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Pyka P, Garbo S, Fioravanti R, Jacob C, Hittinger M, Handzlik J, Zwergel C, Battistelli C. Selenium-containing compounds: a new hope for innovative treatments in Alzheimer's disease and Parkinson's disease. Drug Discov Today 2024; 29:104062. [PMID: 38871111 DOI: 10.1016/j.drudis.2024.104062] [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: 01/31/2024] [Revised: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
Neurodegenerative diseases are challenging to cure. To date, no cure has been found for Alzheimer's disease or Parkinson's disease, and current treatments are able only to slow the progression of the diseases and manage their symptoms. After an introduction to the complex biology of these diseases, we discuss the beneficial effect of selenium-containing agents, which show neuroprotective effects in vitro or in vivo. Indeed, selenium is an essential trace element that is being incorporated into innovative organoselenium compounds, which can improve outcomes in rodent or even primate models with neurological deficits. Herein, we critically discuss recent findings in the field of selenium-based applications in neurological disorders.
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Affiliation(s)
- Patryk Pyka
- Department of Technology and Biotechnology of Drugs, Jagiellonian University, Medical College, Medyczna 9, 30-688 Krakow, Poland; Doctoral School of Medical and Health Sciences, Jagiellonian University Medical College, św. Łazarza 15, 31-530 Krakow, Poland; Istituto Pasteur Italia, Fondazione Cenci-Bolognetti, Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Sabrina Garbo
- Istituto Pasteur Italia, Fondazione Cenci-Bolognetti, Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy
| | - Rossella Fioravanti
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Claus Jacob
- Division of Bioorganic Chemistry, School of Pharmacy, Saarland University, Campus B 2.1, D-66123 Saarbrücken, Germany
| | - Marius Hittinger
- Pharmbiotec gGmbH, Department of Drug Discovery, Nußkopf 39, 66578 Schiffweiler, Germany
| | - Jadwiga Handzlik
- Department of Technology and Biotechnology of Drugs, Jagiellonian University, Medical College, Medyczna 9, 30-688 Krakow, Poland.
| | - Clemens Zwergel
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; Division of Bioorganic Chemistry, School of Pharmacy, Saarland University, Campus B 2.1, D-66123 Saarbrücken, Germany; Pharmbiotec gGmbH, Department of Drug Discovery, Nußkopf 39, 66578 Schiffweiler, Germany.
| | - Cecilia Battistelli
- Istituto Pasteur Italia, Fondazione Cenci-Bolognetti, Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161, Rome, Italy.
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Tung HH, Kuo CY, Lee PL, Chang CW, Chou KH, Lin CP, Chen LK. Efficacy of Digital Dance on Brain Imagery, Cognition, and Health: Randomized Controlled Trial. J Med Internet Res 2024; 26:e57694. [PMID: 39078687 PMCID: PMC11322681 DOI: 10.2196/57694] [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: 02/24/2024] [Revised: 05/13/2024] [Accepted: 07/05/2024] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND Multidomain interventions have demonstrable benefits for promoting healthy aging, but self-empowerment strategies to sustain long-term gains remain elusive. OBJECTIVE This study evaluated the effects of digital somatosensory dance game participation on brain imagery changes as primary outcomes and other physical and mental health measures as secondary outcomes related to healthy aging. METHODS Between August 31, 2020, and June 27, 2021, this randomized controlled trial recruited 60 eligible participants older than 55 years with no recent engagement in digital dance games. A computer-generated randomization sequence was used to allocate participants 1:1, without stratification, to an intervention group (n=30) who underwent digital somatosensory dance game training or a control group (n=30). An anonymized code masked the intervention allocations from the investigators, and individuals who assigned the interventions were not involved in analyzing the study data. The intervention entailed two 30-minute dance game sessions per week for 6 months, and the control group received healthy aging education. Primary outcomes were brain imagery changes. All variables were measured at baseline and the 6-month follow-up, and intervention effects were estimated using t tests with intention-to-treat analyses. RESULTS Compared with the control group, intervention participants had significantly different brain imagery in the gray matter volume (GMV) of the left putamen (estimate 0.016, 95% CI 0.008 to 0.024; P<.001), GMV of the left pallidum (estimate 0.02, 95% CI 0.006 to 0.034; P=.004), and fractional amplitude of low frequency fluctuations of the left pallidum (estimate 0.262, 95% CI 0.084 to 0.439; P=.004). Additionally, the intervention group had different imagery in the cerebellum VI GMV (estimate 0.011, 95% CI 0.003 to 0.02; P=.01). The intervention group also had improved total Montreal Cognitive Assessment scores (estimate 1.2, 95% CI 0.27 to -2.13; P<.01), quality of life (estimate 7.08, 95% CI 2.35 to 11.82; P=.004), and time spent sitting on weekdays (estimate -1.96, 95% CI -3.33 to -0.60; P=.005). Furthermore, dance performance was significantly associated with cognitive performance (P=.003), health status (P=.14), resilience (P=.007), and demoralization (P<.001). CONCLUSIONS Digital somatosensory dance game participation for 6 months was associated with brain imagery changes in multiple regions involving somatosensory, motor, visual, and attention functions, which were consistent with phenotypic improvements associated with healthy aging. TRIAL REGISTRATION ClinicalTrials.gov NCT05411042; https://clinicaltrials.gov/study/NCT05411042.
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Affiliation(s)
- Heng-Hsin Tung
- Department of Nursing, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Tungs' Taichung MetroHarbor Hospital, Taichung, Taiwan
- Center for Healthy Longevity and Aging Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chen-Yuan Kuo
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Pei-Lin Lee
- Center for Healthy Longevity and Aging Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chih-Wen Chang
- Center for Healthy Longevity and Aging Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Kun-Hsien Chou
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ching-Po Lin
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Education and Research, Taipei City Hospital, Taipei, Taiwan
| | - Liang-Kung Chen
- Center for Healthy Longevity and Aging Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Center for Geriatrics and Gerontology, Taipei Veterans General Hospital, Taipei, Taiwan
- Taipei Municipal Gan-Dau Hospital, Taipei, Taiwan
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Aschner M, Skalny AV, Santamaria A, Rocha JBT, Mansouri B, Tizabi Y, Madeddu R, Lu R, Lee E, Tinkov AA. Epigenetic Mechanisms of Aluminum-Induced Neurotoxicity and Alzheimer's Disease: A Focus on Non-Coding RNAs. Neurochem Res 2024:10.1007/s11064-024-04214-9. [PMID: 39060769 DOI: 10.1007/s11064-024-04214-9] [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: 04/12/2024] [Revised: 06/16/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024]
Abstract
Aluminum (Al) is known to induce neurotoxic effects, potentially contributing to Alzheimer's disease (AD) pathogenesis. Recent studies suggest that epigenetic modification may contribute to Al neurotoxicity, although the mechanisms are still debatable. Therefore, the objective of the present study was to summarize existing data on the involvement of epigenetic mechanisms in Al-induced neurotoxicity, especially AD-type pathology. Existing data demonstrate that Al exposure induces disruption in DNA methylation, histone modifications, and non-coding RNA expression in brains. Alterations in DNA methylation following Al exposure were shown to be mediated by changes in expression and activity of DNA methyltransferases (DNMTs) and ten-eleven translocation proteins (TETs). Al exposure was shown to reduce histone acetylation by up-regulating expression of histone deacetylases (HDACs) and impair histone methylation, ultimately contributing to down-regulation of brain-derived neurotrophic factor (BDNF) expression and activation of nuclear factor κB (NF-κB) signaling. Neurotoxic effects of Al exposure were also associated with aberrant expression of non-coding RNAs, especially microRNAs (miR). Al-induced patterns of miR expression were involved in development of AD-type pathology by increasing amyloid β (Aβ) production through up-regulation of Aβ precursor protein (APP) and β secretase (BACE1) expression (down-regulation of miR-29a/b, miR-101, miR-124, and Let-7c expression), increasing in neuroinflammation through NF-κB signaling (up-regulation of miR-9, miR-125b, miR-128, and 146a), as well as modulating other signaling pathways. Furthermore, reduced global DNA methylation, altered histone modification, and aberrant miRNA expression were associated with cognitive decline in Al-exposed subjects. However, further studies are required to evaluate the contribution of epigenetic mechanisms to Al-induced neurotoxicity and/or AD development.
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Affiliation(s)
- Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Anatoly V Skalny
- Laboratory of Ecobiomonitoring and Quality Control, Yaroslavl State University, Sovetskaya Str. 14, Yaroslavl, 150000, Russia
- Laboratory of Molecular Dietetics, IM Sechenov First Moscow State Medical University (Sechenov University), Bolshaya Pirogovskaya St., 2-4, Moscow, 119146, Russia
| | - Abel Santamaria
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico
- Laboratorio de Nanotecnología y Nanomedicina, Departamento de Atención a la Salud, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, 04960, Mexico
| | - Joao B T Rocha
- Departamento de Bioquímica e Biologia Molecular, CCNE, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Borhan Mansouri
- Substance Abuse Prevention Research Center, Research Institute for Health, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Yousef Tizabi
- Department of Pharmacology, Howard University College of Medicine, Washington, DC, 20059, USA
| | - Roberto Madeddu
- Department of Biomedical Sciences-Histology, University of Sassari, Viale San Pietro 43/B, 07100, Sassari, Italy
| | - Rongzu Lu
- Department of Preventive Medicine and Public Health Laboratory Science, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, People's Republic of China
| | - Eunsook Lee
- Department of Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, 32307, USA
| | - Alexey A Tinkov
- Laboratory of Ecobiomonitoring and Quality Control, Yaroslavl State University, Sovetskaya Str. 14, Yaroslavl, 150000, Russia.
- Laboratory of Molecular Dietetics, IM Sechenov First Moscow State Medical University (Sechenov University), Bolshaya Pirogovskaya St., 2-4, Moscow, 119146, Russia.
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4
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Bayazid AB, Lim BO. Therapeutic Effects of Plant Anthocyanin against Alzheimer's Disease and Modulate Gut Health, Short-Chain Fatty Acids. Nutrients 2024; 16:1554. [PMID: 38892488 PMCID: PMC11173718 DOI: 10.3390/nu16111554] [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: 04/23/2024] [Revised: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia and neurogenerative disease (NDD), and it is also one of the leading causes of death worldwide. The number of AD patients is over 55 million according to 2020 Alzheimer's Disease International (ADI), and the number is increasing drastically without any effective cure. In this review, we discuss and analyze the potential role of anthocyanins (ACNs) against AD while understanding the molecular mechanisms. ACNs have been reported as having neuroprotective effects by mitigating cognitive impairments, apoptotic markers, neuroinflammation, aberrant amyloidogenesis, and tauopathy. Taken together, ACNs could be an important therapeutic agent for combating or delaying the onset of AD.
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Affiliation(s)
- Al Borhan Bayazid
- Medicinal Biosciences, Department of Applied Biological Sciences, Graduate School, BK21 Program, Konkuk University, Chungju 27478, Republic of Korea
| | - Beong Ou Lim
- Medicinal Biosciences, Department of Applied Biological Sciences, Graduate School, BK21 Program, Konkuk University, Chungju 27478, Republic of Korea
- Human Bioscience Corporate R&D Center, Human Bioscience Corp., 268 Chungwondaero, Chungju 27478, Republic of Korea
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Chen H, Zhang CJ, Zhao ZY, Gao YY, Zhao JT, Li XX, Zhang M, Wang H. Mechanisms underlying LncRNA SNHG1 regulation of Alzheimer's disease involve DNA methylation. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2024; 87:428-435. [PMID: 38551404 DOI: 10.1080/15287394.2024.2334248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease associated with long non-coding RNAs and DNA methylation; however, the mechanisms underlying the role of lncRNA small nucleolar RNA host gene 1 (lncRNA SNHG1) and subsequent involvement of DNA methylation in AD development are not known. The aim of this study was to examine the regulatory mechanisms attributed to lncRNA SNHG1 gene utilizing 2 strains of senescence-accelerated mouse prone 8 (SAMP8) model of AD and compared to senescence-accelerated mouse resistant (SAMR) considered a control. Both strains of the mouse were transfected with either blank virus, psLenti-U6-SNHG1(low gene expression) virus, and psLenti-pA-SNHG1(gene overexpression) virus via a single injection into the brains for 2 weeks. At 2 weeks mice were subjected to a Morris water maze to determine any behavioral effects followed by sacrifice to extract hippocampal tissue for Western blotting to measure protein expression of p-tau, DNMT1, DNMT3A, DNMT3B, TET1, and p-Akt. No marked alterations were noted in any parameters following blank virus transfection. In SAMP8 mice, a significant decrease was noted in protein expression of DNMT1, DNMT3A, DNMT3B, and p-Akt associated with rise in p-tau and TET1. Transfection with ps-Lenti-U6-SNHG1 alone in SAMR1 mice resulted in a significant rise in DNMTs and p-Akt and a fall in p-tau and TET1. Transfection of SAMP8 with ps-Lenti-U6-SNHG1 blocked effects on overexpression noted in this mouse strain. However, knockdown of lncRNA SNHG1 yielded the opposite results as found in SAMR1 mice. In conclusion, the knockdown of lncRNA SNHG1 enhanced DNA methylation through the PI3K/Akt signaling pathway, thereby reducing the phosphorylation levels of tau in SAMP8 AD model mice with ameliorating brain damage attributed to p-tau accumulation with consequent neuroprotection.
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Affiliation(s)
- Hong Chen
- Institute of Neuroscience and Medical Technology, Department of Anatomy, Baotou Medical College, Inner Mongolia, China
| | - Chun-Jie Zhang
- Institute of Neuroscience and Medical Technology, Department of Anatomy, Baotou Medical College, Inner Mongolia, China
- Center of Collaborative Innovation in Translational Medicine, Baotou Medical College, Inner Mongolia, China
| | - Zhi-Ying Zhao
- Institute of Neuroscience and Medical Technology, Department of Anatomy, Baotou Medical College, Inner Mongolia, China
| | - Yang-Yang Gao
- Institute of Neuroscience and Medical Technology, Department of Anatomy, Baotou Medical College, Inner Mongolia, China
| | - Jian-Tian Zhao
- Institute of Public Health, Baotou Medical College, Inner Mongolia, China
| | - Xiao-Xu Li
- Institute of Neuroscience and Medical Technology, Department of Anatomy, Baotou Medical College, Inner Mongolia, China
| | - Ming Zhang
- Institute of Neuroscience and Medical Technology, Department of Anatomy, Baotou Medical College, Inner Mongolia, China
| | - He Wang
- School of Health Sciences, University of Newcastle, Newcastle, Australia
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6
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Ramos-Campoy O, Comas-Albertí A, Hervás D, Borrego-Écija S, Bosch B, Sandoval J, Fort-Aznar L, Moreno-Izco F, Fernández-Villullas G, Molina-Porcel L, Balasa M, Lladó A, Sánchez-Valle R, Antonell A. Genome-Wide DNA Methylation in Early-Onset-Dementia Patients Brain Tissue and Lymphoblastoid Cell Lines. Int J Mol Sci 2024; 25:5445. [PMID: 38791483 PMCID: PMC11121630 DOI: 10.3390/ijms25105445] [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: 04/23/2024] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Epigenetics, a potential underlying pathogenic mechanism of neurodegenerative diseases, has been in the scope of several studies performed so far. However, there is a gap in regard to analyzing different forms of early-onset dementia and the use of Lymphoblastoid cell lines (LCLs). We performed a genome-wide DNA methylation analysis on sixty-four samples (from the prefrontal cortex and LCLs) including those taken from patients with early-onset forms of Alzheimer's disease (AD) and frontotemporal dementia (FTD) and healthy controls. A beta regression model and adjusted p-values were used to obtain differentially methylated positions (DMPs) via pairwise comparisons. A correlation analysis of DMP levels with Clariom D array gene expression data from the same cohort was also performed. The results showed hypermethylation as the most frequent finding in both tissues studied in the patient groups. Biological significance analysis revealed common pathways altered in AD and FTD patients, affecting neuron development, metabolism, signal transduction, and immune system pathways. These alterations were also found in LCL samples, suggesting the epigenetic changes might not be limited to the central nervous system. In the brain, CpG methylation presented an inverse correlation with gene expression, while in LCLs, we observed mainly a positive correlation. This study enhances our understanding of the biological pathways that are associated with neurodegeneration, describes differential methylation patterns, and suggests LCLs are a potential cell model for studying neurodegenerative diseases in earlier clinical phases than brain tissue.
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Affiliation(s)
- Oscar Ramos-Campoy
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Aina Comas-Albertí
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - David Hervás
- Department of Applied Statistics and Operations Research and Quality, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Sergi Borrego-Écija
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Beatriz Bosch
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Juan Sandoval
- Epigenomics Core Facility, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Laura Fort-Aznar
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Fermín Moreno-Izco
- Cognitive Disorders Unit, Department of Neurology, Hospital Universitario Donostia, 20014 San Sebastian, Spain
- Instituto de Investigación Sanitaria Biogipuzkoa, Neurosciences Area, Group of Neurodegenerative Diseases, 20014 San Sebastian, Spain
| | - Guadalupe Fernández-Villullas
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Laura Molina-Porcel
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
- Neurological Tissue Bank, Biobank-Hospital Clinic-IDIBAPS, 08036 Barcelona, Spain
| | - Mircea Balasa
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Albert Lladó
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Raquel Sánchez-Valle
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
- Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Anna Antonell
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
- Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona (UB), 08036 Barcelona, Spain
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Eulalio T, Sun MW, Gevaert O, Greicius MD, Montine TJ, Nachun D, Montgomery SB. regionalpcs: improved discovery of DNA methylation associations with complex traits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.590171. [PMID: 38746367 PMCID: PMC11092597 DOI: 10.1101/2024.05.01.590171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
We have developed the regional principal components (rPCs) method, a novel approach for summarizing gene-level methylation. rPCs address the challenge of deciphering complex epigenetic mechanisms in diseases like Alzheimer's disease (AD). In contrast to traditional averaging, rPCs leverage principal components analysis to capture complex methylation patterns across gene regions. Our method demonstrated a 54% improvement in sensitivity over averaging in simulations, offering a robust framework for identifying subtle epigenetic variations. Applying rPCs to the AD brain methylation data in ROSMAP, combined with cell type deconvolution, we uncovered 838 differentially methylated genes associated with neuritic plaque burden-significantly outperforming conventional methods. Integrating methylation quantitative trait loci (meQTL) with genome-wide association studies (GWAS) identified 17 genes with potential causal roles in AD, including MS4A4A and PICALM. Our approach is available in the Bioconductor package regionalpcs, opening avenues for research and facilitating a deeper understanding of the epigenetic landscape in complex diseases.
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Affiliation(s)
- Tiffany Eulalio
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Min Woo Sun
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Olivier Gevaert
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Michael D Greicius
- Department of Neurology & Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Daniel Nachun
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
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Shreeya T, Ansari MS, Kumar P, Saifi M, Shati AA, Alfaifi MY, Elbehairi SEI. Senescence: A DNA damage response and its role in aging and Neurodegenerative Diseases. FRONTIERS IN AGING 2024; 4:1292053. [PMID: 38596783 PMCID: PMC11002673 DOI: 10.3389/fragi.2023.1292053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/09/2023] [Indexed: 04/11/2024]
Abstract
Senescence is a complicated, multi-factorial, irreversible cell cycle halt that has a tumor-suppressing effect in addition to being a significant factor in aging and neurological diseases. Damaged DNA, neuroinflammation, oxidative stress and disrupted proteostasis are a few of the factors that cause senescence. Senescence is triggered by DNA damage which initiates DNA damage response. The DNA damage response, which includes the formation of DNA damage foci containing activated H2AX, which is a key factor in cellular senescence, is provoked by a double strand DNA break. Oxidative stress impairs cognition, inhibits neurogenesis, and has an accelerated aging effect. Senescent cells generate pro-inflammatory mediators known as senescence-associated secretory phenotype (SASP). These pro-inflammatory cytokines and chemokines have an impact on neuroinflammation, neuronal death, and cell proliferation. While it is tempting to think of neurodegenerative diseases as manifestations of accelerated aging and senescence, this review will present information on brain ageing and neurodegeneration as a result of senescence and DNA damage response.
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Affiliation(s)
- Tejal Shreeya
- Institute of Biophysics, Biological Research Center, Szeged, Hungary
- Doctoral School of Theoretical Medicine, University of Szeged, Szeged, Hungary
| | - Mohd Saifullah Ansari
- Institute of Genetics, Biological Research Center, Szeged, Hungary
- Doctoral School of Biology, University of Szeged, Szeged, Hungary
| | - Prabhat Kumar
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
- Centre for Neuroscience, University of Pécs, Pécs, Hungary
| | | | - Ali A. Shati
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Y. Alfaifi
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
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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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10
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Wang X, Liu L, Jiang X, Saredy J, Xi H, Cueto R, Sigler D, Khan M, Wu S, Ji Y, Snyder NW, Hu W, Yang X, Wang H. Identification of methylation-regulated genes modulating microglial phagocytosis in hyperhomocysteinemia-exacerbated Alzheimer's disease. Alzheimers Res Ther 2023; 15:164. [PMID: 37789414 PMCID: PMC10546779 DOI: 10.1186/s13195-023-01311-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/20/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND Hyperhomocysteinemia (HHcy) has been linked to development of Alzheimer's disease (AD) neuropathologically characterized by the accumulation of amyloid β (Aβ). Microglia (MG) play a crucial role in uptake of Aβ fibrils, and its dysfunction worsens AD. However, the effect of HHcy on MG Aβ phagocytosis remains unstudied. METHODS We isolated MG from the cerebrum of HHcy mice with genetic cystathionine-β-synthase deficiency (Cbs-/-) and performed bulk RNA-seq. We performed meta-analysis over transcriptomes of Cbs-/- mouse MG, human and mouse AD MG, MG Aβ phagocytosis model, human AD methylome, and GWAS AD genes. RESULTS HHcy and hypomethylation conditions were identified in Cbs-/- mice. Through Cbs-/- MG transcriptome analysis, 353 MG DEGs were identified. Phagosome formation and integrin signaling pathways were found suppressed in Cbs-/- MG. By analyzing MG transcriptomes from 4 AD patient and 7 mouse AD datasets, 409 human and 777 mouse AD MG DEGs were identified, of which 37 were found common in both species. Through further combinatory analysis with transcriptome from MG Aβ phagocytosis model, we identified 130 functional-validated Aβ phagocytic AD MG DEGs (20 in human AD, 110 in mouse AD), which reflected a compensatory activation of Aβ phagocytosis. Interestingly, we identified 14 human Aβ phagocytic AD MG DEGs which represented impaired MG Aβ phagocytosis in human AD. Finally, through a cascade of meta-analysis of transcriptome of AD MG, functional phagocytosis, HHcy MG, and human AD brain methylome dataset, we identified 5 HHcy-suppressed phagocytic AD MG DEGs (Flt1, Calponin 3, Igf1, Cacna2d4, and Celsr) which were reported to regulate MG/MΦ migration and Aβ phagocytosis. CONCLUSIONS We established molecular signatures for a compensatory response of Aβ phagocytosis activation in human and mouse AD MG and impaired Aβ phagocytosis in human AD MG. Our discoveries suggested that hypomethylation may modulate HHcy-suppressed MG Aβ phagocytosis in AD.
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Affiliation(s)
- Xianwei Wang
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Lu Liu
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Xiaohua Jiang
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Jason Saredy
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Hang Xi
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Ramon Cueto
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Danni Sigler
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Mohsin Khan
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Sheng Wu
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Yong Ji
- Key Laboratory of Cardiovascular Disease and Molecular Intervention, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Nathaniel W Snyder
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Wenhui Hu
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Xiaofeng Yang
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA
| | - Hong Wang
- Center for Metabolic Disease Research, Department of Cardiovascular Science, Lewis Kats School of Medicine, Temple University, MERB, Room 1060, 3500 N. Broad Street, Philadelphia, USA.
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11
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Kawakami S, Yamato R, Kitamura K, Watanabe Y, Kabasawa K, Takahashi A, Saito T, Kobayashi R, Oshiki R, Takachi R, Tsugane S, Yamazaki O, Watanabe K, Nakamura K. Alcohol consumption, smoking, and risk of dementia in community-dwelling Japanese people aged 40-74 years: The Murakami cohort study. Maturitas 2023; 176:107788. [PMID: 37356262 DOI: 10.1016/j.maturitas.2023.107788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 05/16/2023] [Accepted: 06/10/2023] [Indexed: 06/27/2023]
Abstract
OBJECTIVE Alcohol drinking and tobacco smoking have impacts on lifestyle-related diseases, but their association with dementia remains a debated topic. This study aimed to examine longitudinal associations between alcohol consumption, smoking, and dementia risk in middle-aged and older Japanese people. METHODS This study used a cohort design with an 8-year follow-up. Participants were community-dwelling Japanese people (N = 13,802) aged 40-74 years. The baseline survey, including a self-administered questionnaire, was conducted in 2011-2013. Predictors were alcohol consumption and tobacco smoking. The outcome was incident dementia obtained from a long-term care insurance database. Covariates were demographics, lifestyle factors, body mass index, general health status, and history of stroke, diabetes, and depression. RESULTS Participant mean age was 59.0 years. The 1-149, 150-299, and 300-449 g ethanol/week groups had significantly lower adjusted hazard ratios (HRs) (0.62, 0.59, and 0.47, respectively) compared with the reference group, with no significant linear association. HRs increased toward 1 when past-drinkers and those with poor health status and a disease history were excluded (0.80, 0.66, and 0.82, respectively). Higher smoking levels were dose-dependently associated with a higher HR (adjusted P for trend = 0.0105), with the ≥20 cigarettes/day group having a significantly higher adjusted HR (1.80). Heavy drinkers (≥449 g ethanol/week) with smoking habits, but not those without smoking habits, had higher dementia risk (P for interaction = 0.0046). CONCLUSION Light-to-moderate alcohol consumption is associated with decreased dementia risk, and smoking is dose-dependently associated with increased dementia risk, with an interaction between high alcohol consumption and smoking on dementia risk.
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Affiliation(s)
| | - Ren Yamato
- School of Medicine, Niigata University, Niigata, Japan
| | - Kaori Kitamura
- Division of Preventive Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yumi Watanabe
- Division of Preventive Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Keiko Kabasawa
- Department of Health Promotion Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Akemi Takahashi
- Department of Rehabilitation, Niigata University of Rehabilitation, Niigata, Japan
| | - Toshiko Saito
- Division of Preventive Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ryosaku Kobayashi
- Department of Rehabilitation, Niigata University of Rehabilitation, Niigata, Japan
| | - Rieko Oshiki
- Department of Rehabilitation, Niigata University of Rehabilitation, Niigata, Japan
| | - Ribeka Takachi
- Department of Food Science and Nutrition, Nara Women's University Graduate School of Humanities and Sciences, Nara, Japan
| | - Shoichiro Tsugane
- Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | | | - Kei Watanabe
- Department of Orthopedic Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kazutoshi Nakamura
- Division of Preventive Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.
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12
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Luz DA, Pinheiro AM, Fontes-Júnior EA, Maia CSF. Neuroprotective, neurogenic, and anticholinergic evidence of Ganoderma lucidum cognitive effects: Crucial knowledge is still lacking. Med Res Rev 2023; 43:1504-1536. [PMID: 37052237 DOI: 10.1002/med.21957] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 12/14/2022] [Accepted: 03/24/2023] [Indexed: 04/14/2023]
Abstract
Ganoderma lucidum is a mushroom that has been widely used for centuries in Asian countries for its antiaging properties. It is popularly known as "Ling Zhi," "Reishi," and "Youngzhi," and because of its benefits, it is known as the "immortality mushroom." Pharmacological assays have revealed that G. lucidum ameliorates cognitive impairments through inhibition of β-amyloid and neurofibrillary tangle formation, antioxidant effect, reduction of inflammatory cytokine release and apoptosis, genic expression modulation, among other activities. Chemical investigations on G. lucidum have revealed the presence of metabolites such as triterpenes, which are the most explored in this field, as well as flavonoids, steroids, benzofurans, and alkaloids; in the literature, these have also been reported to have mnemonic activity. These properties of the mushroom make it a potential source of new drugs to prevent or reverse memory disorders, as actual medications are able to only alleviate some symptoms but are unable to stop the progress of cognitive impairments, with no impact on social, familiar, and personal relevance. In this review, we discuss the cognitive findings of G. lucidum reported in the literature, converging the proposed mechanisms through the several pathways that underlie memory and cognition processes. In addition, we highlight the gaps that deserve particular attention to support future studies.
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Affiliation(s)
- Diandra A Luz
- Laboratory of Pharmacology of Inflammation and Behavior, Institute of Health Science, Faculty of Pharmacy, Federal University of Pará, Belém, Pará, Brazil
| | - Alana M Pinheiro
- Laboratory of Pharmacology of Inflammation and Behavior, Institute of Health Science, Faculty of Pharmacy, Federal University of Pará, Belém, Pará, Brazil
| | - Enéas A Fontes-Júnior
- Laboratory of Pharmacology of Inflammation and Behavior, Institute of Health Science, Faculty of Pharmacy, Federal University of Pará, Belém, Pará, Brazil
| | - Cristiane S F Maia
- Laboratory of Pharmacology of Inflammation and Behavior, Institute of Health Science, Faculty of Pharmacy, Federal University of Pará, Belém, Pará, Brazil
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13
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Li W, Rang Y, Liu H, Liu C. Update on new trends and progress of natural active ingredients in the intervention of Alzheimer's disease, based on understanding of traditional Chinese and Western relevant theories: A review. Phytother Res 2023; 37:3744-3764. [PMID: 37380605 DOI: 10.1002/ptr.7908] [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: 10/26/2022] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/30/2023]
Abstract
Alzheimer's disease (AD) is one of the major neurological disorders causing death in the elderly worldwide. As a neurodegenerative disease that is difficult to prevent and cure, the pathogenesis of AD is complex and there is no effective cure. A variety of natural products derived from plants have been reported to have promising anti-AD activities, including flavonoids, terpenes, phenolic acids and alkaloids, which can effectively relieve the symptoms of AD in a variety of ways. This paper mainly reviews the pharmacological activity and mechanisms of natural products against AD. Although the clinical efficacy of these plants still needs to be determined by further high-quality studies, it may also provide a basis for future researchers to study anti-AD in depth.
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Affiliation(s)
- Weiye Li
- College of Food Science, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Food Quality and Safety of Guangdong Province, Guangzhou, China
| | - Yifeng Rang
- College of Food Science, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Food Quality and Safety of Guangdong Province, Guangzhou, China
| | - Huan Liu
- College of Food Science, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Food Quality and Safety of Guangdong Province, Guangzhou, China
| | - Chunhong Liu
- College of Food Science, South China Agricultural University, Guangzhou, China
- The Key Laboratory of Food Quality and Safety of Guangdong Province, Guangzhou, China
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14
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Qin H, Liu J, Fang C, Deng Y, Zhang Y. DNA methylation: The epigenetic mechanism of Alzheimer's disease. IBRAIN 2023; 9:463-472. [PMID: 38680511 PMCID: PMC11045197 DOI: 10.1002/ibra.12121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/11/2023] [Accepted: 07/18/2023] [Indexed: 05/01/2024]
Abstract
Nowadays, with the development of the social health care system, there is an increasing trend towards an aging society. The incidence of Alzheimer's disease (AD) is also on the rise. AD is a kind of neurodegenerative disease that can be found in any age group. For years, scientists have been committing to discovering the cause of AD. DNA methylation is one of the most common epigenetic mechanisms in mammals and plays a vital role in the pathogenesis of several diseases, including tumors. Studying chemical changes in the epigenome, or DNA methylation can help us understand the effects of our environment and life on diseases, such as smoking, depression, and menopause, which may affect people's chances of developing Alzheimer's or other diseases. Recent studies have identified some crucial genes like ANK1, RHBDF2, ABCA7, and BIN1, linking DNA methylation to AD. This review focuses on elucidating the relationship between DNA methylation and the pathogenesis of AD and provides an outlook on possible targeted therapeutic modalities.
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Affiliation(s)
- Hao‐Yue Qin
- Department of AnesthesiologySouthwest Medical UniversityLuzhouSichuanChina
| | - Jiao‐Yan Liu
- Department of AnesthesiologySouthwest Medical UniversityLuzhouSichuanChina
| | - Chang‐Le Fang
- Faculty of Health SciencesUniversity of AdelaideMelbourneVICAustralia
| | - Yan‐Ping Deng
- Department of AnesthesiologySouthwest Medical UniversityLuzhouSichuanChina
| | - Ying Zhang
- State Key Laboratories for Quality Research in Chinese Medicines, Faculty of PharmacyMacau University of Science and TechnologyMacauChina
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15
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Ulaganathan S, Pitchaimani A. Spontaneous and familial models of Alzheimer's disease: Challenges and advances in preclinical research. Life Sci 2023:121918. [PMID: 37422070 DOI: 10.1016/j.lfs.2023.121918] [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: 05/31/2023] [Revised: 06/28/2023] [Accepted: 07/05/2023] [Indexed: 07/10/2023]
Abstract
Alzheimer's disease (AD) is a debilitating neurodegenerative disorder that is progressive and irreversible in nature. Even after decades of dedicated research and paradigm-shifting hypotheses of AD etiology, very few well-founded credible improvements have been foreseen in understanding the actual underlying mechanisms involved in the development of the disorder. As for any disease to be well-comprehended, AD also requires optimal modelling strategies, which will then pave way for effective therapeutic interventions. Most of the clinical trials and research towards better treatment of AD fail in translation, due to the inefficacy of explored animal models to mimic the actual AD pathology, precisely. The majority of the existing AD models are developed based on the mutations found in the familial form of AD (fAD) which accounts for less than 5 % of the incidence of AD. Further, the investigations also face more challenges due to the additional complexities and lacunae found in etiology of sporadic form of AD (sAD), which accounts for 95 % of total AD. This review illustrates the gaps found in different models of AD, both sporadic and familial variants with additional focus on recent avenues for accurate simulation of AD pathology using in vitro and chimeric AD models.
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Affiliation(s)
- Suryapriya Ulaganathan
- Precision Nanomedicine and Microfluidic Lab, Centre for Biomaterials, Cellular and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore 632014, TN, India; School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, TN, India
| | - Arunkumar Pitchaimani
- Precision Nanomedicine and Microfluidic Lab, Centre for Biomaterials, Cellular and Molecular Theranostics (CBCMT), Vellore Institute of Technology (VIT), Vellore 632014, TN, India; School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore 632014, TN, India.
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16
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Liu T, Du D, Zhao R, Xie Q, Dong Z. Gut microbes influence the development of central nervous system disorders through epigenetic inheritance. Microbiol Res 2023; 274:127440. [PMID: 37343494 DOI: 10.1016/j.micres.2023.127440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
Central nervous system (CNS) disorders, such as depression, anxiety, and Alzheimer's disease (AD), affect quality of life of patients and pose significant economic and social burdens worldwide. Due to their obscure and complex pathogeneses, current therapies for these diseases have limited efficacy. Over the past decade, the gut microbiome has been shown to exhibit direct and indirect influences on the structure and function of the CNS, affecting multiple pathological pathways. In addition to the direct interactions between the gut microbiota and CNS, the gut microbiota and their metabolites can regulate epigenetic processes, including DNA methylation, histone modification, and regulation of non-coding RNAs. In this review, we discuss the tripartite relationship among gut microbiota, epigenetic inheritance, and CNS disorders. We suggest that gut microbes and their metabolites influence the pathogenesis of CNS disorders at the epigenetic level, which may inform the development of effective therapeutic strategies for CNS disorders.
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Affiliation(s)
- Tianyou Liu
- West China School of Medicine, Sichuan University, Chengdu 610072, PR China
| | - Dongru Du
- West China School of Medicine, Sichuan University, Chengdu 610072, PR China
| | - Rui Zhao
- West China School of Medicine, Sichuan University, Chengdu 610072, PR China
| | - Qinglian Xie
- Department of Outpatient, West China Hospital of Sichuan University, Chengdu 610041, PR China
| | - Zaiquan Dong
- Mental Health Center, West China Hospital, Sichuan University, Chengdu 610041, PR China.
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17
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Milicic L, Porter T, Vacher M, Laws SM. Utility of DNA Methylation as a Biomarker in Aging and Alzheimer's Disease. J Alzheimers Dis Rep 2023; 7:475-503. [PMID: 37313495 PMCID: PMC10259073 DOI: 10.3233/adr-220109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/23/2023] [Indexed: 06/15/2023] Open
Abstract
Epigenetic mechanisms such as DNA methylation have been implicated in a number of diseases including cancer, heart disease, autoimmune disorders, and neurodegenerative diseases. While it is recognized that DNA methylation is tissue-specific, a limitation for many studies is the ability to sample the tissue of interest, which is why there is a need for a proxy tissue such as blood, that is reflective of the methylation state of the target tissue. In the last decade, DNA methylation has been utilized in the design of epigenetic clocks, which aim to predict an individual's biological age based on an algorithmically defined set of CpGs. A number of studies have found associations between disease and/or disease risk with increased biological age, adding weight to the theory of increased biological age being linked with disease processes. Hence, this review takes a closer look at the utility of DNA methylation as a biomarker in aging and disease, with a particular focus on Alzheimer's disease.
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Affiliation(s)
- Lidija Milicic
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Tenielle Porter
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
| | - Michael Vacher
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- CSIRO Health and Biosecurity, Australian e-Health Research Centre, Floreat, Western Australia
| | - Simon M. Laws
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
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18
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Hu S, Tao J, Peng M, Ye Z, Chen Z, Chen H, Yu H, Wang B, Fan JB, Ni B. Accurate detection of early-stage lung cancer using a panel of circulating cell-free DNA methylation biomarkers. Biomark Res 2023; 11:45. [PMID: 37101220 PMCID: PMC10134678 DOI: 10.1186/s40364-023-00486-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/14/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Lung cancer remains the leading cause of cancer mortality worldwide. Early detection of lung cancer helps improve treatment and survival. Numerous aberrant DNA methylations have been reported in early-stage lung cancer. Here, we sought to identify novel DNA methylation biomarkers that could potentially be used for noninvasive early diagnosis of lung cancers. METHODS This prospective-specimen collection and retrospective-blinded-evaluation trial enrolled a total of 317 participants (198 tissues and 119 plasmas) comprising healthy controls, patients with lung cancer and benign disease between January 2020 and December 2021. Tissue and plasma samples were subjected to targeted bisulfite sequencing with a lung cancer specific panel targeting 9,307 differential methylation regions (DMRs). DMRs associated with lung cancer were identified by comparing the methylation profiles of tissue samples from patients with lung cancer and benign disease. Markers were selected with minimum redundancy and maximum relevance algorithm. A prediction model for lung cancer diagnosis was built through logistic regression algorithm and validated independently in tissue samples. Furthermore, the performance of this developed model was evaluated in a set of plasma cell-free DNA (cfDNA) samples. RESULTS We identified 7 DMRs corresponding to 7 differentially methylated genes (DMGs) including HOXB4, HOXA7, HOXD8, ITGA4, ZNF808, PTGER4, and B3GNTL1 that were highly associated with lung cancer by comparing the methylation profiles of lung cancer and benign nodule tissue. Based on the 7-DMR biomarker panel, we developed a new diagnostic model in tissue samples, termed "7-DMR model", to distinguish lung cancers from benign diseases, achieving AUCs of 0.97 (95%CI: 0.93-1.00)/0.96 (0.92-1.00), sensitivities of 0.89 (0.82-0.95)/0.92 (0.86-0.98), specificities of 0.94 (0.89-0.99)/1.00 (1.00-1.00), and accuracies of 0.90 (0.84-0.96)/0.94 (0.89-0.99) in the discovery cohort (n = 96) and the independent validation cohort (n = 81), respectively. Furthermore, the 7-DMR model was applied to noninvasive discrimination of lung cancers and non-lung cancers including benign lung diseases and healthy controls in an independent validation cohort of plasma samples (n = 106), yielding an AUC of 0.94 (0.86-1.00), sensitivity of 0.81 (0.73-0.88), specificity of 0.98 (0.95-1.00), and accuracy of 0.93 (0.89-0.98). CONCLUSION The 7 novel DMRs could be promising methylation biomarkers that merits further development as a noninvasive test for early detection of lung cancer.
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Affiliation(s)
- Shuo Hu
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | | | | | - Zhujia Ye
- Anchordx Medical Co., Ltd, Guangzhou, China
| | - Zhiwei Chen
- Anchordx Medical Co., Ltd, Guangzhou, China
- AnchorDx Inc, Fremont, CA, USA
| | | | - Haifeng Yu
- The Fifth People's Hospital of Wuxi, Wuxi, China
| | - Bo Wang
- Anchordx Medical Co., Ltd, Guangzhou, China.
| | - Jian-Bing Fan
- Anchordx Medical Co., Ltd, Guangzhou, China.
- Department of Pathology, Southern Medical University, Guangzhou, China.
| | - Bin Ni
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.
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Mathur S, Gawas C, Ahmad IZ, Wani M, Tabassum H. Neurodegenerative disorders: Assessing the impact of natural vs drug-induced treatment options. Aging Med (Milton) 2023; 6:82-97. [PMID: 36911087 PMCID: PMC10000287 DOI: 10.1002/agm2.12243] [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: 12/30/2022] [Revised: 01/15/2023] [Accepted: 01/29/2023] [Indexed: 02/24/2023] Open
Abstract
Neurodegenerative illnesses refer to the gradual, cumulative loss of neural activity. Neurological conditions are considered to be the second leading cause of mortality in the modern world and the two most prevalent ones are Parkinson's disease and Alzheimer's disease. The negative side effects of pharmaceutical use are a major global concern, despite the availability of many different treatments for therapy. We concentrated on different types of neurological problems and their influence on targets, in vitro, in vivo, and in silico methods toward neurological disorders, as well as the molecular approaches influencing the same, in the first half of the review. The bulk of the second half of the review focuses on the many categories of treatment possibilities, including natural and artificial. Nevertheless, herbal treatment solutions are piquing scholarly attention due to their anti-oxidative properties and accessibility. However, more quality investigations and innovations are undoubtedly needed to back up these conclusions.
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Affiliation(s)
- Sakshi Mathur
- Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth Pune Maharashtra India
| | - Chaitali Gawas
- Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth Pune Maharashtra India
| | | | - Minal Wani
- Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth Pune Maharashtra India
| | - Heena Tabassum
- Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth Pune Maharashtra India
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Monteiro AR, Barbosa DJ, Remião F, Silva R. Alzheimer’s disease: insights and new prospects in disease pathophysiology, biomarkers and disease-modifying drugs. Biochem Pharmacol 2023; 211:115522. [PMID: 36996971 DOI: 10.1016/j.bcp.2023.115522] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023]
Abstract
Alzheimer's disease (AD) is one of the most prevalent neurodegenerative diseases that affect millions of people worldwide, with both prevalence and incidence increasing with age. It is characterized by cognitive decline associated, specifically, with degeneration of cholinergic neurons. The problem of this disease is even more fundamental as the available therapies remain fairly limited and mainly focused on symptoms' relief. Although the aetiology of the disease remains elusive, two main pathological hallmarks are described: i) presence of neurofibrillary tangles formed by unfolded protein aggregates (hyperphosphorylated Tau protein) and ii) presence of extracellular aggregates of amyloid-beta peptide. Given the complexity surrounding the pathogenesis of the disease, several potential targets have been highlighted and interrelated upon its progression, such as oxidative stress and the accumulation of metal ions. Thus, advances have been made on the development of innovative multitarget therapeutical compounds to delay the disease progression and restore cell function. This review focuses the ongoing research on new insights and emerging disease-modifying drugs for AD treatment. Furthermore, classical and novel potential biomarkers for early diagnosis of the disease, and their role in assisting on the improvement of targeted therapies will also be approached.
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Affiliation(s)
- Ana R Monteiro
- UCIBIO - Applied Molecular Biosciences Unit, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, Porto University, 4050-313 Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Daniel J Barbosa
- TOXRUN - Toxicology Research Unit, Department of Sciences, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal; Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Fernando Remião
- UCIBIO - Applied Molecular Biosciences Unit, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, Porto University, 4050-313 Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Renata Silva
- UCIBIO - Applied Molecular Biosciences Unit, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, Porto University, 4050-313 Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal.
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21
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Gallardo VJ, Vila-Pueyo M, Pozo-Rosich P. The impact of epigenetic mechanisms in migraine: Current knowledge and future directions. Cephalalgia 2023; 43:3331024221145916. [PMID: 36759209 DOI: 10.1177/03331024221145916] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
BACKGROUND Epigenetic mechanisms, including DNA methylation, microRNAs and histone modifications, may modulate the genetic expression in migraine and its interaction with internal and external factors, such as lifestyle and environmental changes. OBJECTIVE To summarize, contextualize and critically analyze the published literature on the current state of epigenetic mechanisms in migraine in a narrative review. FINDINGS The studies published to date have used different approaches and methodologies to determine the role of epigenetic mechanisms in migraine. Epigenetic changes seem to be involved in migraine and are increasing our knowledge of the disease. CONCLUSIONS Changes in DNA methylation, microRNA expression and histone modifications could be utilized as biomarkers that would be highly valuable for patient stratification, molecular diagnosis, and precision medicine in migraine.
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Affiliation(s)
- Víctor José Gallardo
- Headache and Neurological Pain Research Group, Vall d'Hebron Institute of Research, Universitat Autònoma de Barcelona, Spain
| | - Marta Vila-Pueyo
- Headache and Neurological Pain Research Group, Vall d'Hebron Institute of Research, Universitat Autònoma de Barcelona, Spain
| | - Patricia Pozo-Rosich
- Headache and Neurological Pain Research Group, Vall d'Hebron Institute of Research, Universitat Autònoma de Barcelona, Spain.,Headache Unit, Neurology Department, Vall d'Hebron University Hospital, Barcelona, Spain
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22
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Jiang D, Li T, Guo C, Tang TS, Liu H. Small molecule modulators of chromatin remodeling: from neurodevelopment to neurodegeneration. Cell Biosci 2023; 13:10. [PMID: 36647159 PMCID: PMC9841685 DOI: 10.1186/s13578-023-00953-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
The dynamic changes in chromatin conformation alter the organization and structure of the genome and further regulate gene transcription. Basically, the chromatin structure is controlled by reversible, enzyme-catalyzed covalent modifications to chromatin components and by noncovalent ATP-dependent modifications via chromatin remodeling complexes, including switch/sucrose nonfermentable (SWI/SNF), inositol-requiring 80 (INO80), imitation switch (ISWI) and chromodomain-helicase DNA-binding protein (CHD) complexes. Recent studies have shown that chromatin remodeling is essential in different stages of postnatal and adult neurogenesis. Chromatin deregulation, which leads to defects in epigenetic gene regulation and further pathological gene expression programs, often causes a wide range of pathologies. This review first gives an overview of the regulatory mechanisms of chromatin remodeling. We then focus mainly on discussing the physiological functions of chromatin remodeling, particularly histone and DNA modifications and the four classes of ATP-dependent chromatin-remodeling enzymes, in the central and peripheral nervous systems under healthy and pathological conditions, that is, in neurodegenerative disorders. Finally, we provide an update on the development of potent and selective small molecule modulators targeting various chromatin-modifying proteins commonly associated with neurodegenerative diseases and their potential clinical applications.
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Affiliation(s)
- Dongfang Jiang
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Tingting Li
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Caixia Guo
- grid.9227.e0000000119573309Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Tie-Shan Tang
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Hongmei Liu
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China
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23
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Jiao L, Liu Y, Yu XY, Pan X, Zhang Y, Tu J, Song YH, Li Y. Ribosome biogenesis in disease: new players and therapeutic targets. Signal Transduct Target Ther 2023; 8:15. [PMID: 36617563 PMCID: PMC9826790 DOI: 10.1038/s41392-022-01285-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 01/10/2023] Open
Abstract
The ribosome is a multi-unit complex that translates mRNA into protein. Ribosome biogenesis is the process that generates ribosomes and plays an essential role in cell proliferation, differentiation, apoptosis, development, and transformation. The mTORC1, Myc, and noncoding RNA signaling pathways are the primary mediators that work jointly with RNA polymerases and ribosome proteins to control ribosome biogenesis and protein synthesis. Activation of mTORC1 is required for normal fetal growth and development and tissue regeneration after birth. Myc is implicated in cancer development by enhancing RNA Pol II activity, leading to uncontrolled cancer cell growth. The deregulation of noncoding RNAs such as microRNAs, long noncoding RNAs, and circular RNAs is involved in developing blood, neurodegenerative diseases, and atherosclerosis. We review the similarities and differences between eukaryotic and bacterial ribosomes and the molecular mechanism of ribosome-targeting antibiotics and bacterial resistance. We also review the most recent findings of ribosome dysfunction in COVID-19 and other conditions and discuss the consequences of ribosome frameshifting, ribosome-stalling, and ribosome-collision. We summarize the role of ribosome biogenesis in the development of various diseases. Furthermore, we review the current clinical trials, prospective vaccines for COVID-19, and therapies targeting ribosome biogenesis in cancer, cardiovascular disease, aging, and neurodegenerative disease.
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Affiliation(s)
- Lijuan Jiao
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Yuzhe Liu
- grid.452829.00000000417660726Department of Orthopedics, the Second Hospital of Jilin University, Changchun, Jilin 130000 P. R. China
| | - Xi-Yong Yu
- grid.410737.60000 0000 8653 1072Key Laboratory of Molecular Target & Clinical Pharmacology and the NMPA State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, Guangdong 511436 P. R. China
| | - Xiangbin Pan
- grid.506261.60000 0001 0706 7839Department of Structural Heart Disease, National Center for Cardiovascular Disease, China & Fuwai Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China ,Key Laboratory of Cardiovascular Appratus Innovation, Beijing, 100037 P. R. China
| | - Yu Zhang
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Junchu Tu
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Yao-Hua Song
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, P. R. China. .,State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, P. R. China.
| | - Yangxin Li
- Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu, 215123, P. R. China.
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Abraham Daniel A, Silzer T, Sun J, Zhou Z, Hall C, Phillips N, Barber R. Hypermethylation at CREBBP Is Associated with Cognitive Impairment in a Mexican American Cohort. J Alzheimers Dis 2023; 92:1229-1239. [PMID: 36872777 PMCID: PMC10200223 DOI: 10.3233/jad-221031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2023] [Indexed: 03/06/2023]
Abstract
BACKGROUND The aging Mexican American (MA) population is the fastest growing ethnic minority group in the US. MAs have a unique metabolic-related risk for Alzheimer's disease (AD) and mild cognitive impairment (MCI), compared to non-Hispanic whites (NHW). This risk for cognitive impairment (CI) is multifactorial involving genetics, environmental, and lifestyle factors. Changes in environment and lifestyle can alter patterns and even possibly reverse derangement of DNA methylation (a form of epigenetic regulation). OBJECTIVE We sought to identify ethnicity-specific DNA methylation profiles that may be associated with CI in MAs and NHWs. METHODS DNA obtained from peripheral blood of 551 participants from the Texas Alzheimer's Research and Care Consortium was typed on the Illumina Infinium® MethylationEPIC chip array, which assesses over 850K CpG genomic sites. Within each ethnic group (N = 299 MAs, N = 252 NHWs), participants were stratified by cognitive status (control versus CI). Beta values, representing relative degree of methylation, were normalized using the Beta MIxture Quantile dilation method and assessed for differential methylation using the Chip Analysis Methylation Pipeline (ChAMP), limma and cate packages in R. RESULTS Two differentially methylated sites were significant: cg13135255 (MAs) and cg27002303 (NHWs) based on an FDR p < 0.05. Three suggestive sites obtained were cg01887506 (MAs) and cg10607142 and cg13529380 (NHWs). Most methylation sites were hypermethylated in CI compared to controls, except cg13529380 which was hypomethylated. CONCLUSION The strongest association with CI was at cg13135255 (FDR-adjusted p = 0.029 in MAs), within the CREBBP gene. Moving forward, identifying additional ethnicity-specific methylation sites may be useful to discern CI risk in MAs.
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Affiliation(s)
- Ann Abraham Daniel
- Department of Microbiology, Immunology and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Talisa Silzer
- Department of Microbiology, Immunology and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Jie Sun
- Department of Microbiology, Immunology and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Zhengyang Zhou
- Department of Biostatistics and Epidemiology, School of Public Health, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Courtney Hall
- Department of Microbiology, Immunology and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Nicole Phillips
- Department of Microbiology, Immunology and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Robert Barber
- Department of Family and Manipulative Medicine, Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX, USA
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Raval M, Mishra S, Tiwari AK. Epigenetic regulons in Alzheimer's disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:185-247. [DOI: 10.1016/bs.pmbts.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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26
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Zhao Y, Zhang Y, Meng S, Chen B, Dong X, Guo X, Guo F, Zhang R, Cui H, Li S. Effects of S-Adenosylmethionine on Cognition in Animals and Humans: A Systematic Review and Meta-Analysis of Randomized Controlled Trials. J Alzheimers Dis 2023; 94:S267-S287. [PMID: 36970898 PMCID: PMC10473070 DOI: 10.3233/jad-221076] [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: 02/24/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND There is increasing evidence that supplementation of S-adenosylmethionine (SAM) can improve cognitive function in animals and humans, although the outcomes are not always inconsistent. OBJECTIVE We conducted a systematic review and meta-analysis to evaluate the correlation between SAM supplementation and improved cognitive function. METHODS We searched studies in the PubMed, Cochrane Library, Embase, Web of Science, and Clinical Trials databases from January 1, 2002 to January 1, 2022. Risk of bias was assessed using the Cochrane risk of bias 2.0 (human studies) and the Systematic Review Center for Laboratory Animal Experimentation risk of bias (animal studies) tools; and evidence quality was evaluated using the Grading of Recommendations Assessment, Development, and Evaluation. STATA software was employed to perform meta-analysis, and the random-effects models was used to evaluate the standardized mean difference with 95% confidence intervals. RESULTS Out of the 2,375 studies screened, 30 studies met the inclusion criteria. Meta-analyses of animal (p = 0.213) and human (p = 0.047) studies showed that there were no significant differences between the SAM supplementation and control groups. The results of the subgroup analyses showed that the animals aged ≤8 weeks (p = 0.027) and the intervention duration >8 weeks (p = 0.009) were significantly different compared to the controls. Additionally, the Morris water maze test (p = 0.005) used to assess the cognitive level of the animals revealed that SAM could enhance spatial learning and memory in animals. CONCLUSION SAM supplementation showed no significant improvement in cognition. Therefore, further studies are needed to assess the effectiveness of SAM supplementation.
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Affiliation(s)
- Yan Zhao
- Department of Anatomy, Hebei Medical University, Shijiazhuang, China
- Neuroscience Research Center, Hebei Medical University, Shijiazhuang, China
- School of Nursing, Hebei Medical University, Shijiazhuang, China
| | - Yizhou Zhang
- Department of Anatomy, Hebei Medical University, Shijiazhuang, China
- Neuroscience Research Center, Hebei Medical University, Shijiazhuang, China
- Hebei Key Laboratory of Neurodegenerative Disease Mechanism, Shijiazhuang, China
| | - Sijia Meng
- School of Nursing, Hebei Medical University, Shijiazhuang, China
| | - Bingyu Chen
- Department of Anatomy, Hebei Medical University, Shijiazhuang, China
- Neuroscience Research Center, Hebei Medical University, Shijiazhuang, China
| | - Xinyi Dong
- School of Nursing, Hebei Medical University, Shijiazhuang, China
| | - Xiaojing Guo
- School of Nursing, Hebei Medical University, Shijiazhuang, China
| | - Fangzhen Guo
- Department of Anatomy, Hebei Medical University, Shijiazhuang, China
- Neuroscience Research Center, Hebei Medical University, Shijiazhuang, China
| | - Runjiao Zhang
- Department of Anatomy, Hebei Medical University, Shijiazhuang, China
- Neuroscience Research Center, Hebei Medical University, Shijiazhuang, China
| | - Huixian Cui
- Department of Anatomy, Hebei Medical University, Shijiazhuang, China
- Neuroscience Research Center, Hebei Medical University, Shijiazhuang, China
- Hebei Key Laboratory of Neurodegenerative Disease Mechanism, Shijiazhuang, China
| | - Sha Li
- Department of Anatomy, Hebei Medical University, Shijiazhuang, China
- Neuroscience Research Center, Hebei Medical University, Shijiazhuang, China
- Hebei Key Laboratory of Neurodegenerative Disease Mechanism, Shijiazhuang, China
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27
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The role of DNA methylation in progression of neurological disorders and neurodegenerative diseases as well as the prospect of using DNA methylation inhibitors as therapeutic agents for such disorders. IBRO Neurosci Rep 2022; 14:28-37. [PMID: 36590248 PMCID: PMC9794904 DOI: 10.1016/j.ibneur.2022.12.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/23/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Genome-wide studies related to neurological disorders and neurodegenerative diseases have pointed to the role of epigenetic changes such as DNA methylation, histone modification, and noncoding RNAs. DNA methylation machinery controls the dynamic regulation of methylation patterns in discrete brain regions. Objective This review aims to describe the role of DNA methylation in inhibiting and progressing neurological and neurodegenerative disorders and therapeutic approaches. Methods A Systematic search of PubMed, Web of Science, and Cochrane Library was conducted for all qualified studies from 2000 to 2022. Results For the current need of time, we have focused on the DNA methylation role in neurological and neurodegenerative diseases and the expression of genes involved in neurodegeneration such as Alzheimer's, Depression, and Rett Syndrome. Finally, it appears that the various epigenetic changes do not occur separately and that DNA methylation and histone modification changes occur side by side and affect each other. We focused on the role of modification of DNA methylation in several genes associated with depression (NR3C1, NR3C2, CRHR1, SLC6A4, BDNF, and FKBP5), Rett syndrome (MECP2), Alzheimer's, depression (APP, BACE1, BIN1 or ANK1) and Parkinson's disease (SNCA), as well as the co-occurring modifications to histones and expression of non-coding RNAs. Understanding these epigenetic changes and their interactions will lead to better treatment strategies. Conclusion This review captures the state of understanding of the epigenetics of neurological and neurodegenerative diseases. With new epigenetic mechanisms and targets undoubtedly on the horizon, pharmacological modulation and regulation of epigenetic processes in the brain holds great promise for therapy.
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Osaka R, Kobayashi N, Shimada K, Ishii A, Oka N, Kondo K. VP26, a herpes simplex virus type 1 capsid protein, increases DNA methylation in COASY promoter region. Brain Behav Immun Health 2022; 26:100545. [PMCID: PMC9636445 DOI: 10.1016/j.bbih.2022.100545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/20/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
| | - Nobuyuki Kobayashi
- Corresponding author. Department of Virology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan.
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Savelieff MG, Chen KS, Elzinga SE, Feldman EL. Diabetes and dementia: Clinical perspective, innovation, knowledge gaps. J Diabetes Complications 2022; 36:108333. [PMID: 36240668 PMCID: PMC10076101 DOI: 10.1016/j.jdiacomp.2022.108333] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/30/2022] [Indexed: 10/31/2022]
Abstract
The world faces a pandemic-level prevalence of type 2 diabetes. In parallel with this massive burden of metabolic disease is the growing prevalence of dementia as the population ages. The two health issues are intertwined. The Lancet Commission on dementia prevention, intervention, and care was convened to tackle the growing global concern of dementia by identifying risk factors. It concluded, along with other studies, that diabetes as well as obesity and the metabolic syndrome more broadly, which are frequently comorbid, raise the risk of developing dementia. Type 2 diabetes is a modifiable risk factor; however, it is uncertain whether anti-diabetic drugs mitigate risk of developing dementia. Reasons are manifold but constitute a critical knowledge gap in the field. This review outlines studies of type 2 diabetes on risk of dementia, illustrating key concepts. Moreover, it identifies knowledge gaps, reviews strategies to help fill these gaps, and concludes with a series of recommendations to mitigate risk and advance understanding of type 2 diabetes and dementia.
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Affiliation(s)
- Masha G Savelieff
- NeuroNetwork for Emerging Therapies, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kevin S Chen
- NeuroNetwork for Emerging Therapies, University of Michigan, Ann Arbor, MI 48109, USA; Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Neurosurgery, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Sarah E Elzinga
- NeuroNetwork for Emerging Therapies, University of Michigan, Ann Arbor, MI 48109, USA; Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Eva L Feldman
- NeuroNetwork for Emerging Therapies, University of Michigan, Ann Arbor, MI 48109, USA; Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA.
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30
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Shireby G, Dempster EL, Policicchio S, Smith RG, Pishva E, Chioza B, Davies JP, Burrage J, Lunnon K, Seiler Vellame D, Love S, Thomas A, Brookes K, Morgan K, Francis P, Hannon E, Mill J. DNA methylation signatures of Alzheimer's disease neuropathology in the cortex are primarily driven by variation in non-neuronal cell-types. Nat Commun 2022; 13:5620. [PMID: 36153390 PMCID: PMC9509387 DOI: 10.1038/s41467-022-33394-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022] Open
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disease characterized by the progressive accumulation of amyloid-beta and neurofibrillary tangles of tau in the neocortex. We profiled DNA methylation in two regions of the cortex from 631 donors, performing an epigenome-wide association study of multiple measures of AD neuropathology. We meta-analyzed our results with those from previous studies of DNA methylation in AD cortex (total n = 2013 donors), identifying 334 cortical differentially methylated positions (DMPs) associated with AD pathology including methylomic variation at loci not previously implicated in dementia. We subsequently profiled DNA methylation in NeuN+ (neuronal-enriched), SOX10+ (oligodendrocyte-enriched) and NeuN-/SOX10- (microglia- and astrocyte-enriched) nuclei, finding that the majority of DMPs identified in 'bulk' cortex tissue reflect DNA methylation differences occurring in non-neuronal cells. Our study highlights the power of utilizing multiple measures of neuropathology to identify epigenetic signatures of AD and the importance of characterizing disease-associated variation in purified cell-types.
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Affiliation(s)
- Gemma Shireby
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Emma L Dempster
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Stefania Policicchio
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Rebecca G Smith
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Ehsan Pishva
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
| | - Barry Chioza
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan P Davies
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Joe Burrage
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Katie Lunnon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Dorothea Seiler Vellame
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Seth Love
- Dementia Research Group, University of Bristol Medical School (Translational Health Sciences), Bristol, UK
| | - Alan Thomas
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Keeley Brookes
- Biosciences, School of Science & Technology, Nottingham Trent University, Nottingham, UK
| | - Kevin Morgan
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Paul Francis
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
- Wolfson Centre for Age-Related Diseases, King's College London, London, UK
| | - Eilis Hannon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK.
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Gao SQ, Zhao JH, Guan Y, Tang YS, Li Y, Liu LY. Mass Spectrometry Imaging technology in metabolomics: a systematic review. Biomed Chromatogr 2022:e5494. [PMID: 36044038 DOI: 10.1002/bmc.5494] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 11/11/2022]
Abstract
Mass spectrometry imaging (MSI) is a powerful label-free analysis technique that can provide simultaneous spatial distribution of multiple compounds in a single experiment. By combining the sensitive and rapid screening of high-throughput mass spectrometry with spatial chemical information, metabolite analysis and morphological characteristics are presented in a single image. MSI can be used for qualitative and quantitative analysis of metabolic profiles and it can provide visual analysis of spatial distribution information of complex biological and microbial systems. Matrix assisted laser desorption ionization, laser ablation electrospray ionization and desorption electrospray ionization are commonly used in MSI. Here, we summarize and compare these three technologies, as well as the applications and prospects of MSI in metabolomics.
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Affiliation(s)
- Si-Qi Gao
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, Harbin, P. R. China
| | - Jin-Hui Zhao
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, Harbin, P. R. China
| | - Yue Guan
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, Harbin, P. R. China
| | - Ying-Shu Tang
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, Harbin, P. R. China
| | - Ying Li
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, Harbin, P. R. China
| | - Li-Yan Liu
- Department of Nutrition and Food Hygiene, Public Health College, Harbin Medical University, Harbin, P. R. China
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Profile of TREM2-Derived circRNA and mRNA Variants in the Entorhinal Cortex of Alzheimer’s Disease Patients. Int J Mol Sci 2022; 23:ijms23147682. [PMID: 35887031 PMCID: PMC9320643 DOI: 10.3390/ijms23147682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 02/04/2023] Open
Abstract
Genetic variants in TREM2, a microglia-related gene, are well-known risk factors for Alzheimer’s disease (AD). Here, we report that TREM2 originates from circular RNAs (circRNAs), a novel class of non-coding RNAs characterized by a covalent and stable closed-loop structure. First, divergent primers were designed to amplify circRNAs by RT-PCR, which were further assessed by Sanger sequencing. Then, additional primer sets were used to confirm back-splicing junctions. In addition, HMC3 cells were used to assess the microglial expression of circTREM2s. Three candidate circTREM2s were identified in control and AD human entorhinal samples. One of the circRNAs, circTREM2_1, was consistently amplified by all divergent primer sets in control and AD entorhinal cortex samples as well as in HMC3 cells. In AD cases, a moderate negative correlation (r = −0.434) was found between the global average area of Aβ deposits in the entorhinal cortex and circTREM2_1 expression level. In addition, by bioinformatics tools, a total of 16 miRNAs were predicted to join with circTREM2s. Finally, TREM2 mRNA corresponding to four isoforms was profiled by RT-qPCR. TREM2 mRNA levels were found elevated in entorhinal samples of AD patients with low or intermediate ABC scores compared to controls. To sum up, a novel circRNA derived from the TREM2 gene, circTREM2_1, has been identified in the human entorhinal cortex and TREM2 mRNA expression has been detected to increase in AD compared to controls. Unraveling the molecular genetics of the TREM2 gene may help to better know the innate immune response in AD.
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Abdelraheem E, Thair B, Varela RF, Jockmann E, Popadić D, Hailes HC, Ward JM, Iribarren AM, Lewkowicz ES, Andexer JN, Hagedoorn PL, Hanefeld U. Methyltransferases, functions and applications. Chembiochem 2022; 23:e202200212. [PMID: 35691829 PMCID: PMC9539859 DOI: 10.1002/cbic.202200212] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/10/2022] [Indexed: 11/25/2022]
Abstract
In this review the current state‐of‐the‐art of S‐adenosylmethionine (SAM)‐dependent methyltransferases and SAM are evaluated. Their structural classification and diversity is introduced and key mechanistic aspects presented which are then detailed further. Then, catalytic SAM as a target for drugs, and approaches to utilise SAM as a cofactor in synthesis are introduced with different supply and regeneration approaches evaluated. The use of SAM analogues are also described. Finally O‐, N‐, C‐ and S‐MTs, their synthetic applications and potential for compound diversification is given.
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Affiliation(s)
| | - Benjamin Thair
- University College London Faculty of Mathematical and Physical Sciences, department of Chemistry, UNITED KINGDOM
| | - Romina Fernández Varela
- Universidad nacional di Quilmes, 3Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, ARGENTINA
| | - Emely Jockmann
- Albert-Ludwigs-Universitat Freiburg Universitatsbibliothek Freiburg, Pharmacie, GERMANY
| | | | - Helen C Hailes
- University College London Faculty of Mathematical and Physical Sciences, department of Chemistry, UNITED KINGDOM
| | - John M Ward
- University College London, Department of Biochemical Engineering, UNITED KINGDOM
| | - Adolfo M Iribarren
- Universidad Nacional de Quilmes, 3Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, ARGENTINA
| | - Elizabeth S Lewkowicz
- Universidad Nacional de Quilmes, Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, ARGENTINA
| | | | | | - Ulf Hanefeld
- Technische Universiteit Delft, Gebouw voor Scheikunde, Julianalaan 136, 2628 BL, Delft, NETHERLANDS
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34
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Chen F, Wang N, He X. Identification of Differential Genes of DNA Methylation Associated With Alzheimer's Disease Based on Integrated Bioinformatics and Its Diagnostic Significance. Front Aging Neurosci 2022; 14:884367. [PMID: 35615586 PMCID: PMC9125150 DOI: 10.3389/fnagi.2022.884367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/19/2022] [Indexed: 12/16/2022] Open
Abstract
Background Alzheimer's disease (AD) is a common neurodegenerative disease. The pathogenesis is complex and has not been clearly elucidated, and there is no effective treatment. Recent studies have demonstrated that DNA methylation is closely associated with the pathogenesis of AD, which sheds light on investigating potential biomarkers for the diagnosis of early AD and related possible therapeutic approaches. Methods Alzheimer's disease patients samples and healthy controls samples were collected from two datasets in the GEO database. Using LIMMA software package in R language to find differentially expressed genes (DEGs). Afterward, DEGs have been subjected to enrichment analysis of GO and KEGG pathways. The PPI networks and Hub genes were created and visualized based on the STRING database and Cytoscape. ROC curves were further constructed to analyze the accuracy of these genes for AD diagnosis. Results Analysis of the GSE109887 and GSE97760 datasets showed 477 significant DEGs. GO and KEGG enrichment analysis showed terms related to biological processes related to these genes. The top ten Hub genes were found on the basis of the PPI network using the CytoHubba plugin, and the AUC areas of these top ranked genes were all greater than 0.7, showing satisfactory diagnostic accuracy. Conclusion The study identified the top 10 Hub genes associated with AD-related DNA methylation, of which RPSA, RPS23, and RPLP0 have high diagnostic accuracy and excellent AD biomarker potential.
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Affiliation(s)
| | | | - Xiaping He
- School of Basic Medical Sciences, Dali University, Dali, China
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35
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Li Z, Guo W, Zeng T, Yin J, Feng K, Huang T, Cai YD. Detecting Brain Structure-Specific Methylation Signatures and Rules for Alzheimer's Disease. Front Neurosci 2022; 16:895181. [PMID: 35585924 PMCID: PMC9108872 DOI: 10.3389/fnins.2022.895181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 04/11/2022] [Indexed: 01/01/2023] Open
Abstract
Alzheimer's disease (AD) is a progressive disease that leads to irreversible behavioral changes, erratic emotions, and loss of motor skills. These conditions make people with AD hard or almost impossible to take care of. Multiple internal and external pathological factors may affect or even trigger the initiation and progression of AD. DNA methylation is one of the most effective regulatory roles during AD pathogenesis, and pathological methylation alterations may be potentially different in the various brain structures of people with AD. Although multiple loci associated with AD initiation and progression have been identified, the spatial distribution patterns of AD-associated DNA methylation in the brain have not been clarified. According to the systematic methylation profiles on different structural brain regions, we applied multiple machine learning algorithms to investigate such profiles. First, the profile on each brain region was analyzed by the Boruta feature filtering method. Some important methylation features were extracted and further analyzed by the max-relevance and min-redundancy method, resulting in a feature list. Then, the incremental feature selection method, incorporating some classification algorithms, adopted such list to identify candidate AD-associated loci at methylation with structural specificity, establish a group of quantitative rules for revealing the effects of DNA methylation in various brain regions (i.e., four brain structures) on AD pathogenesis. Furthermore, some efficient classifiers based on essential methylation sites were proposed to identify AD samples. Results revealed that methylation alterations in different brain structures have different contributions to AD pathogenesis. This study further illustrates the complex pathological mechanisms of AD.
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Affiliation(s)
- ZhanDong Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tao Zeng
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jie Yin
- Cancer Institute, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Human Genetics, Institute of Genetics, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - KaiYan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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Guemri J, Pierre-Jean M, Brohard S, Oussada N, Horgues C, Bonnet E, Mauger F, Deleuze JF. Methylated ccfDNA from plasma biomarkers of Alzheimer's disease using targeted bisulfite sequencing. Epigenomics 2022; 14:451-468. [PMID: 35416052 DOI: 10.2217/epi-2021-0491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Noninvasive biomarkers such as methylated ccfDNA from plasma could help to support the diagnosis of Alzheimer's disease (AD). Methods: A targeted sequencing protocol was developed to identify candidate biomarkers of AD in methylated ccfDNA extracted from plasma. Results: The authors identified differentially methylated CpGs, regions of which were the same as those identified in previous AD studies. Specifically, a differentially methylated CpG of the LHX2 gene previously identified in a plasma study of AD was replicated in the study. The MBP and DUSP22 regions have been identified in other brain studies of AD and in the authors' study. Conclusion: Although these biomarkers must be validated in other cohorts, methylated ccfDNA could be a relevant noninvasive biomarker in AD.
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Affiliation(s)
- Julien Guemri
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Morgane Pierre-Jean
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Solène Brohard
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Nouara Oussada
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Caroline Horgues
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Eric Bonnet
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Florence Mauger
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
| | - Jean-François Deleuze
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Recherche en Génomique Humaine, Evry, 91057, France
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37
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Personalized Management and Treatment of Alzheimer's Disease. Life (Basel) 2022; 12:life12030460. [PMID: 35330211 PMCID: PMC8951963 DOI: 10.3390/life12030460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 11/16/2022] Open
Abstract
Alzheimer’s disease (AD) is a priority health problem with a high cost to society and a large consumption of medical and social resources. The management of AD patients is complex and multidisciplinary. Over 90% of patients suffer from concomitant diseases and require personalized therapeutic regimens to reduce adverse drug reactions (ADRs), drug−drug interactions (DDIs), and unnecessary costs. Men and women show substantial differences in their AD-related phenotypes. Genomic, epigenetic, neuroimaging, and biochemical biomarkers are useful for predictive and differential diagnosis. The most frequent concomitant diseases include hypertension (>25%), obesity (>70%), diabetes mellitus type 2 (>25%), hypercholesterolemia (40%), hypertriglyceridemia (20%), metabolic syndrome (20%), hepatobiliary disorder (15%), endocrine/metabolic disorders (>20%), cardiovascular disorder (40%), cerebrovascular disorder (60−90%), neuropsychiatric disorders (60−90%), and cancer (10%). Over 90% of AD patients require multifactorial treatments with risk of ADRs and DDIs. The implementation of pharmacogenetics in clinical practice can help optimize the limited therapeutic resources available to treat AD and personalize the use of anti-dementia drugs, in combination with other medications, for the treatment of concomitant disorders.
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Cacabelos R, Naidoo V, Martínez-Iglesias O, Corzo L, Cacabelos N, Pego R, Carril JC. Pharmacogenomics of Alzheimer's Disease: Novel Strategies for Drug Utilization and Development. Methods Mol Biol 2022; 2547:275-387. [PMID: 36068470 DOI: 10.1007/978-1-0716-2573-6_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Alzheimer's disease (AD) is a priority health problem in developed countries with a high cost to society. Approximately 20% of direct costs are associated with pharmacological treatment. Over 90% of patients require multifactorial treatments, with risk of adverse drug reactions (ADRs) and drug-drug interactions (DDIs) for the treatment of concomitant diseases such as hypertension (>25%), obesity (>70%), diabetes mellitus type 2 (>25%), hypercholesterolemia (40%), hypertriglyceridemia (20%), metabolic syndrome (20%), hepatobiliary disorder (15%), endocrine/metabolic disorders (>20%), cardiovascular disorder (40%), cerebrovascular disorder (60-90%), neuropsychiatric disorders (60-90%), and cancer (10%).For the past decades, pharmacological studies in search of potential treatments for AD focused on the following categories: neurotransmitter enhancers (11.38%), multitarget drugs (2.45%), anti-amyloid agents (13.30%), anti-tau agents (2.03%), natural products and derivatives (25.58%), novel synthetic drugs (8.13%), novel targets (5.66%), repository drugs (11.77%), anti-inflammatory drugs (1.20%), neuroprotective peptides (1.25%), stem cell therapy (1.85%), nanocarriers/nanotherapeutics (1.52%), and other compounds (<1%).Pharmacogenetic studies have shown that the therapeutic response to drugs in AD is genotype-specific in close association with the gene clusters that constitute the pharmacogenetic machinery (pathogenic, mechanistic, metabolic, transporter, pleiotropic genes) under the regulatory control of epigenetic mechanisms (DNA methylation, histone/chromatin remodeling, microRNA regulation). Most AD patients (>60%) are carriers of over ten pathogenic genes. The genes that most frequently (>50%) accumulate pathogenic variants in the same AD case are A2M (54.38%), ACE (78.94%), BIN1 (57.89%), CLU (63.15%), CPZ (63.15%), LHFPL6 (52.63%), MS4A4E (50.87%), MS4A6A (63.15%), PICALM (54.38%), PRNP (80.7059), and PSEN1 (77.19%). There is also an accumulation of 15 to 26 defective pharmagenes in approximately 85% of AD patients. About 50% of AD patients are carriers of at least 20 mutant pharmagenes, and over 80% are deficient metabolizers for the most common drugs, which are metabolized via the CYP2D6, CYP2C9, CYP2C19, and CYP3A4/5 enzymes.The implementation of pharmacogenetics can help optimize drug development and the limited therapeutic resources available to treat AD, and personalize the use of anti-dementia drugs in combination with other medications for the treatment of concomitant disorders.
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Affiliation(s)
- Ramón Cacabelos
- Department of Genomic Medicine, International Center of Neuroscience and Genomic Medicine, EuroEspes Biomedical Research Center, Corunna, Spain.
| | - Vinogran Naidoo
- Department of Neuroscience, International Center of Neuroscience and Genomic Medicine, EuroEspes Biomedical Research Center, Corunna, Spain
| | - Olaia Martínez-Iglesias
- Department of Medical Epigenetics, International Center of Neuroscience and Genomic Medicine, EuroEspes Biomedical Research Center, Corunna, Spain
| | - Lola Corzo
- Department of Medical Biochemistry, International Center of Neuroscience and Genomic Medicine, EuroEspes Biomedical Research Center, Corunna, Spain
| | - Natalia Cacabelos
- Department of Medical Documentation, International Center of Neuroscience and Genomic Medicine, EuroEspes Biomedical Research Center, Corunna, Spain
| | - Rocío Pego
- Department of Neuropsychology, International Center of Neuroscience and Genomic Medicine, EuroEspes Biomedical Research Center, Corunna, Spain
| | - Juan C Carril
- Department of Genomics and Pharmacogenomics, International Center of Neuroscience and Genomic Medicine, EuroEspes Biomedical Research Center, Corunna, Spain
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Kloske CM, Dugan AJ, Weekman EM, Winder Z, Patel E, Nelson PT, Fardo DW, Wilcock DM. Inflammatory Pathways Are Impaired in Alzheimer Disease and Differentially Associated With Apolipoprotein E Status. J Neuropathol Exp Neurol 2021; 80:922-932. [PMID: 34486652 PMCID: PMC8557334 DOI: 10.1093/jnen/nlab085] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Alzheimer disease (AD) is a neurodegenerative disease characterized by a cognitive decline leading to dementia. The most impactful genetic risk factor is apolipoprotein E (APOE). APOE-ε4 significantly increases AD risk, APOE-ε3 is the most common gene variant, and APOE-ε2 protects against AD. However, the underlying mechanisms of APOE-ε4 on AD risk remains unclear, with APOE-ε4 impacting many pathways. We investigated how the APOE isoforms associated with the neuroinflammatory state of the brain with and without AD pathology. Frozen brain tissue from the superior and middle temporal gyrus was analyzed from APOE-ε3/3 (n = 9) or APOE-ε4/4 (n = 10) participants with AD pathology and APOE-ε3/3 (n = 9) participants without AD pathology. We determined transcript levels of 757 inflammatory related genes using the NanoString Human Neuroinflammation Panel. We found significant pathways impaired in APOE-ε4/4-AD individuals compared to APOE-ε3/3-AD. Of interest, expression of genes related to microglial activation (SALL1), motility (FSCN1), epigenetics (DNMT1), and others showed altered expression. Additionally, we performed immunohistochemistry of P2RY12 to confirm reduced microglial activation. Our results suggest APOE-ε3 responds to AD pathology while potentially having a harmful long-term inflammatory response, while APOE-ε4 shows a weakened response to pathology. Overall, APOE isoforms appear to modulate the brain immune response to AD-type pathology.
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Affiliation(s)
- Courtney M Kloske
- From the Department of Physiology, Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Adam J Dugan
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, Kentucky, USA
| | - Erica M Weekman
- From the Department of Physiology, Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Zachary Winder
- From the Department of Physiology, Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Ela Patel
- Department of Pathology and Laboratory Medicine, Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Peter T Nelson
- Department of Pathology and Laboratory Medicine, Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - David W Fardo
- Department of Biostatics, Sanders-Brown Center on Aging, College of Public Health, University of Kentucky, Lexington, Kentucky, USA
| | - Donna M Wilcock
- From the Department of Physiology, Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, Kentucky, USA
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40
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Wei X, Du P, Zhao Z. Impacts of DNA methylation on Tau protein related genes in the brains of patients with Alzheimer's disease. Neurosci Lett 2021; 763:136196. [PMID: 34437990 DOI: 10.1016/j.neulet.2021.136196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 08/09/2021] [Accepted: 08/20/2021] [Indexed: 01/01/2023]
Abstract
As the most common cause of dementia, Alzheimer's disease (AD) is progressively neurodegenerative disease. In the initial stage, Alzheimer's disease is related to the memory disorder, followed by a serious progressive decline in cognitive function, and finally died. Neurofibrillary tangles (NFTs) deposited in neurons form one of the histopathological features of AD. NFTs are composed of abnormally modified forms, such as hyperphosphorylation, of tau protein. DNA methylation on Tau protein related genes in the brains of AD patients plays an important role in AD pathogenesis. In this paper, the process and role of gene methylation in abnormal Tau modification and aggregation in the development of Alzheimer's disease were discussed. The effect of DNA methylation on tau protein in the brain of patients with Alzheimer's disease will help to find new targets in the development of drugs for treating Alzheimer's disease.
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Affiliation(s)
- Xieze Wei
- Institute of Anesthesia, Department of Anatomy, Baotou Medical College, Baotou, Inner Mongolia, China; Xinxiang Central Hospital, China
| | | | - Zhiying Zhao
- Institute of Anesthesia, Department of Anatomy, Baotou Medical College, Baotou, Inner Mongolia, China.
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41
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New RNA-Based Breakthroughs in Alzheimer's Disease Diagnosis and Therapeutics. Pharmaceutics 2021; 13:pharmaceutics13091397. [PMID: 34575473 PMCID: PMC8471423 DOI: 10.3390/pharmaceutics13091397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 01/25/2023] Open
Abstract
Dementia is described as the fifth leading cause of death worldwide and Alzheimer’s disease (AD) is recognized as the most common, causing a huge impact on health costs and quality of patients’ lives. The main hallmarks that are commonly associated with the pathologic process are amyloid deposition, pathologic Tau phosphorylation and neurodegeneration. It is still unclear how these events are linked to the disease progression, due to the complex pathologic mechanisms. Nevertheless, several hypotheses have been proposed for a better understanding of AD. The AD diagnosis is performed by using a combination of several tools to detect β-amyloid peptide (Aβ) deposits and modifications in cognitive performance, sometimes being expensive and invasive. In the treatment field, there is still an absence of effective treatments to delay or stop the progression of the disease, with most of the approved drugs used to relieve symptoms, and all of them with significant adverse side effects. Considering all limitations, the need to establish new and more effective diagnostic and therapeutic strategies becomes clear. This review aims not only to describe the disease and its impact but also to collect the currently available diagnostic and therapeutic strategies, highlighting new promising RNA-based strategies for AD.
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Murthy M, Cheng YY, Holton JL, Bettencourt C. Neurodegenerative movement disorders: An epigenetics perspective and promise for the future. Neuropathol Appl Neurobiol 2021; 47:897-909. [PMID: 34318515 PMCID: PMC9291277 DOI: 10.1111/nan.12757] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/12/2021] [Indexed: 02/02/2023]
Abstract
Neurodegenerative movement disorders (NMDs) are age‐dependent disorders that are characterised by the degeneration and loss of neurons, typically accompanied by pathological accumulation of different protein aggregates in the brain, which lead to motor symptoms. NMDs include Parkinson's disease, multiple system atrophy, progressive supranuclear palsy, and Huntington's disease, among others. Epigenetic modifications are responsible for functional gene regulation during development, adult life and ageing and have progressively been implicated in complex diseases such as cancer and more recently in neurodegenerative diseases, such as NMDs. DNA methylation is by far the most widely studied epigenetic modification and consists of the reversible addition of a methyl group to the DNA without changing the DNA sequence. Although this research field is still in its infancy in relation to NMDs, an increasing number of studies point towards a role for DNA methylation in disease processes. This review addresses recent advances in epigenetic and epigenomic research in NMDs, with a focus on human brain DNA methylation studies. We discuss the current understanding of the DNA methylation changes underlying these disorders, the potential for use of these DNA modifications in peripheral tissues as biomarkers in early disease detection, classification and progression as well as a promising role in future disease management and therapy.
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Affiliation(s)
- Megha Murthy
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.,Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Yun Yung Cheng
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Janice L Holton
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.,Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Conceição Bettencourt
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.,Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
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Wang F, Xu CS, Chen WH, Duan SW, Xu SJ, Dai JJ, Wang QW. Identification of Blood-Based Glycolysis Gene Associated with Alzheimer's Disease by Integrated Bioinformatics Analysis. J Alzheimers Dis 2021; 83:163-178. [PMID: 34308907 DOI: 10.3233/jad-210540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Alzheimer's disease (AD) is one of many common neurodegenerative diseases without ideal treatment, but early detection and intervention can prevent the disease progression. OBJECTIVE This study aimed to identify AD-related glycolysis gene for AD diagnosis and further investigation by integrated bioinformatics analysis. METHODS 122 subjects were recruited from the affiliated hospitals of Ningbo University between 1 October 2015 and 31 December 2016. Their clinical information and methylation levels of 8 glycolysis genes were assessed. Machine learning algorithms were used to establish an AD prediction model. Receiver operating characteristic curve (AUC) and decision curve analysis (DCA) were used to assess the model. An AD risk factor model was developed by SHapley Additive exPlanations (SHAP) to extract features that had important impacts on AD. Finally, gene expression of AD-related glycolysis genes were validated by AlzData. RESULTS An AD prediction model was developed using random forest algorithm with the best average ROC_AUC (0.969544). The threshold probability of the model was positive in the range of 0∼0.9875 by DCA. Eight glycolysis genes (GAPDHS, PKLR, PFKFB3, LDHC, DLD, ALDOC, LDHB, HK3) were identified by SHAP. Five of these genes (PFKFB3, DLD, ALDOC, LDHB, LDHC) have significant differences in gene expression between AD and control groups by Alzdata, while three of the genes (HK3, ALDOC, PKLR) are related to the pathogenesis of AD. GAPDHS is involved in the regulatory network of AD risk genes. CONCLUSION We identified 8 AD-related glycolysis genes (GAPDHS, PFKFB3, LDHC, HK3, ALDOC, LDHB, PKLR, DLD) as promising candidate biomarkers for early diagnosis of AD by integrated bioinformatics analysis. Machine learning has the advantage in identifying genes.
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Affiliation(s)
- Fng Wang
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China.,Zhejiang Pharmaceutical College, Ningbo, China
| | - Chun-Shuang Xu
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - Wei-Hua Chen
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - Shi-Wei Duan
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - Shu-Jun Xu
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
| | - Jun-Jie Dai
- Affiliated Lihuili Hospital of Ningbo University, Ningbo, China
| | - Qin-Wen Wang
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, China
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Xu H, Li S, Liu YS. Roles and Mechanisms of DNA Methylation in Vascular Aging and Related Diseases. Front Cell Dev Biol 2021; 9:699374. [PMID: 34262910 PMCID: PMC8273304 DOI: 10.3389/fcell.2021.699374] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/07/2021] [Indexed: 12/20/2022] Open
Abstract
Vascular aging is a pivotal risk factor promoting vascular dysfunction, the development and progression of vascular aging-related diseases. The structure and function of endothelial cells (ECs), vascular smooth muscle cells (VSMCs), fibroblasts, and macrophages are disrupted during the aging process, causing vascular cell senescence as well as vascular dysfunction. DNA methylation, an epigenetic mechanism, involves the alteration of gene transcription without changing the DNA sequence. It is a dynamically reversible process modulated by methyltransferases and demethyltransferases. Emerging evidence reveals that DNA methylation is implicated in the vascular aging process and plays a central role in regulating vascular aging-related diseases. In this review, we seek to clarify the mechanisms of DNA methylation in modulating ECs, VSMCs, fibroblasts, and macrophages functions and primarily focus on the connection between DNA methylation and vascular aging-related diseases. Therefore, we represent many vascular aging-related genes which are modulated by DNA methylation. Besides, we concentrate on the potential clinical application of DNA methylation to serve as a reliable diagnostic tool and DNA methylation-based therapeutic drugs for vascular aging-related diseases.
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Affiliation(s)
- Hui Xu
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, China.,Institute of Aging and Age-Related Disease Research, Central South University, Changsha, China
| | - Shuang Li
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, China.,Institute of Aging and Age-Related Disease Research, Central South University, Changsha, China
| | - You-Shuo Liu
- Department of Geriatrics, The Second Xiangya Hospital, Central South University, Changsha, China.,Institute of Aging and Age-Related Disease Research, Central South University, Changsha, China
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Hu J, Yang Y, Lv X, Lao Z, Yu L. Dichlorodiphenyltrichloroethane metabolites inhibit DNMT1 activity which confers methylation-specific modulation of the sex determination pathway. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 279:116828. [PMID: 33765505 DOI: 10.1016/j.envpol.2021.116828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/11/2021] [Accepted: 02/21/2021] [Indexed: 06/12/2023]
Abstract
Dichlorodiphenyltrichloroethane (DDT) poses a significant health risk to humans which is associated with genomic DNA hypomethylation. However, the mechanism and biological consequences remain poorly understood. In vitro assays confirmed that the DDT metabolites 2,2-bis(p-chlorophenyl)-acetic acid (DDA) and 1-chloro-2,2-bis-(p-chlorophenyl)ethylene (DDMU), but not other DDT metabolites, significantly inhibited DNA methyltransferase 1 (DNMT1) activity, leading to genomic hypomethylation in cell culture assays. DNMT1 as a target for DNA hypomethylation induced by DDT metabolites was also confirmed using cell cultures in which DNMT1 was silenced or highly expressed. DDA and DDMU can modify methylation markers in the promoter regions of sexual development-related genes, and change the expression of Sox9 and Oct4 in embryonic stem cells. Molecular docking indicated that DDA and DDMU bound to DNMT1 with high binding affinity. Molecular dynamic simulation revealed that DDA and DDMU acted as allosteric modulators that reshaped the conformation of the catalytic domain of DNMT1. These findings provide a new insight into DDT-induced abnormalities in sexual development and demonstrate that selective binding to DNMT1 by DDA and DDMU can interfere with human DNMT1 activity and regulate the expression of the Sox9 and Oct4 genes.
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Affiliation(s)
- Junjie Hu
- School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan, 523808, Guangdong, PR China
| | - Yan Yang
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, PR China; Synergy Innovation Institute of GDUT, Shantou, 515041, China
| | - Xiaomei Lv
- School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan, 523808, Guangdong, PR China
| | - Zhilang Lao
- School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan, 523808, Guangdong, PR China
| | - Lili Yu
- Translational Medicine Collaborative Innovation Center, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, 1017 Dongmen North Road, Luohu District, Shenzhen, 518020, Guangdong, China.
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Himalian R, Singh SK, Singh MP. Ameliorative Role of Nutraceuticals on Neurodegenerative Diseases Using the Drosophila melanogaster as a Discovery Model to Define Bioefficacy. J Am Coll Nutr 2021; 41:511-539. [PMID: 34125661 DOI: 10.1080/07315724.2021.1904305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Neurodegeneration is the destruction of neurons, and once the neurons degenerate they can't revive. This is one of the most concerned health conditions among aged population, more than ∼70% of the elderly people are suffering from neurodegeneration. Among all of the neurodegenerative diseases, Alzheimer's disease (AD), Parkinson's disease (PD) and Poly-glutamine disease (Poly-Q) are the major one and affecting most of the people around the world and posing excessive burden on the society. In order to understand this disease in non-human animal models it is pertinent to examine in model organism and various animal model are being used for such diseases like rat, mice and non-vertebrate model like Drosophila. Drosophila melanogaster is one of the best animal proven by several eminent scientist and had received several Nobel prizes for uncovering mechanism of human related genes and highly efficient model for studying neurodegenerative diseases due to its great affinity with human disease-related genes. Another factor is also employed to act as therapeutic or preventive method that is nutraceuticals. Nutraceuticals are functional natural compounds with antioxidant properties and had extensively showed the neuroprotective effect in different organisms. These nutraceuticals having antioxidant properties act through scavenging free radicals or by increasing endogenous cellular antioxidant defense molecules. For the best benefit, we are trying to utilize these nutraceuticals, which will have no or negligible side effects. In this review, we are dealing with various types of such nutraceuticals which have potent value in the prevention and curing of the diseases related to neurodegeneration.HighlightsNeurodegeneration is the silently progressing disease which shows its symptoms when it is well rooted.Many chemical drugs (almost all) have only symptomatic relief with side effects.Potent mechanism of neurodegeneration and improvement effect by nutraceuticals is proposed.Based on the Indian Cuisine scientists are trying to find the medicine from the food or food components having antioxidant properties.The best model to study the neurodegenerative diseases is Drosophila melanogaster.Many nutraceuticals having antioxidant properties have been studied and attenuated various diseases are discussed.
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Affiliation(s)
- Ranjana Himalian
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Sandeep Kumar Singh
- Indian Scientific Education and Technology (ISET) Foundation, Lucknow, India
| | - Mahendra Pratap Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
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Shao W, Xiang S, Zhang Z, Huang K, Zhang J. Hyper-graph based sparse canonical correlation analysis for the diagnosis of Alzheimer's disease from multi-dimensional genomic data. Methods 2021; 189:86-94. [PMID: 32360353 DOI: 10.1016/j.ymeth.2020.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/30/2020] [Accepted: 04/23/2020] [Indexed: 10/24/2022] Open
Abstract
The effective and accurate diagnosis of Alzheimer's disease (AD), especially in the early stage (i.e., mild cognitive impairment (MCI)) remains a big challenge in AD research. So far, multiple biomarkers have been associated with AD diagnosis and progression. However, most of the existing research only utilized single modality data for diagnostic biomarker identification, which did not take the advantages of multi-modal data that provide comprehensive and complementary information at multiple levels into consideration. In this paper, we integrate multi-modal genomic data from postmortem AD brains (i.e., mRNA, miRNA and epigenomic data) and propose a hyper-graph based sparse canonical correlation analysis (HGSCCA) method to extract the most correlated multi-modal biomarkers associated with AD and MCI. Specifically, our model utilizes the sparse canonical correlation analysis framework (SCCA), which aims at finding the best linear projections for each input modality so that the strongest correlation within the selected features of multi-dimensional genomic data can be captured. In addition, with the consideration of high-order relationships among different subjects, we also introduce a hyper-graph-based regularization term that will lead to the selection of more discriminative biomarkers. To evaluate the effectiveness of the proposed method, we conduct the experiments on the well-known AD cohort study, The Religious Orders Study and Memory and Aging Project (ROSMAP) dataset, and the results show that our method can not only identify meaningful biomarkers for the diagnosis AD disease, but also achieve superior classification performance than the comparing methods.
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Affiliation(s)
- Wei Shao
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Shunian Xiang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University, Shenzhen 518060, China; Department of Medical & Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA
| | - Zuoyi Zhang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202 USA; Regenstrief Institute, Indianapolis, IN 46202, USA
| | - Kun Huang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202 USA; Regenstrief Institute, Indianapolis, IN 46202, USA.
| | - Jie Zhang
- Department of Medical & Molecular Genetics, Indiana University, Indianapolis, IN 46202, USA.
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Sun Q, Huang M, Wei Y. Diversity of the reaction mechanisms of SAM-dependent enzymes. Acta Pharm Sin B 2021; 11:632-650. [PMID: 33777672 PMCID: PMC7982431 DOI: 10.1016/j.apsb.2020.08.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/30/2020] [Accepted: 08/08/2020] [Indexed: 02/08/2023] Open
Abstract
S-adenosylmethionine (SAM) is ubiquitous in living organisms and is of great significance in metabolism as a cofactor of various enzymes. Methyltransferases (MTases), a major group of SAM-dependent enzymes, catalyze methyl transfer from SAM to C, O, N, and S atoms in small-molecule secondary metabolites and macromolecules, including proteins and nucleic acids. MTases have long been a hot topic in biomedical research because of their crucial role in epigenetic regulation of macromolecules and biosynthesis of natural products with prolific pharmacological moieties. However, another group of SAM-dependent enzymes, sharing similar core domains with MTases, can catalyze nonmethylation reactions and have multiple functions. Herein, we mainly describe the nonmethylation reactions of SAM-dependent enzymes in biosynthesis. First, we compare the structural and mechanistic similarities and distinctions between SAM-dependent MTases and the non-methylating SAM-dependent enzymes. Second, we summarize the reactions catalyzed by these enzymes and explore the mechanisms. Finally, we discuss the structural conservation and catalytical diversity of class I-like non-methylating SAM-dependent enzymes and propose a possibility in enzymes evolution, suggesting future perspectives for enzyme-mediated chemistry and biotechnology, which will help the development of new methods for drug synthesis.
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Traversi D, Pulliero A, Izzotti A, Franchitti E, Iacoviello L, Gianfagna F, Gialluisi A, Izzi B, Agodi A, Barchitta M, Calabrò GE, Hoxhaj I, Sassano M, Sbrogiò LG, Del Sole A, Marchiori F, Pitini E, Migliara G, Marzuillo C, De Vito C, Tamburro M, Sammarco ML, Ripabelli G, Villari P, Boccia S. Precision Medicine and Public Health: New Challenges for Effective and Sustainable Health. J Pers Med 2021; 11:135. [PMID: 33669364 PMCID: PMC7920275 DOI: 10.3390/jpm11020135] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/11/2021] [Accepted: 02/14/2021] [Indexed: 02/06/2023] Open
Abstract
The development of high-throughput omics technologies represents an unmissable opportunity for evidence-based prevention of adverse effects on human health. However, the applicability and access to multi-omics tests are limited. In Italy, this is due to the rapid increase of knowledge and the high levels of skill and economic investment initially necessary. The fields of human genetics and public health have highlighted the relevance of an implementation strategy at a national level in Italy, including integration in sanitary regulations and governance instruments. In this review, the emerging field of public health genomics is discussed, including the polygenic scores approach, epigenetic modulation, nutrigenomics, and microbiomes implications. Moreover, the Italian state of implementation is presented. The omics sciences have important implications for the prevention of both communicable and noncommunicable diseases, especially because they can be used to assess the health status during the whole course of life. An effective population health gain is possible if omics tools are implemented for each person after a preliminary assessment of effectiveness in the medium to long term.
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Affiliation(s)
- Deborah Traversi
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126 Torino, Italy;
| | - Alessandra Pulliero
- Department of Health Sciences School of Medicine, University of Genoa, 16132 Genova, Italy;
| | - Alberto Izzotti
- Department of Experimental Medicine, University of Genoa, 16132 Genova, Italy;
- IRCCS Ospedale Policlinico San Martino, 161632 Genova, Italy
| | - Elena Franchitti
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126 Torino, Italy;
| | - Licia Iacoviello
- Research Center in Epidemiology and Preventive Medicine (EPIMED), Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy; (L.I.); (F.G.)
- Department of Epidemiology and Prevention, IRCCS NEUROMED, 86077 Pozzilli, Italy; (A.G.); (B.I.)
| | - Francesco Gianfagna
- Research Center in Epidemiology and Preventive Medicine (EPIMED), Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy; (L.I.); (F.G.)
- Mediterranea Cardiocentro, 80122 Napoli, Italy
| | - Alessandro Gialluisi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, 86077 Pozzilli, Italy; (A.G.); (B.I.)
| | - Benedetta Izzi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, 86077 Pozzilli, Italy; (A.G.); (B.I.)
| | - Antonella Agodi
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, 95123 Catania, Italy; (A.A.); (M.B.)
| | - Martina Barchitta
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, 95123 Catania, Italy; (A.A.); (M.B.)
| | - Giovanna Elisa Calabrò
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
| | - Ilda Hoxhaj
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
| | - Michele Sassano
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
| | - Luca Gino Sbrogiò
- Dipartimento di Prevenzione, Az. ULSS3 Serenissima, 30174 Venezia, Italy;
| | | | | | - Erica Pitini
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Giuseppe Migliara
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Carolina Marzuillo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Corrado De Vito
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Manuela Tamburro
- Department of Medicine and Health Sciences “Vincenzo Tiberio”, University of Molise, 86100 Campobasso, Italy; (M.T.); (M.L.S.); (G.R.)
| | - Michela Lucia Sammarco
- Department of Medicine and Health Sciences “Vincenzo Tiberio”, University of Molise, 86100 Campobasso, Italy; (M.T.); (M.L.S.); (G.R.)
| | - Giancarlo Ripabelli
- Department of Medicine and Health Sciences “Vincenzo Tiberio”, University of Molise, 86100 Campobasso, Italy; (M.T.); (M.L.S.); (G.R.)
| | - Paolo Villari
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Stefania Boccia
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
- Department of Woman and Child Health and Public Health-Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Roma, Italy
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He C, Huang ZS, Yu CC, Wang HH, Zhou H, Kong LH. Epigenetic Regulation of Amyloid-beta Metabolism in Alzheimer's Disease. Curr Med Sci 2021; 40:1022-1030. [PMID: 33428129 DOI: 10.1007/s11596-020-2283-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 10/05/2020] [Indexed: 11/28/2022]
Abstract
Senile plaques (SPs) are one of the pathological features of Alzheimer's disease (AD) and they are formed by the overproduction and aggregation of amyloid-beta (Aβ) peptides derived from the abnormal cleavage of amyloid precursor protein (APP). Thus, understanding the regulatory mechanisms during Aβ metabolism is of great importance to elucidate AD pathogenesis. Recent studies have shown that epigenetic modulation-including DNA methylation, non-coding RNA alterations, and histone modifications-is of great significance in regulating Aβ metabolism. In this article, we review the aberrant epigenetic regulation of Aβ metabolism.
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Affiliation(s)
- Chuan He
- Hubei University of Chinese Medicine, Wuhan, 430060, China
| | | | - Chao-Chao Yu
- Department of Tuina, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518000, China.,The 4th Clinical College of Guangzhou University of Chinese Medicine, Shenzhen, 518000, China
| | - Hai-Hua Wang
- Hospital of Traditional Chinese Medicine of Fengrun District, Tangshan, 064000, China
| | - Hua Zhou
- Hubei University of Chinese Medicine, Wuhan, 430060, China.
| | - Li-Hong Kong
- Hubei University of Chinese Medicine, Wuhan, 430060, China.
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