, the methylation level of three CpG sites showed a weak relationship with age and exhibited a low concordance between the data obtained from the two technologies. The construction of the epigenetic clock involved the utilization of different machine-learning models, including linear models, deep neural networks (DNN), and gradient-boosted decision trees (GBDT). The results obtained from these models were compared with each other and with the outcomes generated by other well-established epigenetic clocks. In our study, the TabNet architecture (deep tabular data learning architecture) exhibited the best performance (best MAE = 5.99). Although our minimized epigenetic clock yielded slightly higher age prediction errors compared to other epigenetic clocks, it still represents a viable alternative to the genome-wide epigenotyping array.
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Affiliation(s)
- Ekaterina Davydova
- Institute of Biology and Biomedicine, Lobachevsky State University, 23 Gagarin Ave., Nizhny Novgorod 603022, Russia (M.V.)
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Kim YA, Mellen M, Kizil C, Santa-Maria I. Mechanisms linking cerebrovascular dysfunction and tauopathy: Adding a layer of epiregulatory complexity. Br J Pharmacol 2024; 181:879-895. [PMID: 37926507 DOI: 10.1111/bph.16280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 09/11/2023] [Accepted: 09/30/2023] [Indexed: 11/07/2023] Open
Abstract
Intracellular accumulation of hyperphosphorylated misfolded tau proteins are found in many neurodegenerative tauopathies, including Alzheimer's disease (AD). Tau pathology can impact cerebrovascular physiology and function through multiple mechanisms. In vitro and in vivo studies have shown that alterations in the blood-brain barrier (BBB) integrity and function can result in synaptic abnormalities and neuronal damage. In the present review, we will summarize how tau proteostasis dysregulation contributes to vascular dysfunction and, conversely, we will examine the factors and pathways leading to tau pathological alterations triggered by cerebrovascular dysfunction. Finally, we will highlight the role epigenetic and epitranscriptomic factors play in regulating the integrity of the cerebrovascular system and the progression of tauopathy including a few observartions on potential therapeutic interventions. LINKED ARTICLES: This article is part of a themed issue From Alzheimer's Disease to Vascular Dementia: Different Roads Leading to Cognitive Decline. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v181.6/issuetoc.
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Affiliation(s)
- Yoon A Kim
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
- Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
| | - Marian Mellen
- Facultad de Ciencias Experimentales, Universidad Francisco de Vitoria, Pozuelo de Alarcon, Madrid, Spain
| | - Caghan Kizil
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Ismael Santa-Maria
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
- Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
- Facultad de Ciencias Experimentales, Universidad Francisco de Vitoria, Pozuelo de Alarcon, Madrid, Spain
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6
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Ramirez P, Sun W, Kazempour Dehkordi S, Zare H, Fongang B, Bieniek KF, Frost B. Nanopore-based DNA long-read sequencing analysis of the aged human brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578450. [PMID: 38370753 PMCID: PMC10871260 DOI: 10.1101/2024.02.01.578450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Aging disrupts cellular processes such as DNA repair and epigenetic control, leading to a gradual buildup of genomic alterations that can have detrimental effects in post-mitotic cells. Genomic alterations in regions of the genome that are rich in repetitive sequences, often termed "dark loci," are difficult to resolve using traditional sequencing approaches. New long-read technologies offer promising avenues for exploration of previously inaccessible regions of the genome. Using nanopore-based long-read whole-genome sequencing of DNA extracted from aged 18 human brains, we identify previously unreported structural variants and methylation patterns within repetitive DNA, focusing on transposable elements ("jumping genes") as crucial sources of variation, particularly in dark loci. Our analyses reveal potential somatic insertion variants and provides DNA methylation frequencies for many retrotransposon families. We further demonstrate the utility of this technology for the study of these challenging genomic regions in brains affected by Alzheimer's disease and identify significant differences in DNA methylation in pathologically normal brains versus those affected by Alzheimer's disease. Highlighting the power of this approach, we discover specific polymorphic retrotransposons with altered DNA methylation patterns. These retrotransposon loci have the potential to contribute to pathology, warranting further investigation in Alzheimer's disease research. Taken together, our study provides the first long-read DNA sequencing-based analysis of retrotransposon sequences, structural variants, and DNA methylation in the aging brain affected with Alzheimer's disease neuropathology.
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Affiliation(s)
- Paulino Ramirez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Wenyan Sun
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
- School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri
| | - Shiva Kazempour Dehkordi
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Habil Zare
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Bernard Fongang
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Biochemistry & Structural Biology, University of Texas Health San Antonio, San Antonio, Texas
| | - Kevin F. Bieniek
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Pathology, University of Texas Health San Antonio, San Antonio, Texas
| | - Bess Frost
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
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7
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Zhao R. Exercise mimetics: a novel strategy to combat neuroinflammation and Alzheimer's disease. J Neuroinflammation 2024; 21:40. [PMID: 38308368 PMCID: PMC10837901 DOI: 10.1186/s12974-024-03031-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/25/2024] [Indexed: 02/04/2024] Open
Abstract
Neuroinflammation is a pathological hallmark of Alzheimer's disease (AD), characterized by the stimulation of resident immune cells of the brain and the penetration of peripheral immune cells. These inflammatory processes facilitate the deposition of amyloid-beta (Aβ) plaques and the abnormal hyperphosphorylation of tau protein. Managing neuroinflammation to restore immune homeostasis and decrease neuronal damage is a therapeutic approach for AD. One way to achieve this is through exercise, which can improve brain function and protect against neuroinflammation, oxidative stress, and synaptic dysfunction in AD models. The neuroprotective impact of exercise is regulated by various molecular factors that can be activated in the same way as exercise by the administration of their mimetics. Recent evidence has proven some exercise mimetics effective in alleviating neuroinflammation and AD, and, additionally, they are a helpful alternative option for patients who are unable to perform regular physical exercise to manage neurodegenerative disorders. This review focuses on the current state of knowledge on exercise mimetics, including their efficacy, regulatory mechanisms, progress, challenges, limitations, and future guidance for their application in AD therapy.
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Affiliation(s)
- Renqing Zhao
- College of Physical Education, Yangzhou University, Yangzhou, China.
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8
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Iskusnykh IY, Zakharova AA, Kryl’skii ED, Popova TN. Aging, Neurodegenerative Disorders, and Cerebellum. Int J Mol Sci 2024; 25:1018. [PMID: 38256091 PMCID: PMC10815822 DOI: 10.3390/ijms25021018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
An important part of the central nervous system (CNS), the cerebellum is involved in motor control, learning, reflex adaptation, and cognition. Diminished cerebellar function results in the motor and cognitive impairment observed in patients with neurodegenerative disorders such as Alzheimer's disease (AD), vascular dementia (VD), Parkinson's disease (PD), Huntington's disease (HD), spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS), Friedreich's ataxia (FRDA), and multiple sclerosis (MS), and even during the normal aging process. In most neurodegenerative disorders, impairment mainly occurs as a result of morphological changes over time, although during the early stages of some disorders such as AD, the cerebellum also serves a compensatory function. Biological aging is accompanied by changes in cerebellar circuits, which are predominantly involved in motor control. Despite decades of research, the functional contributions of the cerebellum and the underlying molecular mechanisms in aging and neurodegenerative disorders remain largely unknown. Therefore, this review will highlight the molecular and cellular events in the cerebellum that are disrupted during the process of aging and the development of neurodegenerative disorders. We believe that deeper insights into the pathophysiological mechanisms of the cerebellum during aging and the development of neurodegenerative disorders will be essential for the design of new effective strategies for neuroprotection and the alleviation of some neurodegenerative disorders.
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Affiliation(s)
- Igor Y. Iskusnykh
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Anastasia A. Zakharova
- Department of Medical Biochemistry, Faculty of Biomedicine, Pirogov Russian National Research Medical University, Ostrovitianov St. 1, Moscow 117997, Russia
| | - Evgenii D. Kryl’skii
- Department of Medical Biochemistry, Molecular and Cell Biology, Voronezh State University, Universitetskaya Sq. 1, Voronezh 394018, Russia; (E.D.K.)
| | - Tatyana N. Popova
- Department of Medical Biochemistry, Molecular and Cell Biology, Voronezh State University, Universitetskaya Sq. 1, Voronezh 394018, Russia; (E.D.K.)
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9
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Reho P, Saez-Atienzar S, Ruffo P, Solaiman S, Shah Z, Chia R, Kaivola K, Traynor BJ, Tilley BS, Gentleman SM, Hodges AK, Aarsland D, Monuki ES, Newell KL, Woltjer R, Albert MS, Dawson TM, Rosenthal LS, Troncoso JC, Pletnikova O, Serrano GE, Beach TG, Easwaran HP, Scholz SW. Differential methylation analysis in neuropathologically confirmed dementia with Lewy bodies. Commun Biol 2024; 7:35. [PMID: 38182665 PMCID: PMC10770032 DOI: 10.1038/s42003-023-05725-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024] Open
Abstract
Dementia with Lewy bodies (DLB) is a common form of dementia in the elderly population. We performed genome-wide DNA methylation mapping of cerebellar tissue from pathologically confirmed DLB cases and controls to study the epigenetic profile of this understudied disease. After quality control filtering, 728,197 CpG-sites in 278 cases and 172 controls were available for the analysis. We undertook an epigenome-wide association study, which found a differential methylation signature in DLB cases. Our analysis identified seven differentially methylated probes and three regions associated with DLB. The most significant CpGs were located in ARSB (cg16086807), LINC00173 (cg18800161), and MGRN1 (cg16250093). Functional enrichment evaluations found widespread epigenetic dysregulation in genes associated with neuron-to-neuron synapse, postsynaptic specialization, postsynaptic density, and CTCF-mediated synaptic plasticity. In conclusion, our study highlights the potential importance of epigenetic alterations in the pathogenesis of DLB and provides insights into the modified genes, regions and pathways that may guide therapeutic developments.
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Affiliation(s)
- Paolo Reho
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Laboratory of Precision Environmental Health, Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Sara Saez-Atienzar
- Neuromuscular Diseases Research Section, National Institute on Aging, Bethesda, MD, USA
| | - Paola Ruffo
- Neuromuscular Diseases Research Section, National Institute on Aging, Bethesda, MD, USA
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Sultana Solaiman
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Zalak Shah
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Ruth Chia
- Neuromuscular Diseases Research Section, National Institute on Aging, Bethesda, MD, USA
| | - Karri Kaivola
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Bryan J Traynor
- Neuromuscular Diseases Research Section, National Institute on Aging, Bethesda, MD, USA
| | - Bension S Tilley
- Neuropathology Unit, Department of Brain Sciences, Imperial College London, London, UK
| | - Steve M Gentleman
- Neuropathology Unit, Department of Brain Sciences, Imperial College London, London, UK
| | - Angela K Hodges
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Dag Aarsland
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Centre for Age-Related Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Edwin S Monuki
- Department of Pathology & Laboratory Medicine, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Kathy L Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Randy Woltjer
- Department of Neurology, Oregon Health & Sciences University, Portland, OR, USA
| | - Marilyn S Albert
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Ted M Dawson
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Neuroregeneration and Stem Cell Programs, Institute of Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Liana S Rosenthal
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Juan C Troncoso
- Department of Pathology (Neuropathology), Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Olga Pletnikova
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Geidy E Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Thomas G Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Hariharan P Easwaran
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA.
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10
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Ndukwe K, Serrano PA, Rockwell P, Xie L, Figueiredo-Pereira M. Histone deacetylase inhibitor RG2833 has therapeutic potential for Alzheimer's disease in females. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.26.573348. [PMID: 38234827 PMCID: PMC10793399 DOI: 10.1101/2023.12.26.573348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Nearly two-thirds of patients with Alzheimer's are women. Identifying therapeutics specific for women is critical to lowering their elevated risk for developing this major cause of adult dementia. Moreover, targeting epigenetic processes that regulate multiple cellular pathways is advantageous given Alzheimer's multifactorial nature. Histone acetylation is an epigenetic process heavily involved in memory consolidation. Its disruption is linked to Alzheimer's. Through our computational studies, we predicted that the investigational drug RG2833 (N-[6-(2-aminoanilino)-6-oxohexyl]-4-methylbenzamide) has repurposing potential for Alzheimer's. RG2833 is a histone deacetylase HDAC1/3 inhibitor that is orally bioavailable and permeates the blood-brain-barrier. We investigated the RG2833 therapeutic potential in TgF344-AD rats, which are a model of Alzheimer's that exhibits age-dependent progression, thus mimicking this aspect of Alzheimer's patients that is difficult to establish in animal models. We investigated the RG2833 effects on cognitive performance, gene expression, and AD-like pathology in 11-month TgF344-AD female and male rats. A total of 89 rats were used: wild type n = 45 (17 females, 28 males), and TgF344-AD n = 44 (24 females, 20 males)] across multiple cohorts. No obvious toxicity was detected in the TgF344-AD rats up to 6 months of RG2833-treatment starting at 5 months of age administering the drug in rodent chow at ∼30mg/kg of body weight. We started treatment early in the course of pathology when therapeutic intervention is predicted to be more effective than in later stages of the disease. The drug-treatment significantly mitigated hippocampal-dependent spatial memory deficits in 11-month TgF344-AD females but not in males, compared to wild type littermates. This female sex-specific drug effect has not been previously reported. RG2833-treatment failed to ameliorate amyloid beta accumulation and microgliosis in female and male TgF344-AD rats. However, RNAseq analysis of hippocampal tissue from TgF344-AD rats showed that drug-treatment in females upregulated the expression of immediate early genes, such as Arc, Egr1 and c-Fos, and other genes involved in synaptic plasticity and memory consolidation. Remarkably, out of 17,168 genes analyzed for each sex, no significant changes in gene expression were detected in males at P < 0.05, false discovery rate < 0.05, and fold-change ≥ 1.5. Our data suggest that histone modifying therapeutics such as RG2833 improve cognitive behavior by modulating the expression of immediate early, neuroprotective and synaptic plasticity genes. Our preclinical study supports that RG2833 has therapeutic potential specifically for female Alzheimer's patients. RG2833 evaluations using other AD-related models is necessary to confirm our findings.
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11
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Kalyakulina A, Yusipov I, Kondakova E, Bacalini MG, Giuliani C, Sivtseva T, Semenov S, Ksenofontov A, Nikolaeva M, Khusnutdinova E, Zakharova R, Vedunova M, Franceschi C, Ivanchenko M. Epigenetics of the far northern Yakutian population. Clin Epigenetics 2023; 15:189. [PMID: 38053163 PMCID: PMC10699032 DOI: 10.1186/s13148-023-01600-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/13/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Yakuts are one of the indigenous populations of the subarctic and arctic territories of Siberia characterized by a continental subarctic climate with severe winters, with the regular January average temperature in the regional capital city of Yakutsk dipping below - 40 °C. The epigenetic mechanisms of adaptation to such ecologies and environments and, in particular, epigenetic age acceleration in the local population have not been studied before. RESULTS This work reports the first epigenetic study of the Yakutian population using whole-blood DNA methylation data, supplemented with the comparison to the residents of Central Russia. Gene set enrichment analysis revealed, among others, geographic region-specific differentially methylated regions associated with adaptation to climatic conditions (water consumption, digestive system regulation), aging processes (actin filament activity, cell fate), and both of them (channel activity, regulation of steroid and corticosteroid hormone secretion). Further, it is demonstrated that the epigenetic age acceleration of the Yakutian representatives is significantly higher than that of Central Russia counterparts. For both geographic regions, we showed that epigenetically males age faster than females, whereas no significant sex differences were found between the regions. CONCLUSIONS We performed the first study of the epigenetic data of the Yakutia cohort, paying special attention to region-specific features, aging processes, age acceleration, and sex specificity.
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Affiliation(s)
- Alena Kalyakulina
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia.
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia.
| | - Igor Yusipov
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Elena Kondakova
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | | | - Cristina Giuliani
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126, Bologna, Italy
| | - Tatiana Sivtseva
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Sergey Semenov
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Artem Ksenofontov
- State Budgetary Institution of the Republic of Sakha (Yakutia) Republican Center for Public Health and Medical Prevention, Yakutsk, 677001, Russia
| | - Maria Nikolaeva
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia, 450054
| | - Raisa Zakharova
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Maria Vedunova
- Institute of Biology and Biomedicine, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
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12
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Lukkahatai N, Park J, Jia HM, Martin D, Li J, Sheng JYS, Gill J, Saligan LN, Stearns V, Carducci M. Feasibility of DNA Methylation Age as a Biomarker of Symptoms and Resilience among Cancer Survivors with Multiple Chronic Conditions. Biomedicines 2023; 11:3076. [PMID: 38002076 PMCID: PMC10669866 DOI: 10.3390/biomedicines11113076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
This study aims to examine the feasibility of DNA methylation age as a biomarker for symptoms and resilience in cancer survivors with multiple chronic conditions (MCCs). We included ten participants from our parent study, an ongoing randomized control trial study. Participants' symptoms and resilience were assessed, and peripheral blood was collected. DNA methylation age calculation was performed using DNAge® analysis. Data were analyzed using Spearman's correlation analysis and the Mann-Whitney U test. Participants in the intervention group tended to have a decrease in DNA methylation age and age acceleration after completing an exercise program (mean difference = -0.83 ± 1.26). The change in DNA methylation age was significantly correlated with the change in resilience score (r = -0.897, p = 0.015). The preliminary results suggest that DNA methylation age can be a potential biomarker for improving resilience in cancer survivors with multiple chronic conditions. This finding is limited by the small sample size, and a larger study is needed.
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Affiliation(s)
- Nada Lukkahatai
- School of Nursing, Johns Hopkins University, Baltimore, MD 21205, USA; (D.M.); (J.L.); (J.G.)
| | - Jongmin Park
- College of Nursing, Research Institute of Nursing Science, Pusan National University, Yangsan-si 50612, Republic of Korea;
| | - Hejingzi Monica Jia
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA;
| | - Daniel Martin
- School of Nursing, Johns Hopkins University, Baltimore, MD 21205, USA; (D.M.); (J.L.); (J.G.)
| | - Junxin Li
- School of Nursing, Johns Hopkins University, Baltimore, MD 21205, USA; (D.M.); (J.L.); (J.G.)
| | - Jennifer Yeong-Shin Sheng
- Johns Hopkins School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21205, USA;
| | - Jessica Gill
- School of Nursing, Johns Hopkins University, Baltimore, MD 21205, USA; (D.M.); (J.L.); (J.G.)
| | - Leorey N. Saligan
- National Institute of Nursing Research, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Vered Stearns
- School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA (M.C.)
| | - Michael Carducci
- School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA (M.C.)
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13
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Almaguer J, Hindle A, Lawrence JJ. The Contribution of Hippocampal All-Trans Retinoic Acid (ATRA) Deficiency to Alzheimer's Disease: A Narrative Overview of ATRA-Dependent Gene Expression in Post-Mortem Hippocampal Tissue. Antioxidants (Basel) 2023; 12:1921. [PMID: 38001775 PMCID: PMC10669734 DOI: 10.3390/antiox12111921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 11/26/2023] Open
Abstract
There is accumulating evidence that vitamin A (VA) deficiency contributes to the pathogenesis and progression of Alzheimer's disease (AD). All-trans retinoic acid (ATRA), a metabolite of VA in the brain, serves distinct roles in the human hippocampus. Agonists of retinoic acid receptors (RAR), including ATRA, promote activation of the non-amyloidogenic pathway by enhancing expression of α-secretases, providing a mechanistic basis for delaying/preventing amyloid beta (Aβ) toxicity. However, whether ATRA is actually deficient in the hippocampi of patients with AD is not clear. Here, using a publicly available human transcriptomic dataset, we evaluated the extent to which ATRA-sensitive genes are dysregulated in hippocampal tissue from post-mortem AD brains, relative to age-matched controls. Consistent with ATRA deficiency, we found significant dysregulation of many ATRA-sensitive genes and significant upregulation of RAR co-repressors, supporting the idea of transcriptional repression of ATRA-mediated signaling. Consistent with oxidative stress and neuroinflammation, Nrf2 and NfkB transcripts were upregulated, respectively. Interestingly, transcriptional targets of Nrf2 were not upregulated, accompanied by upregulation of several histone deacetylases. Overall, our investigation of ATRA-sensitive genes in the human hippocampus bolsters the scientific premise of ATRA depletion in AD and that epigenetic factors should be considered and addressed as part of VA supplementation.
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Affiliation(s)
- Joey Almaguer
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA;
| | - Ashly Hindle
- Department of Pharmacology and Neuroscience and Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA;
| | - J. Josh Lawrence
- Department of Pharmacology and Neuroscience, Garrison Institute on Aging, Center of Excellence for Translational Neuroscience and Therapeutics, and Center of Excellence for Integrated Health, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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14
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Watanabe R, Nakachi Y, Matsubara H, Ueda J, Ishii T, Ukai W, Hashimoto E, Kasai K, Simizu S, Kato T, Bundo M, Iwamoto K. Identification of epigenetically active L1 promoters in the human brain and their relationship with psychiatric disorders. Neurosci Res 2023; 195:37-51. [PMID: 37141946 DOI: 10.1016/j.neures.2023.05.001] [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: 02/02/2023] [Revised: 04/09/2023] [Accepted: 05/01/2023] [Indexed: 05/06/2023]
Abstract
Long interspersed nuclear element-1 (LINE-1, L1) affects the transcriptome landscape in multiple ways. Promoter activity within its 5'UTR plays a critical role in regulating diverse L1 activities. However, the epigenetic status of L1 promoters in adult brain cells and their relationship with psychiatric disorders remain poorly understood. Here, we examined DNA methylation and hydroxymethylation of the full-length L1s in neurons and nonneurons and identified "epigenetically active" L1s. Notably, some of epigenetically active L1s were retrotransposition competent, which even had chimeric transcripts from the antisense promoters at their 5'UTRs. We also identified differentially methylated L1s in the prefrontal cortices of patients with psychiatric disorders. In nonneurons of bipolar disorder patients, one L1 was significantly hypomethylated and showed an inverse correlation with the expression level of the overlapping gene NREP. Finally, we observed that altered DNA methylation levels of L1 in patients with psychiatric disorders were not affected by the surrounding genomic regions but originated from the L1 sequences. These results suggested that altered epigenetic regulation of the L1 5'UTR in the brain was involved in the pathophysiology of psychiatric disorders.
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Affiliation(s)
- Risa Watanabe
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yutaka Nakachi
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hikari Matsubara
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Junko Ueda
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Takao Ishii
- Department of Occupational Therapy, Sapporo Medical University School of Health Sciences, Sapporo, Japan
| | - Wataru Ukai
- Department of Neuropsychiatry, Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - Eri Hashimoto
- Department of Neuropsychiatry, Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; The International Research Center for Neurointelligence (WPI-IRCN), University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, Tokyo, Japan; University of Tokyo Institute for Diversity and Adaptation of Human Mind (UTIDAHM), The University of Tokyo, Tokyo, Japan; UTokyo Center for Integrative Science of Human Behaviour (CiSHuB), The University of Tokyo, Tokyo, Japan
| | - Siro Simizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Tadafumi Kato
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan; Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Miki Bundo
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan; Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Saitama, Japan.
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan; Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Saitama, Japan.
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15
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Jeremic D, Jiménez-Díaz L, Navarro-López JD. Targeting epigenetics: A novel promise for Alzheimer's disease treatment. Ageing Res Rev 2023; 90:102003. [PMID: 37422087 DOI: 10.1016/j.arr.2023.102003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/30/2023] [Accepted: 07/03/2023] [Indexed: 07/10/2023]
Abstract
So far, the search for a cure for Alzheimer Disease (AD) has been unsuccessful. The only approved drugs attenuate some symptoms, but do not halt the progress of this disease, which affects 50 million people worldwide and will increase its incidence in the coming decades. Such scenario demands new therapeutic approaches to fight against this devastating dementia. In recent years, multi-omics research and the analysis of differential epigenetic marks in AD subjects have contributed to our understanding of AD; however, the impact of epigenetic research is yet to be seen. This review integrates the most recent data on pathological processes and epigenetic changes relevant for aging and AD, as well as current therapies targeting epigenetic machinery in clinical trials. Evidence shows that epigenetic modifications play a key role in gene expression, which could provide multi-target preventative and therapeutic approaches in AD. Both novel and repurposed drugs are employed in AD clinical trials due to their epigenetic effects, as well as increasing number of natural compounds. Given the reversible nature of epigenetic modifications and the complexity of gene-environment interactions, the combination of epigenetic-based therapies with environmental strategies and drugs with multiple targets might be needed to properly help AD patients.
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Affiliation(s)
- Danko Jeremic
- University of Castilla-La Mancha, NeuroPhysiology & Behavior Lab, Biomedical Research Center (CRIB), School of Medicine of Ciudad Real, Spain
| | - Lydia Jiménez-Díaz
- University of Castilla-La Mancha, NeuroPhysiology & Behavior Lab, Biomedical Research Center (CRIB), School of Medicine of Ciudad Real, Spain.
| | - Juan D Navarro-López
- University of Castilla-La Mancha, NeuroPhysiology & Behavior Lab, Biomedical Research Center (CRIB), School of Medicine of Ciudad Real, Spain.
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16
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Armstrong MJ, Jin Y, Vattathil SM, Huang Y, Schroeder JP, Bennet DA, Qin ZS, Wingo TS, Jin P. Role of TET1-mediated epigenetic modulation in Alzheimer's disease. Neurobiol Dis 2023; 185:106257. [PMID: 37562656 PMCID: PMC10530206 DOI: 10.1016/j.nbd.2023.106257] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/30/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder influenced by a complex interplay of environmental, epigenetic, and genetic factors. DNA methylation (5mC) and hydroxymethylation (5hmC) are DNA modifications that serve as tissue-specific and temporal regulators of gene expression. TET family enzymes dynamically regulate these epigenetic modifications in response to environmental conditions, connecting environmental factors with gene expression. Previous epigenetic studies have identified 5mC and 5hmC changes associated with AD. In this study, we performed targeted resequencing of TET1 on a cohort of early-onset AD (EOAD) and control samples. Through gene-wise burden analysis, we observed significant enrichment of rare TET1 variants associated with AD (p = 0.04). We also profiled 5hmC in human postmortem brain tissues from AD and control groups. Our analysis identified differentially hydroxymethylated regions (DhMRs) in key genes responsible for regulating the methylome: TET3, DNMT3L, DNMT3A, and MECP2. To further investigate the role of Tet1 in AD pathogenesis, we used the 5xFAD mouse model with a Tet1 KO allele to examine how Tet1 loss influences AD pathogenesis. We observed significant changes in neuropathology, 5hmC, and RNA expression associated with Tet1 loss, while the behavioral alterations were not significant. The loss of Tet1 significantly increased amyloid plaque burden in the 5xFAD mouse (p = 0.044) and lead to a non-significant trend towards exacerbated AD-associated stress response in 5xFAD mice. At the molecular level, we found significant DhMRs enriched in genes involved in pathways responsible for neuronal projection organization, dendritic spine development and organization, and myelin assembly. RNA-Seq analysis revealed a significant increase in the expression of AD-associated genes such as Mpeg1, Ctsd, and Trem2. In conclusion, our results suggest that TET enzymes, particularly TET1, which regulate the methylome, may contribute to AD pathogenesis, as the loss of TET function increases AD-associated pathology.
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Affiliation(s)
- Matthew J Armstrong
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yulin Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Selina M Vattathil
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yanting Huang
- Department of Computer Science, Emory University, Atlanta, GA 30322, USA
| | - Jason P Schroeder
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - David A Bennet
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Zhaohui S Qin
- Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health, Atlanta, GA 30322, USA
| | - Thomas S Wingo
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
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17
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Abdolmaleky HM, Zhou JR. Underlying Mechanisms of Brain Aging and Neurodegenerative Diseases as Potential Targets for Preventive or Therapeutic Strategies Using Phytochemicals. Nutrients 2023; 15:3456. [PMID: 37571393 PMCID: PMC10473240 DOI: 10.3390/nu15153456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
During aging, several tissues and biological systems undergo a progressive decline in function, leading to age-associated diseases such as neurodegenerative, inflammatory, metabolic, and cardiovascular diseases and cancer. In this review, we focus on the molecular underpinning of senescence and neurodegeneration related to age-associated brain diseases, in particular, Alzheimer's and Parkinson's diseases, along with introducing nutrients or phytochemicals that modulate age-associated molecular dysfunctions, potentially offering preventive or therapeutic benefits. Based on current knowledge, the dysregulation of microglia genes and neuroinflammation, telomere attrition, neuronal stem cell degradation, vascular system dysfunction, reactive oxygen species, loss of chromosome X inactivation in females, and gut microbiome dysbiosis have been seen to play pivotal roles in neurodegeneration in an interactive manner. There are several phytochemicals (e.g., curcumin, EGCG, fucoidan, galangin, astin C, apigenin, resveratrol, phytic acid, acacetin, daucosterol, silibinin, sulforaphane, withaferin A, and betulinic acid) that modulate the dysfunction of one or several key genes (e.g., TREM2, C3, C3aR1, TNFA, NF-kb, TGFB1&2, SIRT1&6, HMGB1, and STING) affected in the aged brain. Although phytochemicals have shown promise in slowing down the progression of age-related brain diseases, more studies to identify their efficacy, alone or in combinations, in preclinical systems can help to design novel nutritional strategies for the management of neurodegenerative diseases in humans.
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Affiliation(s)
| | - Jin-Rong Zhou
- Nutrition/Metabolism Laboratory, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA;
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18
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O'Connor LM, O'Connor BA, Lim SB, Zeng J, Lo CH. Integrative multi-omics and systems bioinformatics in translational neuroscience: A data mining perspective. J Pharm Anal 2023; 13:836-850. [PMID: 37719197 PMCID: PMC10499660 DOI: 10.1016/j.jpha.2023.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 09/19/2023] Open
Abstract
Bioinformatic analysis of large and complex omics datasets has become increasingly useful in modern day biology by providing a great depth of information, with its application to neuroscience termed neuroinformatics. Data mining of omics datasets has enabled the generation of new hypotheses based on differentially regulated biological molecules associated with disease mechanisms, which can be tested experimentally for improved diagnostic and therapeutic targeting of neurodegenerative diseases. Importantly, integrating multi-omics data using a systems bioinformatics approach will advance the understanding of the layered and interactive network of biological regulation that exchanges systemic knowledge to facilitate the development of a comprehensive human brain profile. In this review, we first summarize data mining studies utilizing datasets from the individual type of omics analysis, including epigenetics/epigenomics, transcriptomics, proteomics, metabolomics, lipidomics, and spatial omics, pertaining to Alzheimer's disease, Parkinson's disease, and multiple sclerosis. We then discuss multi-omics integration approaches, including independent biological integration and unsupervised integration methods, for more intuitive and informative interpretation of the biological data obtained across different omics layers. We further assess studies that integrate multi-omics in data mining which provide convoluted biological insights and offer proof-of-concept proposition towards systems bioinformatics in the reconstruction of brain networks. Finally, we recommend a combination of high dimensional bioinformatics analysis with experimental validation to achieve translational neuroscience applications including biomarker discovery, therapeutic development, and elucidation of disease mechanisms. We conclude by providing future perspectives and opportunities in applying integrative multi-omics and systems bioinformatics to achieve precision phenotyping of neurodegenerative diseases and towards personalized medicine.
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Affiliation(s)
- Lance M. O'Connor
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Blake A. O'Connor
- School of Pharmacy, University of Wisconsin, Madison, WI, 53705, USA
| | - Su Bin Lim
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499, South Korea
| | - Jialiu Zeng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Chih Hung Lo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
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19
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Vijay Kumar MJ, Morales R, Tsvetkov AS. G-quadruplexes and associated proteins in aging and Alzheimer's disease. FRONTIERS IN AGING 2023; 4:1164057. [PMID: 37323535 PMCID: PMC10267416 DOI: 10.3389/fragi.2023.1164057] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
Aging is a prominent risk factor for many neurodegenerative disorders, such as Alzheimer's disease (AD). Alzheimer's disease is characterized by progressive cognitive decline, memory loss, and neuropsychiatric and behavioral symptoms, accounting for most of the reported dementia cases. This disease is now becoming a major challenge and burden on modern society, especially with the aging population. Over the last few decades, a significant understanding of the pathophysiology of AD has been gained by studying amyloid deposition, hyperphosphorylated tau, synaptic dysfunction, oxidative stress, calcium dysregulation, and neuroinflammation. This review focuses on the role of non-canonical secondary structures of DNA/RNA G-quadruplexes (G4s, G4-DNA, and G4-RNA), G4-binding proteins (G4BPs), and helicases, and their roles in aging and AD. Being critically important for cellular function, G4s are involved in the regulation of DNA and RNA processes, such as replication, transcription, translation, RNA localization, and degradation. Recent studies have also highlighted G4-DNA's roles in inducing DNA double-strand breaks that cause genomic instability and G4-RNA's participation in regulating stress granule formation. This review emphasizes the significance of G4s in aging processes and how their homeostatic imbalance may contribute to the pathophysiology of AD.
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Affiliation(s)
- M. J. Vijay Kumar
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
| | - Rodrigo Morales
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- Centro Integrativo de Biologia y Quimica Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Andrey S. Tsvetkov
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
- UTHealth Consortium on Aging, The University of Texas McGovern Medical School, Houston, TX, United States
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20
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Sommerer Y, Dobricic V, Schilling M, Ohlei O, Sabet SS, Wesse T, Fuß J, Franzenburg S, Franke A, Parkkinen L, Lill CM, Bertram L. Entorhinal cortex epigenome-wide association study highlights four novel loci showing differential methylation in Alzheimer's disease. Alzheimers Res Ther 2023; 15:92. [PMID: 37149695 PMCID: PMC10163801 DOI: 10.1186/s13195-023-01232-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/15/2023] [Indexed: 05/08/2023]
Abstract
BACKGROUND Studies on DNA methylation (DNAm) in Alzheimer's disease (AD) have recently highlighted several genomic loci showing association with disease onset and progression. METHODS Here, we conducted an epigenome-wide association study (EWAS) using DNAm profiles in entorhinal cortex (EC) from 149 AD patients and control brains and combined these with two previously published EC datasets by meta-analysis (total n = 337). RESULTS We identified 12 cytosine-phosphate-guanine (CpG) sites showing epigenome-wide significant association with either case-control status or Braak's tau-staging. Four of these CpGs, located in proximity to CNFN/LIPE, TENT5A, PALD1/PRF1, and DIRAS1, represent novel findings. Integrating DNAm levels with RNA sequencing-based mRNA expression data generated in the same individuals showed significant DNAm-mRNA correlations for 6 of the 12 significant CpGs. Lastly, by calculating rates of epigenetic age acceleration using two recently proposed "epigenetic clock" estimators we found a significant association with accelerated epigenetic aging in the brains of AD patients vs. controls. CONCLUSION In summary, our study represents the hitherto most comprehensive EWAS in AD using EC and highlights several novel differentially methylated loci with potential effects on gene expression.
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Affiliation(s)
- Yasmine Sommerer
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, Haus V50, 1St Floor, Room 319, 23562, Lübeck, Germany
| | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, Haus V50, 1St Floor, Room 319, 23562, Lübeck, Germany
| | - Marcel Schilling
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, Haus V50, 1St Floor, Room 319, 23562, Lübeck, Germany
| | - Olena Ohlei
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, Haus V50, 1St Floor, Room 319, 23562, Lübeck, Germany
| | - Sanaz Sedghpour Sabet
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Tanja Wesse
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Janina Fuß
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Sören Franzenburg
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Laura Parkkinen
- Nuffield Department of Clinical Neurosciences, Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
| | - Christina M Lill
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, Haus V50, 1St Floor, Room 319, 23562, Lübeck, Germany
- Ageing Epidemiology Unit (AGE), School of Public Health, Imperial College London, London, UK
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Lübeck, Ratzeburger Allee 160, Haus V50, 1St Floor, Room 319, 23562, Lübeck, Germany.
- Center for Lifespan Changes in Brain and Cognition (LCBC), Department of Psychology, University of Oslo, Oslo, Norway.
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21
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Fingelkurts AA, Fingelkurts AA. Turning Back the Clock: A Retrospective Single-Blind Study on Brain Age Change in Response to Nutraceuticals Supplementation vs. Lifestyle Modifications. Brain Sci 2023; 13:brainsci13030520. [PMID: 36979330 PMCID: PMC10046544 DOI: 10.3390/brainsci13030520] [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: 02/20/2023] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND There is a growing consensus that chronological age (CA) is not an accurate indicator of the aging process and that biological age (BA) instead is a better measure of an individual's risk of age-related outcomes and a more accurate predictor of mortality than actual CA. In this context, BA measures the "true" age, which is an integrated result of an individual's level of damage accumulation across all levels of biological organization, along with preserved resources. The BA is plastic and depends upon epigenetics. Brain state is an important factor contributing to health- and lifespan. METHODS AND OBJECTIVE Quantitative electroencephalography (qEEG)-derived brain BA (BBA) is a suitable and promising measure of brain aging. In the present study, we aimed to show that BBA can be decelerated or even reversed in humans (N = 89) by using customized programs of nutraceutical compounds or lifestyle changes (mean duration = 13 months). RESULTS We observed that BBA was younger than CA in both groups at the end of the intervention. Furthermore, the BBA of the participants in the nutraceuticals group was 2.83 years younger at the endpoint of the intervention compared with their BBA score at the beginning of the intervention, while the BBA of the participants in the lifestyle group was only 0.02 years younger at the end of the intervention. These results were accompanied by improvements in mental-physical health comorbidities in both groups. The pre-intervention BBA score and the sex of the participants were considered confounding factors and analyzed separately. CONCLUSIONS Overall, the obtained results support the feasibility of the goal of this study and also provide the first robust evidence that halting and reversal of brain aging are possible in humans within a reasonable (practical) timeframe of approximately one year.
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Murthy M, Shireby G, Miki Y, Viré E, Lashley T, Warner TT, Mill J, Bettencourt C. Epigenetic age acceleration is associated with oligodendrocyte proportions in MSA and control brain tissue. Neuropathol Appl Neurobiol 2023; 49:e12872. [PMID: 36542090 PMCID: PMC10107510 DOI: 10.1111/nan.12872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/15/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
AIMS Epigenetic clocks are widely applied as surrogates for biological age in different tissues and/or diseases, including several neurodegenerative diseases. Despite white matter (WM) changes often being observed in neurodegenerative diseases, no study has investigated epigenetic ageing in white matter. METHODS We analysed the performances of two DNA methylation-based clocks, DNAmClockMulti and DNAmClockCortical , in post-mortem WM tissue from multiple subcortical regions and the cerebellum, and in oligodendrocyte-enriched nuclei. We also examined epigenetic ageing in control and multiple system atrophy (MSA) (WM and mixed WM and grey matter), as MSA is a neurodegenerative disease comprising pronounced WM changes and α-synuclein aggregates in oligodendrocytes. RESULTS Estimated DNA methylation (DNAm) ages showed strong correlations with chronological ages, even in WM (e.g., DNAmClockCortical , r = [0.80-0.97], p < 0.05). However, performances and DNAm age estimates differed between clocks and brain regions. DNAmClockMulti significantly underestimated ages in all cohorts except in the MSA prefrontal cortex mixed tissue, whereas DNAmClockCortical tended towards age overestimations. Pronounced age overestimations in the oligodendrocyte-enriched cohorts (e.g., oligodendrocyte-enriched nuclei, p = 6.1 × 10-5 ) suggested that this cell type ages faster. Indeed, significant positive correlations were observed between estimated oligodendrocyte proportions and DNAm age acceleration estimated by DNAmClockCortical (r > 0.31, p < 0.05), and similar trends were obtained with DNAmClockMulti . Although increased age acceleration was observed in MSA compared with controls, no significant differences were detected upon adjustment for possible confounders (e.g., cell-type proportions). CONCLUSIONS Our findings show that oligodendrocyte proportions positively influence epigenetic age acceleration across brain regions and highlight the need to further investigate this in ageing and neurodegeneration.
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Affiliation(s)
- Megha Murthy
- Queen Square Brain Bank, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
- Department of Clinical and Movement NeurosciencesUCL Queen Square Institute of NeurologyLondonUK
| | - Gemma Shireby
- University of Exeter Medical SchoolUniversity of ExeterExeterUK
| | - Yasuo Miki
- Queen Square Brain Bank, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
- Department of Neuropathology, Institute of Brain ScienceHirosaki University Graduate School of MedicineHirosakiJapan
| | - Emmanuelle Viré
- UCL Institute of Prion Diseases, MRC Prion Unit at UCLUniversity College LondonLondonUK
| | - Tammaryn Lashley
- Queen Square Brain Bank, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
- Department of Neurodegenerative Disease, Queen Square Brain Bank for Neurological DisordersUCL Queen Square Institute of Neurology1 Wakefield StreetLondonWC1N 1PJUK
| | - Thomas T. Warner
- Queen Square Brain Bank, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
- Department of Clinical and Movement NeurosciencesUCL Queen Square Institute of NeurologyLondonUK
- Reta Lila Weston InstituteUCL Queen Square Institute of NeurologyLondonUK
| | - Jonathan Mill
- University of Exeter Medical SchoolUniversity of ExeterExeterUK
| | - Conceição Bettencourt
- Queen Square Brain Bank, UCL Queen Square Institute of NeurologyUniversity College LondonLondonUK
- Department of Neurodegenerative Disease, Queen Square Brain Bank for Neurological DisordersUCL Queen Square Institute of Neurology1 Wakefield StreetLondonWC1N 1PJUK
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23
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Shirokova O, Zaborskaya O, Pchelin P, Kozliaeva E, Pershin V, Mukhina I. Genetic and Epigenetic Sexual Dimorphism of Brain Cells during Aging. Brain Sci 2023; 13:brainsci13020195. [PMID: 36831738 PMCID: PMC9954625 DOI: 10.3390/brainsci13020195] [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: 12/22/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
In recent years, much of the attention paid to theoretical and applied biomedicine, as well as neurobiology, has been drawn to various aspects of sexual dimorphism due to the differences that male and female brain cells demonstrate during aging: (a) a dimorphic pattern of response to therapy for neurodegenerative disorders, (b) different age of onset and different degrees of the prevalence of such disorders, and (c) differences in their symptomatic manifestations in men and women. The purpose of this review is to outline the genetic and epigenetic differences in brain cells during aging in males and females. As a result, we hereby show that the presence of brain aging patterns in males and females is due to a complex of factors associated with the effects of sex chromosomes, which subsequently entails a change in signal cascades in somatic cells.
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Affiliation(s)
- Olesya Shirokova
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
- Correspondence:
| | - Olga Zaborskaya
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
| | - Pavel Pchelin
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, 23 Gagarin Avenue, Nizhny Novgorod 603002, Russia
| | - Elizaveta Kozliaeva
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
| | - Vladimir Pershin
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, 23 Gagarin Avenue, Nizhny Novgorod 603002, Russia
| | - Irina Mukhina
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, 23 Gagarin Avenue, Nizhny Novgorod 603002, Russia
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24
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Iannuzzi V, Bacalini MG, Franceschi C, Giuliani C. The role of genetics and epigenetics in sex differences in human survival. GENUS 2023. [DOI: 10.1186/s41118-023-00181-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
AbstractSex differences in human survival have been extensively investigated in many studies that have in part uncovered the biological determinants that promote a longer life in females with respect to males. Moreover, researches performed in the past years have prompted increased awareness about the biological effects of environmental factors that can modulate the magnitude of the sex gap in survival. Besides the genetic background, epigenetic modifications like DNA methylation, that can modulate cell function, have been particularly studied in this framework. In this review, we aim to summarize the role of the genetic and epigenetic mechanisms in promoting female advantage from the early in life (“INNATE” features), and in influencing the magnitude of the gap in sex differences in survival and ageing (“VARIABLE” features). After briefly discussing the biological bases of sex determination in humans, we will provide much evidence showing that (i) “innate” mechanisms common to all males and to all females (both genetic and epigenetic) play a major role in sex differences in lifespan; (ii) “variable” genetic and epigenetic patterns, that vary according to context, populations and exposures to different environments, can affect the magnitude of the gap in sex differences in survival. Then we will describe recent findings in the use of epigenetic clocks to uncover sex differences in biological age and thus potentially in mortality. In conclusion, we will discuss how environmental factors cannot be kept apart from the biological factors providing evidence from the field of human ecology.
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25
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Dynamic Regulation of DNA Methylation and Brain Functions. BIOLOGY 2023; 12:biology12020152. [PMID: 36829430 PMCID: PMC9952911 DOI: 10.3390/biology12020152] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
DNA cytosine methylation is a principal epigenetic mechanism underlying transcription during development and aging. Growing evidence suggests that DNA methylation plays a critical role in brain function, including neurogenesis, neuronal differentiation, synaptogenesis, learning, and memory. However, the mechanisms underlying aberrant DNA methylation in neurodegenerative diseases remain unclear. In this review, we provide an overview of the contribution of 5-methycytosine (5mC) and 5-hydroxylcytosine (5hmC) to brain development and aging, with a focus on the roles of dynamic 5mC and 5hmC changes in the pathogenesis of neurodegenerative diseases, particularly Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD). Identification of aberrant DNA methylation sites could provide potential candidates for epigenetic-based diagnostic and therapeutic strategies for neurodegenerative diseases.
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26
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Kumar R, Fatima F, Yadav G, Singh S, Haldar S, Alexiou A, Ashraf GM. Epigenetic Modifications by Estrogen and Androgen in Alzheimer's Disease. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2023; 22:6-17. [PMID: 35232367 DOI: 10.2174/1871527321666220225110501] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 12/16/2022]
Abstract
For the development and maintenance of neuron networks in the brain, epigenetic mechanisms are necessary, as indicated by recent findings. This includes some of the high-order brain processes, such as behavior and cognitive functions. Epigenetic mechanisms could influence the pathophysiology or etiology of some neuronal diseases, altering disease susceptibility and therapy responses. Recent studies support epigenetic dysfunctions in neurodegenerative and psychiatric conditions, such as Alzheimer's disease (AD). These dysfunctions in epigenetic mechanisms also play crucial roles in the transgenerational effects of the environment on the brain and subsequently in the inheritance of pathologies. The possible role of gonadal steroids in the etiology and progression of neurodegenerative diseases, including Alzheimer's disease, has become the subject of a growing body of research over the last 20 years. Recent scientific findings suggest that epigenetic changes, driven by estrogen and androgens, play a vital role in brain functioning. Therefore, exploring the role of estrogen and androgen-based epigenetic changes in the brain is critical for the deeper understanding of AD. This review highlights the epigenetic modifications caused by these two gonadal steroids and the possible therapeutic strategies for AD.
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Affiliation(s)
- Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Uttar Pradesh, India
| | - Faiza Fatima
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Uttar Pradesh, India
| | - Garima Yadav
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Uttar Pradesh, India
| | - Simran Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Uttar Pradesh, India
| | - Subhagata Haldar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Uttar Pradesh, India
| | - Athanasios Alexiou
- Novel Global Community Educational Foundation, Hebersham, 2770 NSW, Australia, and AFNP Med Austria, 1010 Wien, Austria
| | - Ghulam Md Ashraf
- Pre-Clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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27
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Schäfer Hackenhaar F, Josefsson M, Nordin Adolfsson A, Landfors M, Kauppi K, Porter T, Milicic L, Laws SM, Hultdin M, Adolfsson R, Degerman S, Pudas S. Sixteen-Year Longitudinal Evaluation of Blood-Based DNA Methylation Biomarkers for Early Prediction of Alzheimer's Disease. J Alzheimers Dis 2023; 94:1443-1464. [PMID: 37393498 PMCID: PMC10473121 DOI: 10.3233/jad-230039] [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] [Accepted: 05/30/2023] [Indexed: 07/03/2023]
Abstract
BACKGROUND DNA methylation (DNAm), an epigenetic mark reflecting both inherited and environmental influences, has shown promise for Alzheimer's disease (AD) prediction. OBJECTIVE Testing long-term predictive ability (>15 years) of existing DNAm-based epigenetic age acceleration (EAA) measures and identifying novel early blood-based DNAm AD-prediction biomarkers. METHODS EAA measures calculated from Illumina EPIC data from blood were tested with linear mixed-effects models (LMMs) in a longitudinal case-control sample (50 late-onset AD cases; 51 matched controls) with prospective data up to 16 years before clinical onset, and post-onset follow-up. Novel DNAm biomarkers were generated with epigenome-wide LMMs, and Sparse Partial Least Squares Discriminant Analysis applied at pre- (10-16 years), and post-AD-onset time-points. RESULTS EAA did not differentiate cases from controls during the follow-up time (p > 0.05). Three new DNA biomarkers showed in-sample predictive ability on average 8 years pre-onset, after adjustment for age, sex, and white blood cell proportions (p-values: 0.022-<0.00001). Our longitudinally-derived panel replicated nominally (p = 0.012) in an external cohort (n = 146 cases, 324 controls). However, its effect size and discriminatory accuracy were limited compared to APOEɛ4-carriership (OR = 1.38 per 1 SD DNAm score increase versus OR = 13.58 for ɛ4-allele carriage; AUCs = 77.2% versus 87.0%). Literature review showed low overlap (n = 4) across 3275 AD-associated CpGs from 8 published studies, and no overlap with our identified CpGs.
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Affiliation(s)
- Fernanda Schäfer Hackenhaar
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
- Umeå Center for Functional Brain Imaging, Umeå University, Umeå, Sweden
| | - Maria Josefsson
- Umeå Center for Functional Brain Imaging, Umeå University, Umeå, Sweden
- Department of Statistics, USBE, Umeå University, Umeå, Sweden
- Center for Ageing and Demographic Research, Umeå University, Umeå, Sweden
| | | | - Mattias Landfors
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Karolina Kauppi
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Tenielle Porter
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Lidija Milicic
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Simon M. Laws
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Magnus Hultdin
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Rolf Adolfsson
- Department of Clinical Sciences, Umeå University, Umeå, Sweden
| | - Sofie Degerman
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Sara Pudas
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
- Umeå Center for Functional Brain Imaging, Umeå University, Umeå, Sweden
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28
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Beadell AV, Zhang Z, Capuano AW, Bennett DA, He C, Zhang W, Arvanitakis Z. Genome-Wide Mapping Implicates 5-Hydroxymethylcytosines in Diabetes Mellitus and Alzheimer's Disease. J Alzheimers Dis 2023; 93:1135-1151. [PMID: 37182870 PMCID: PMC10490934 DOI: 10.3233/jad-221113] [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] [Indexed: 05/16/2023]
Abstract
BACKGROUND Diabetes mellitus (DM) is a recognized risk factor for dementia. Because DM is a potentially modifiable condition, greater understanding of the mechanisms linking DM to the clinical expression of Alzheimer's disease dementia may provide insights into much needed dementia therapeutics. OBJECTIVE In this feasibility study, we investigated DM as a dementia risk factor by examining genome-wide distributions of the epigenetic DNA modification 5-hydroxymethylcytosine (5hmC). METHODS We obtained biologic samples from the Rush Memory and Aging Project and used the highly sensitive 5hmC-Seal technique to perform genome-wide profiling of 5hmC in circulating cell-free DNA (cfDNA) from antemortem serum samples and in genomic DNA from postmortem prefrontal cortex brain tissue from 80 individuals across four groups: Alzheimer's disease neuropathologically defined (AD), DM clinically defined, AD with DM, and individuals with neither disease (controls). RESULTS Distinct 5hmC signatures and biological pathways were enriched in persons with both AD and DM versus AD alone, DM alone, or controls, including genes inhibited by EGFR signaling in oligodendroglia and those activated by constitutive RHOA. We also demonstrate the potential diagnostic value of 5hmC profiling in circulating cfDNA. Specifically, an 11-gene weighted model distinguished AD from non-AD/non-DM controls (AUC = 91.8%; 95% CI, 82.9-100.0%), while a 4-gene model distinguished DM-associated AD from AD alone (AUC = 87.9%; 95% CI, 77.5-98.3%). CONCLUSION We demonstrate in this small sample, the feasibility of detecting and characterizing 5hmC in DM-associated AD and of using 5hmC information contained in circulating cfDNA to detect AD in high-risk individuals, such as those with diabetes.
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Affiliation(s)
- Alana V Beadell
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Zhou Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ana W Capuano
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Zoe Arvanitakis
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
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29
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Huntingtin and Other Neurodegeneration-Associated Proteins in the Development of Intracellular Pathologies: Potential Target Search for Therapeutic Intervention. Int J Mol Sci 2022; 23:ijms232415533. [PMID: 36555175 PMCID: PMC9779313 DOI: 10.3390/ijms232415533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Neurodegenerative diseases are currently incurable. Numerous experimental data accumulated over the past fifty years have brought us closer to understanding the molecular and cell mechanisms responsible for their development. However, these data are not enough for a complete understanding of the genesis of these diseases, nor to suggest treatment methods. It turns out that many cellular pathologies developing during neurodegeneration coincide from disease to disease. These observations give hope to finding a common intracellular target(s) and to offering a universal method of treatment. In this review, we attempt to analyze data on similar cellular disorders among neurodegenerative diseases in general, and polyglutamine neurodegenerative diseases in particular, focusing on the interaction of various proteins involved in the development of neurodegenerative diseases with various cellular organelles. The main purposes of this review are: (1) to outline the spectrum of common intracellular pathologies and to answer the question of whether it is possible to find potential universal target(s) for therapeutic intervention; (2) to identify specific intracellular pathologies and to speculate about a possible general approach for their treatment.
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30
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Fišar Z. Linking the Amyloid, Tau, and Mitochondrial Hypotheses of Alzheimer's Disease and Identifying Promising Drug Targets. Biomolecules 2022; 12:1676. [PMID: 36421690 PMCID: PMC9687482 DOI: 10.3390/biom12111676] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/23/2022] [Accepted: 11/09/2022] [Indexed: 08/27/2023] Open
Abstract
Damage or loss of brain cells and impaired neurochemistry, neurogenesis, and synaptic and nonsynaptic plasticity of the brain lead to dementia in neurodegenerative diseases, such as Alzheimer's disease (AD). Injury to synapses and neurons and accumulation of extracellular amyloid plaques and intracellular neurofibrillary tangles are considered the main morphological and neuropathological features of AD. Age, genetic and epigenetic factors, environmental stressors, and lifestyle contribute to the risk of AD onset and progression. These risk factors are associated with structural and functional changes in the brain, leading to cognitive decline. Biomarkers of AD reflect or cause specific changes in brain function, especially changes in pathways associated with neurotransmission, neuroinflammation, bioenergetics, apoptosis, and oxidative and nitrosative stress. Even in the initial stages, AD is associated with Aβ neurotoxicity, mitochondrial dysfunction, and tau neurotoxicity. The integrative amyloid-tau-mitochondrial hypothesis assumes that the primary cause of AD is the neurotoxicity of Aβ oligomers and tau oligomers, mitochondrial dysfunction, and their mutual synergy. For the development of new efficient AD drugs, targeting the elimination of neurotoxicity, mutual potentiation of effects, and unwanted protein interactions of risk factors and biomarkers (mainly Aβ oligomers, tau oligomers, and mitochondrial dysfunction) in the early stage of the disease seems promising.
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Affiliation(s)
- Zdeněk Fišar
- Department of Psychiatry, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 11, 120 00 Prague, Czech Republic
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31
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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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32
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Fernandes V, Preeti K, Sood A, Nair KP, Khan S, Rao BSS, Khatri DK, Singh SB. Neuroepigenetic Changes in DNA Methylation Affecting Diabetes-Induced Cognitive Impairment. Cell Mol Neurobiol 2022:10.1007/s10571-022-01278-5. [PMID: 36138280 DOI: 10.1007/s10571-022-01278-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022]
Abstract
Chronic diabetic conditions have been associated with certain cerebral complications, that include neurobehavioral dysfunctional patterns and morphological alterations of neurons, especially the hippocampus. Neuroanatomical studies done by the authors have shown decreased total dendritic length, intersections, dendritic length per branch order and nodes in the CA1 hippocampal region of the diabetic brain as compared to its normal control group, indicating reduced dendritic arborization of the hippocampal CA1 neurons. Epigenetic alterations in the brain are well known to affect age-associated disorders, however its association with the evolving diabetes-induced damage in the brain is still not fully understood. DNA hypermethylation within the neurons, tend to silent the gene expression of several regulatory proteins. The findings in the study have shown an increase in global DNA methylation in palmitic acid-induced lipotoxic Neuro-2a cells as well as within the diabetic mice brain. Inhibiting DNA methylation, restored the levels of HSF1 and certain HSPs, suggesting plausible effect of DNMTs in maintaining the proteostasis and synaptic fidelity. Neuroinflammation, as exhibited by the astrocyte activation (GFAP), were further significantly decreased in the 5-azadeoxycytidine group (DNMT inhibitor). This was further evidenced by decrease in proinflammatory cytokines TNF⍺, IL-6, and mediators iNOS and Phospho-NFkB. Our results suggest that changes in DNA methylation advocate epigenetic dysregulation and its involvement in disrupting the synaptic exactitude in the hippocampus of diabetic mice model, providing an insight into the pathophysiology of diabetes-induced neuroepigenetic changes.
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Affiliation(s)
- Valencia Fernandes
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Kumari Preeti
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Anika Sood
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - Kala P Nair
- Department of Neurophysiology, National Institute of Mental Health and Neuroscience (NIMHANS), Bengaluru, Karnataka, 560029, India
| | - Sabiya Khan
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India
| | - B S Shankaranarayana Rao
- Department of Neurophysiology, National Institute of Mental Health and Neuroscience (NIMHANS), Bengaluru, Karnataka, 560029, India
| | - Dharmendra Kumar Khatri
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India.
| | - Shashi Bala Singh
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad, Telangana, 500037, India.
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Gonzales MM, Garbarino VR, Pollet E, Palavicini JP, Kellogg DL, Kraig E, Orr ME. Biological aging processes underlying cognitive decline and neurodegenerative disease. J Clin Invest 2022; 132:e158453. [PMID: 35575089 PMCID: PMC9106343 DOI: 10.1172/jci158453] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Alzheimer's disease and related dementias (ADRD) are among the top contributors to disability and mortality in later life. As with many chronic conditions, aging is the single most influential factor in the development of ADRD. Even among older adults who remain free of dementia throughout their lives, cognitive decline and neurodegenerative changes are appreciable with advancing age, suggesting shared pathophysiological mechanisms. In this Review, we provide an overview of changes in cognition, brain morphology, and neuropathological protein accumulation across the lifespan in humans, with complementary and mechanistic evidence from animal models. Next, we highlight selected aging processes that are differentially regulated in neurodegenerative disease, including aberrant autophagy, mitochondrial dysfunction, cellular senescence, epigenetic changes, cerebrovascular dysfunction, inflammation, and lipid dysregulation. We summarize research across clinical and translational studies to link biological aging processes to underlying ADRD pathogenesis. Targeting fundamental processes underlying biological aging may represent a yet relatively unexplored avenue to attenuate both age-related cognitive decline and ADRD. Collaboration across the fields of geroscience and neuroscience, coupled with the development of new translational animal models that more closely align with human disease processes, is necessary to advance novel therapeutic discovery in this realm.
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Affiliation(s)
- Mitzi M. Gonzales
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases
- Department of Neurology
| | | | - Erin Pollet
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases
| | - Juan P. Palavicini
- Barshop Institute for Longevity and Aging Studies, and
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Dean L. Kellogg
- Barshop Institute for Longevity and Aging Studies, and
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
- Geriatric Research and Education Center, South Texas Veterans Health Care System, San Antonio, Texas, USA
| | - Ellen Kraig
- Barshop Institute for Longevity and Aging Studies, and
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Miranda E. Orr
- Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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Seale K, Horvath S, Teschendorff A, Eynon N, Voisin S. Making sense of the ageing methylome. Nat Rev Genet 2022; 23:585-605. [PMID: 35501397 DOI: 10.1038/s41576-022-00477-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2022] [Indexed: 12/22/2022]
Abstract
Over time, the human DNA methylation landscape accrues substantial damage, which has been associated with a broad range of age-related diseases, including cardiovascular disease and cancer. Various age-related DNA methylation changes have been described, including at the level of individual CpGs, such as differential and variable methylation, and at the level of the whole methylome, including entropy and correlation networks. Here, we review these changes in the ageing methylome as well as the statistical tools that can be used to quantify them. We detail the evidence linking DNA methylation to ageing phenotypes and the longevity strategies aimed at altering both DNA methylation patterns and machinery to extend healthspan and lifespan. Lastly, we discuss theories on the mechanistic causes of epigenetic ageing.
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Affiliation(s)
- Kirsten Seale
- Institute for Health and Sport (iHeS), Victoria University, Footscray, Melbourne, Victoria, Australia
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,Altos Labs, San Diego, CA, USA
| | - Andrew Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China.,UCL Cancer Institute, University College London, London, UK
| | - Nir Eynon
- Institute for Health and Sport (iHeS), Victoria University, Footscray, Melbourne, Victoria, Australia.
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University, Footscray, Melbourne, Victoria, Australia.
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Bouvier DS, Fixemer S, Heurtaux T, Jeannelle F, Frauenknecht KBM, Mittelbronn M. The Multifaceted Neurotoxicity of Astrocytes in Ageing and Age-Related Neurodegenerative Diseases: A Translational Perspective. Front Physiol 2022; 13:814889. [PMID: 35370777 PMCID: PMC8969602 DOI: 10.3389/fphys.2022.814889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
In a healthy physiological context, astrocytes are multitasking cells contributing to central nervous system (CNS) homeostasis, defense, and immunity. In cell culture or rodent models of age-related neurodegenerative diseases (NDDs), such as Alzheimer’s disease (AD) and Parkinson’s disease (PD), numerous studies have shown that astrocytes can adopt neurotoxic phenotypes that could enhance disease progression. Chronic inflammatory responses, oxidative stress, unbalanced phagocytosis, or alteration of their core physiological roles are the main manifestations of their detrimental states. However, if astrocytes are directly involved in brain deterioration by exerting neurotoxic functions in patients with NDDs is still controversial. The large spectrum of NDDs, with often overlapping pathologies, and the technical challenges associated with the study of human brain samples complexify the analysis of astrocyte involvement in specific neurodegenerative cascades. With this review, we aim to provide a translational overview about the multi-facets of astrocyte neurotoxicity ranging from in vitro findings over mouse and human cell-based studies to rodent NDDs research and finally evidence from patient-related research. We also discuss the role of ageing in astrocytes encompassing changes in physiology and response to pathologic stimuli and how this may prime detrimental responses in NDDs. To conclude, we discuss how potentially therapeutic strategies could be adopted to alleviate or reverse astrocytic toxicity and their potential to impact neurodegeneration and dementia progression in patients.
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Affiliation(s)
- David S. Bouvier
- National Center of Pathology (NCP), Laboratoire National de Santé (LNS), Dudelange, Luxembourg
- Luxembourg Center of Systems Biomedicine (LCSB), University of Luxembourg (UL), Belvaux, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), Dudelange, Luxembourg
- *Correspondence: David S. Bouvier,
| | - Sonja Fixemer
- Luxembourg Center of Systems Biomedicine (LCSB), University of Luxembourg (UL), Belvaux, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), Dudelange, Luxembourg
| | - Tony Heurtaux
- Luxembourg Center of Neuropathology (LCNP), Dudelange, Luxembourg
- Systems Biology Group, Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Félicia Jeannelle
- National Center of Pathology (NCP), Laboratoire National de Santé (LNS), Dudelange, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), Dudelange, Luxembourg
| | - Katrin B. M. Frauenknecht
- National Center of Pathology (NCP), Laboratoire National de Santé (LNS), Dudelange, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), Dudelange, Luxembourg
- Institute of Neuropathology, Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Michel Mittelbronn
- National Center of Pathology (NCP), Laboratoire National de Santé (LNS), Dudelange, Luxembourg
- Luxembourg Center of Systems Biomedicine (LCSB), University of Luxembourg (UL), Belvaux, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), Dudelange, Luxembourg
- Department of Cancer Research (DOCR), Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
- Faculty of Science, Technology, and Medicine (FSTM), University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Michel Mittelbronn,
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Luo W, Wen H, Ge S, Tang C, Liu X, Lu L. Development of a Sex-Specific Risk Scoring System for the Prediction of Cognitively Normal People to Patients With Mild Cognitive Impairment (SRSS-CNMCI). Front Aging Neurosci 2022; 13:774804. [PMID: 35145390 PMCID: PMC8823413 DOI: 10.3389/fnagi.2021.774804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/15/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE We aimed to develop a sex-specific risk scoring system, abbreviated as SRSS-CNMCI, for the prediction of the conversion of cognitively normal (CN) people into patients with Mild Cognitive Impairment (MCI) to provide a reliable tool for the prevention of MCI. METHODS CN at baseline participants 61-90 years of age were selected from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database with at least one follow-up. Multivariable Cox proportional hazards models were used to identify the major risk factors associated with the conversion from CN to MCI and to develop the SRSS-CNMCI. Receiver operating characteristic (ROC) curve analysis was used to determine risk cutoff points corresponding to an optimal prediction. The results were externally validated, including evaluation of the discrimination and calibration in the Harvard Aging Brain Study (HABS) database. RESULTS A total of 471 participants, including 240 female (51%) and 231 male participants (49%) aged from 61 to 90 years, were included in the study cohort. The final multivariable models and the SRSS-CNMCI included age, APOE e4, mini mental state examination (MMSE) and clinical dementia rating (CDR). The C-statistics of the SRSS-CNMCI were 0.902 in the female subgroup and 0.911 in the male subgroup. The cutoff point of high and low risks was 33% in the female subgroup, indicating that more than 33% female participants were considered to have a high risk, and more than 9% participants were considered to have a high risk in the male subgroup. The SRSS-CNMCI performed well in the external cohort: the C-statistics were 0.950 in the female subgroup and 0.965 in the male subgroup. CONCLUSION The SRSS-CNMCI performs well in various cohorts and provides an accurate prediction and a generalization.
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Affiliation(s)
- Wen Luo
- School of Medical Information Engineering, Guangzhou University of Chinese Medicine, Guangzhou, China
- Evidence-Based Medicine and Data Science Centre, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hao Wen
- Department of Neurology, The Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shuqi Ge
- Evidence-Based Medicine and Data Science Centre, Guangzhou University of Chinese Medicine, Guangzhou, China
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Chunzhi Tang
- Evidence-Based Medicine and Data Science Centre, Guangzhou University of Chinese Medicine, Guangzhou, China
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiufeng Liu
- School of Medical Information Engineering, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Liming Lu
- Evidence-Based Medicine and Data Science Centre, Guangzhou University of Chinese Medicine, Guangzhou, China
- South China Research Center for Acupuncture and Moxibustion, Medical College of Acu-Moxi and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
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Zimmer-Bensch G, Zempel H. DNA Methylation in Genetic and Sporadic Forms of Neurodegeneration: Lessons from Alzheimer's, Related Tauopathies and Genetic Tauopathies. Cells 2021; 10:3064. [PMID: 34831288 PMCID: PMC8624300 DOI: 10.3390/cells10113064] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 12/14/2022] Open
Abstract
Genetic and sporadic forms of tauopathies, the most prevalent of which is Alzheimer's Disease, are a scourge of the aging society, and in the case of genetic forms, can also affect children and young adults. All tauopathies share ectopic expression, mislocalization, or aggregation of the microtubule associated protein TAU, encoded by the MAPT gene. As TAU is a neuronal protein widely expressed in the CNS, the overwhelming majority of tauopathies are neurological disorders. They are characterized by cognitive dysfunction often leading to dementia, and are frequently accompanied by movement abnormalities such as parkinsonism. Tauopathies can lead to severe neurological deficits and premature death. For some tauopathies there is a clear genetic cause and/or an epigenetic contribution. However, for several others the disease etiology is unclear, with few tauopathies being environmentally triggered. Here, we review current knowledge of tauopathies listing known genetic and important sporadic forms of these disease. Further, we discuss how DNA methylation as a major epigenetic mechanism emerges to be involved in the disease pathophysiology of Alzheimer's, and related genetic and non-genetic tauopathies. Finally, we debate the application of epigenetic signatures in peripheral blood samples as diagnostic tools and usages of epigenetic therapy strategies for these diseases.
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Affiliation(s)
- Geraldine Zimmer-Bensch
- Functional Epigenetics in the Animal Model, Institute for Biology II, RWTH Aachen University, 52074 Aachen, Germany
- Research Training Group 2416 MultiSenses-MultiScales, Institute for Biology II, RWTH Aachen University, 52074 Aachen, Germany
| | - Hans Zempel
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
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Kondakova EV, Vershinina OS, Lopatenko MV, Franceschi C, Ivanchenko MV, Vedunova MV. Sex-Specific Age-Related Changes in Methylation of Certain Genes. Sovrem Tekhnologii Med 2021; 13:26-31. [PMID: 34603752 PMCID: PMC8482819 DOI: 10.17691/stm2021.13.3.03] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Indexed: 11/30/2022] Open
Abstract
The aim of the study was to conduct a functional analysis of sex-specific age-related changes in DNA methylation.
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Affiliation(s)
- E V Kondakova
- Assistant, Department of General and Medical Genetics, Institute of Biology and Biomedicine; National Research Lobachevsky State University of Nizhni Novgorod, 23 Prospekt Gagarina, Nizhny Novgorod, 603950, Russia
| | - O S Vershinina
- Junior Researcher, Department of Applied Mathematics, Institute of Information Technologies, Mathematics and Mechanics; National Research Lobachevsky State University of Nizhni Novgorod, 23 Prospekt Gagarina, Nizhny Novgorod, 603950, Russia
| | - M V Lopatenko
- Student, Institute of Biology and Biomedicine; National Research Lobachevsky State University of Nizhni Novgorod, 23 Prospekt Gagarina, Nizhny Novgorod, 603950, Russia
| | - C Franceschi
- Professor Emeritus, Senior Researcher, Photonics Center, Department of Fundamental and Applied Research; National Research Lobachevsky State University of Nizhni Novgorod, 23 Prospekt Gagarina, Nizhny Novgorod, 603950, Russia; Mater Studiorum; University of Bologna, 33 Via Zamboni, Bologna, 40126, Italy
| | - M V Ivanchenko
- Head of the Department of Applied Mathematics, Institute of Information Technologies, Mathematics and Mechanics; National Research Lobachevsky State University of Nizhni Novgorod, 23 Prospekt Gagarina, Nizhny Novgorod, 603950, Russia
| | - M V Vedunova
- Head of the Department of General and Medical Genetics, Institute of Biology and Biomedicine; National Research Lobachevsky State University of Nizhni Novgorod, 23 Prospekt Gagarina, Nizhny Novgorod, 603950, Russia; Director of the Institute of Biology and Biomedicine; National Research Lobachevsky State University of Nizhni Novgorod, 23 Prospekt Gagarina, Nizhny Novgorod, 603950, Russia
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Hägg S, Jylhävä J. Sex differences in biological aging with a focus on human studies. eLife 2021; 10:e63425. [PMID: 33982659 PMCID: PMC8118651 DOI: 10.7554/elife.63425] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 05/04/2021] [Indexed: 02/06/2023] Open
Abstract
Aging is a complex biological process characterized by hallmark features accumulating over the life course, shaping the individual's aging trajectory and subsequent disease risks. There is substantial individual variability in the aging process between men and women. In general, women live longer than men, consistent with lower biological ages as assessed by molecular biomarkers, but there is a paradox. Women are frailer and have worse health at the end of life, while men still perform better in physical function examinations. Moreover, many age-related diseases show sex-specific patterns. In this review, we aim to summarize the current knowledge on sexual dimorphism in human studies, with support from animal research, on biological aging and illnesses. We also attempt to place it in the context of the theories of aging, as well as discuss the explanations for the sex differences, for example, the sex-chromosome linked mechanisms and hormonally driven differences.
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Affiliation(s)
- Sara Hägg
- Department of Medical Epidemiology and Biostatistics, Karolinska InstitutetStockholmSweden
| | - Juulia Jylhävä
- Department of Medical Epidemiology and Biostatistics, Karolinska InstitutetStockholmSweden
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