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Kwok AJ, Lu J, Huang J, Ip BY, Mok VCT, Lai HM, Ko H. High-resolution omics of vascular ageing and inflammatory pathways in neurodegeneration. Semin Cell Dev Biol 2024; 155:30-49. [PMID: 37380595 DOI: 10.1016/j.semcdb.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 06/07/2023] [Indexed: 06/30/2023]
Abstract
High-resolution omics, particularly single-cell and spatial transcriptomic profiling, are rapidly enhancing our comprehension of the normal molecular diversity of gliovascular cells, as well as their age-related changes that contribute to neurodegeneration. With more omic profiling studies being conducted, it is becoming increasingly essential to synthesise valuable information from the rapidly accumulating findings. In this review, we present an overview of the molecular features of neurovascular and glial cells that have been recently discovered through omic profiling, with a focus on those that have potentially significant functional implications and/or show cross-species differences between human and mouse, and that are linked to vascular deficits and inflammatory pathways in ageing and neurodegenerative disorders. Additionally, we highlight the translational applications of omic profiling, and discuss omic-based strategies to accelerate biomarker discovery and facilitate disease course-modifying therapeutics development for neurodegenerative conditions.
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Affiliation(s)
- Andrew J Kwok
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Jianning Lu
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Junzhe Huang
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Bonaventure Y Ip
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Vincent C T Mok
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hei Ming Lai
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Ho Ko
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
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Giannini LAA, Boers RG, van der Ende EL, Poos JM, Jiskoot LC, Boers JB, van IJcken WFJ, Dopper EG, Pijnenburg YAL, Seelaar H, Meeter LH, van Rooij JGJ, Scheper W, Gribnau J, van Swieten JC. Distinctive cell-free DNA methylation characterizes presymptomatic genetic frontotemporal dementia. Ann Clin Transl Neurol 2024; 11:744-756. [PMID: 38481040 DOI: 10.1002/acn3.51997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/01/2023] [Accepted: 12/27/2023] [Indexed: 03/27/2024] Open
Abstract
OBJECTIVE Methylation of plasma cell-free DNA (cfDNA) has potential as a marker of brain damage in neurodegenerative diseases such as frontotemporal dementia (FTD). Here, we study methylation of cfDNA in presymptomatic and symptomatic carriers of genetic FTD pathogenic variants, next to healthy controls. METHODS cfDNA was isolated from cross-sectional plasma of 10 presymptomatic carriers (4 C9orf72, 4 GRN, and 2 MAPT), 10 symptomatic carriers (4 C9orf72, 4 GRN, and 2 MAPT), and 9 healthy controls. Genome-wide methylation of cfDNA was determined using a high-resolution sequencing technique (MeD-seq). Cumulative scores based on the identified differentially methylated regions (DMRs) were estimated for presymptomatic carriers (vs. controls and symptomatic carriers), and reevaluated in a validation cohort (8 presymptomatic: 3 C9orf72, 3 GRN, and 2 MAPT; 26 symptomatic: 7 C9orf72, 6 GRN, 12 MAPT, and 1 TARDBP; 13 noncarriers from genetic FTD families). RESULTS Presymptomatic carriers showed a distinctive methylation profile compared to healthy controls and symptomatic carriers. Cumulative DMR scores in presymptomatic carriers enabled to significantly differentiate presymptomatic carriers from healthy controls (p < 0.001) and symptomatic carriers (p < 0.001). In the validation cohort, these scores differentiated presymptomatic carriers from symptomatic carriers (p ≤ 0.007) only. Transcription-start-site methylation in presymptomatic carriers, generally associated with gene downregulation, was enriched for genes involved in ubiquitin-dependent processes, while gene body methylation, generally associated with gene upregulation, was enriched for genes involved in neuronal cell processes. INTERPRETATION A distinctive methylation profile of cfDNA characterizes the presymptomatic stage of genetic FTD, and could reflect neuronal death in this stage.
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Affiliation(s)
- Lucia A A Giannini
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ruben G Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Emma L van der Ende
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Jackie M Poos
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lize C Jiskoot
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joachim B Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Elise G Dopper
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yolande A L Pijnenburg
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit, Amsterdam UMC location Vumc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
| | - Harro Seelaar
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lieke H Meeter
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen G J van Rooij
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wiep Scheper
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Faculty of Science, Vrije Universiteit, Amsterdam, The Netherlands
- Department of Human Genetics, Vrije Universiteit, Amsterdam UMC location Vumc, Amsterdam, The Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - John C van Swieten
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
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Lukacsovich D, O’Shea D, Huang H, Zhang W, Young JI, Steven Chen X, Dietrich ST, Kunkle B, Martin ER, Wang L. MIAMI-AD (Methylation in Aging and Methylation in AD): an integrative knowledgebase that facilitates explorations of DNA methylation across sex, aging, and Alzheimer's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.04.23299412. [PMID: 38105943 PMCID: PMC10723513 DOI: 10.1101/2023.12.04.23299412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disorder with a significant impact on aging populations. DNA methylation (DNAm) alterations have been implicated in both the aging processes and the development of AD. Given that AD affects more women than men, it is also important to explore DNAm changes that occur specifically in each sex. We created MIAMI-AD, a comprehensive knowledge base containing manually curated summary statistics from 97 published tables in 37 studies, all of which included at least 100 participants. MIAMI-AD enables easy browsing, querying, and downloading DNAm associations at multiple levels - at individual CpG, gene, genomic regions, or genome-wide, in one or multiple studies. Moreover, it also offers tools to perform integrative analyses, such as comparing DNAm associations across different phenotypes or tissues, as well as interactive visualizations. Using several use case examples, we demonstrated that MIAMI-AD facilitates our understanding of age-associated CpGs in AD and the sex-specific roles of DNAm in AD. This open-access resource is freely available to the research community, and all the underlying data can be downloaded. MIAMI-AD (https://miami-ad.org/) facilitates integrative explorations to better understand the interplay between DNAm across aging, sex, and AD.
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Affiliation(s)
- David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Deirdre O’Shea
- Department of Neurology, Comprehensive Center for Brain Health, University of Miami Miller School of Medicine, Boca Raton, FL, 33433
| | - Hanchen Huang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Juan I. Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - X. Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Sven-Thorsten Dietrich
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Brian Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Eden R. Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
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Yang T, Xiao Y, Cheng Y, Huang J, Wei Q, Li C, Shang H. Epigenetic clocks in neurodegenerative diseases: a systematic review. J Neurol Neurosurg Psychiatry 2023; 94:1064-1070. [PMID: 36963821 DOI: 10.1136/jnnp-2022-330931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/03/2023] [Indexed: 03/26/2023]
Abstract
BACKGROUND Biological ageing is one of the principal risk factors for neurodegenerative diseases. It is becoming increasingly clear that acceleration of DNA methylation age, as measured by the epigenetic clock, is closely associated with many age-related diseases. METHODS We searched the PubMed and Web of Science databases to identify eligible studies reporting epigenetic clocks in several neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS) and Huntington's disease (HD). RESULTS Twenty-three studies (12 for AD, 4 for PD, 5 for ALS, and 2 for HD) were included. We systematically summarised the clinical utility of 11 epigenetic clocks (based on blood and brain tissues) in assessing the risk factors, age of onset, diagnosis, progression, prognosis and pathology of AD, PD, ALS and HD. We also critically described our current understandings to these evidences, and further discussed key challenges, potential mechanisms and future perspectives of epigenetic ageing in neurodegenerative diseases. CONCLUSIONS Epigenetic clocks hold great potential in neurodegenerative diseases. Further research is encouraged to evaluate the clinical utility and promote the application. PROSPERO REGISTRATION NUMBER CRD42022365233.
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Affiliation(s)
- Tianmi Yang
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Yi Xiao
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Yangfan Cheng
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Jingxuan Huang
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Qianqian Wei
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Chunyu Li
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
| | - Huifang Shang
- Department of Neurology, Sichuan University, Chengdu, Sichuan, China
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Huang H, Xie B, Liu Y, Dong GH, Liu R, Gui Z, Chen L, Li S, Guo Y, Yang L, Chen G. Long-term exposure to PM 2.5 compositions and O 3 and their interactive effects on DNA methylation of peripheral brain-derived neurotrophic factor promoter. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2023:1-12. [PMID: 37939783 DOI: 10.1080/09603123.2023.2280157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/01/2023] [Indexed: 11/10/2023]
Abstract
This study examined the associations of long-term exposure to ambient fine particulate matter (PM2.5) compositions/ozone with methylation of peripheral brain-derived neurotrophic factor (BDNF) promoters. A total of 101 participants were recruited from a cohort in Shijiazhuang, Hebei province, China. They underwent baseline and follow-up surveys in 2011 and 2015. DNA methylation levels were detected by bisulfite-PCR amplification and pyrosequencing. Participants' three-year average levels of PM2.5 compositions and ozone were estimated. Bayesian kernel machine regression (BKMR) models were used to examine the joint effects of pollutants on methylation levels. Exposure to PM2.5 compositions and ozone mixtures at the 75th percentile was associated with increased methylation levels at CpG2 of BDNF promoter (203%, 95% CI: 89, 316) than the lowest level of exposure, and sulfate dominated the effect in the BKMR models.Our findings provide clues to the epigenetic mechanisms for the associations of PM2.5 compositions and ozone with BDNF.
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Affiliation(s)
- Haoyu Huang
- Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Bing Xie
- College of Forensic Medicine, Hebei Medical University, Shijiazhuang, China
- Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang, China
| | - Yuewei Liu
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Guang-Hui Dong
- Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Ruqing Liu
- Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Zhaohuan Gui
- Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Lijun Chen
- College of Information Engineering, Hubei University of Chinese Medicine, Wuhan, China
| | - Shanshan Li
- Climate, Air Quality Research Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Yuming Guo
- Climate, Air Quality Research Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Lei Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Hebei Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang, China
| | - Gongbo Chen
- Climate, Air Quality Research Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
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Salvioli S, Basile MS, Bencivenga L, Carrino S, Conte M, Damanti S, De Lorenzo R, Fiorenzato E, Gialluisi A, Ingannato A, Antonini A, Baldini N, Capri M, Cenci S, Iacoviello L, Nacmias B, Olivieri F, Rengo G, Querini PR, Lattanzio F. Biomarkers of aging in frailty and age-associated disorders: State of the art and future perspective. Ageing Res Rev 2023; 91:102044. [PMID: 37647997 DOI: 10.1016/j.arr.2023.102044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/01/2023]
Abstract
According to the Geroscience concept that organismal aging and age-associated diseases share the same basic molecular mechanisms, the identification of biomarkers of age that can efficiently classify people as biologically older (or younger) than their chronological (i.e. calendar) age is becoming of paramount importance. These people will be in fact at higher (or lower) risk for many different age-associated diseases, including cardiovascular diseases, neurodegeneration, cancer, etc. In turn, patients suffering from these diseases are biologically older than healthy age-matched individuals. Many biomarkers that correlate with age have been described so far. The aim of the present review is to discuss the usefulness of some of these biomarkers (especially soluble, circulating ones) in order to identify frail patients, possibly before the appearance of clinical symptoms, as well as patients at risk for age-associated diseases. An overview of selected biomarkers will be discussed in this regard, in particular we will focus on biomarkers related to metabolic stress response, inflammation, and cell death (in particular in neurodegeneration), all phenomena connected to inflammaging (chronic, low-grade, age-associated inflammation). In the second part of the review, next-generation markers such as extracellular vesicles and their cargos, epigenetic markers and gut microbiota composition, will be discussed. Since recent progresses in omics techniques have allowed an exponential increase in the production of laboratory data also in the field of biomarkers of age, making it difficult to extract biological meaning from the huge mass of available data, Artificial Intelligence (AI) approaches will be discussed as an increasingly important strategy for extracting knowledge from raw data and providing practitioners with actionable information to treat patients.
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Affiliation(s)
- Stefano Salvioli
- Department of Medical and Surgical Science, University of Bologna, Bologna, Italy; IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.
| | | | - Leonardo Bencivenga
- Department of Translational Medical Sciences, University of Naples Federico II, Napoli, Italy
| | - Sara Carrino
- Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Maria Conte
- Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Sarah Damanti
- IRCCS Ospedale San Raffaele and Vita-Salute San Raffaele University, Milano, Italy
| | - Rebecca De Lorenzo
- IRCCS Ospedale San Raffaele and Vita-Salute San Raffaele University, Milano, Italy
| | - Eleonora Fiorenzato
- Parkinson's Disease and Movement Disorders Unit, Center for Rare Neurological Diseases (ERN-RND), Department of Neurosciences, University of Padova, Padova, Italy
| | - Alessandro Gialluisi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, Italy; EPIMED Research Center, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Assunta Ingannato
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy; IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Angelo Antonini
- Parkinson's Disease and Movement Disorders Unit, Center for Rare Neurological Diseases (ERN-RND), Department of Neurosciences, University of Padova, Padova, Italy; Center for Neurodegenerative Disease Research (CESNE), Department of Neurosciences, University of Padova, Padova, Italy
| | - Nicola Baldini
- IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Miriam Capri
- Department of Medical and Surgical Science, University of Bologna, Bologna, Italy
| | - Simone Cenci
- IRCCS Ospedale San Raffaele and Vita-Salute San Raffaele University, Milano, Italy
| | - Licia Iacoviello
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, Italy; EPIMED Research Center, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Benedetta Nacmias
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy; IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Fabiola Olivieri
- Department of Clinical and Molecular Sciences, Università Politecnica Delle Marche, Ancona, Italy; Clinic of Laboratory and Precision Medicine, IRCCS INRCA, Ancona, Italy
| | - Giuseppe Rengo
- Department of Translational Medical Sciences, University of Naples Federico II, Napoli, Italy; Istituti Clinici Scientifici Maugeri IRCCS, Scientific Institute of Telese Terme, Telese Terme, Italy
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Lee NY, Hum M, Tan GP, Seah AC, Kin PT, Tan NC, Law HY, Lee ASG. Degradation of methylation signals in cryopreserved DNA. Clin Epigenetics 2023; 15:147. [PMID: 37697422 PMCID: PMC10496221 DOI: 10.1186/s13148-023-01565-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/06/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Blood-based DNA methylation has shown great promise as a biomarker in a wide variety of diseases. Studies of DNA methylation in blood often utilize samples which have been cryopreserved for years or even decades. Therefore, changes in DNA methylation associated with long-term cryopreservation can introduce biases or otherwise mislead methylation analyses of cryopreserved DNA. However, previous studies have presented conflicting results with studies reporting hypomethylation, no effect, or even hypermethylation of DNA following long-term cryopreservation. These studies may have been limited by insufficient sample sizes, or by their profiling of methylation only on an aggregate global scale, or profiling of only a few CpGs. RESULTS We analyzed two large prospective cohorts: a discovery (n = 126) and a validation (n = 136) cohort, where DNA was cryopreserved for up to four years. In both cohorts there was no detectable change in mean global methylation across increasing storage durations as DNA. However, when analysis was performed on the level of individual CpG methylation both cohorts exhibited a greater number of hypomethylated than hypermethylated CpGs at q-value < 0.05 (4049 hypomethylated but only 50 hypermethylated CpGs in discovery, and 63 hypomethylated but only 6 hypermethylated CpGs in validation). The results were the same even after controlling for age, storage duration as buffy coat prior to DNA extraction, and estimated cell type composition. Furthermore, we find that in both cohorts, CpGs have a greater likelihood to be hypomethylated the closer they are to a CpG island; except for CpGs at the CpG islands themselves which are less likely to be hypomethylated. CONCLUSION Cryopreservation of DNA after a few years results in a detectable bias toward hypomethylation at the level of individual CpG methylation, though when analyzed in aggregate there is no detectable change in mean global methylation. Studies profiling methylation in cryopreserved DNA should be mindful of this hypomethylation bias, and more attention should be directed at developing more stable methods of DNA cryopreservation for biomedical research or clinical use.
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Affiliation(s)
- Ning Yuan Lee
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
| | - Melissa Hum
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore
| | - Guek Peng Tan
- DNA Diagnostic and Research Laboratory, KK Women's and Children's Hospital, 100 Bukit Timah Rd, Singapore, 229899, Singapore
| | - Ai Choo Seah
- SingHealth Polyclinics, 167 Jalan Bukit Merah, Singapore, 150167, Singapore
| | - Patricia T Kin
- SingHealth Polyclinics, 167 Jalan Bukit Merah, Singapore, 150167, Singapore
| | - Ngiap Chuan Tan
- SingHealth Polyclinics, 167 Jalan Bukit Merah, Singapore, 150167, Singapore
- SingHealth Duke-NUS Family Medicine Academic Clinical Programme, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Hai-Yang Law
- DNA Diagnostic and Research Laboratory, KK Women's and Children's Hospital, 100 Bukit Timah Rd, Singapore, 229899, Singapore
| | - Ann S G Lee
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Singapore.
- SingHealth Duke-NUS Oncology Academic Clinical Programme (ONCO ACP), Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore, 117593, Singapore.
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Wu S, Yang F, Chao S, Wang B, Wang W, Li H, Yu L, He L, Li X, Sun L, Qin S. Altered DNA methylome profiles of blood leukocytes in Chinese patients with mild cognitive impairment and Alzheimer's disease. Front Genet 2023; 14:1175864. [PMID: 37388929 PMCID: PMC10300350 DOI: 10.3389/fgene.2023.1175864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023] Open
Abstract
Objective: DNA methylation plays a potential role in the pathogenesis of Alzheimer's disease (AD). However, little is known about the global changes of blood leukocyte DNA methylome profiles from Chinese patients with mild cognitive impairment (MCI) and with AD, or the specific DNA methylation-based signatures associated with MCI and AD. In this study, we sought to dissect the characteristics of blood DNA methylome profiles in MCI- and AD-affected Chinese patients with the aim of identifying novel DNA methylation biomarkers for AD. Methods: In this study, we profiled the DNA methylome of peripheral blood leukocytes from 20 MCI- and 20 AD-affected Chinese patients and 20 cognitively healthy controls (CHCs) with the Infinium Methylation EPIC BeadChip array. Results: We identified significant alterations of the methylome profiles in MCI and AD blood leukocytes. A total of 2,582 and 20,829 CpG sites were significantly and differentially methylated in AD and MCI compared with CHCs (adjusted p < 0.05), respectively. Furthermore, 441 differentially methylated positions (DMPs), aligning to 213 unique genes, were overlapped by the three comparative groups of AD versus CHCs, MCI versus CHCs, and AD versus MCI, of which 6 and 5 DMPs were continuously hypermethylated and hypomethylated in MCI and AD relative to CHCs (adjusted p < 0.05), respectively, such as FLNC cg20186636 and AFAP1 cg06758191. The DMPs with an area under the curve >0.900, such as cg18771300, showed high potency for predicting MCI and AD. In addition, gene ontology and pathway enrichment results showed that these overlapping genes were mainly involved in neurotransmitter transport, GABAergic synaptic transmission, signal release from synapse, neurotransmitter secretion, and the regulation of neurotransmitter levels. Furthermore, tissue expression enrichment analysis revealed a subset of potentially cerebral cortex-enriched genes associated with MCI and AD, including SYT7, SYN3, and KCNT1. Conclusion: This study revealed a number of potential biomarkers for MCI and AD, also highlighted the presence of epigenetically dysregulated gene networks that may engage in the underlying pathological events resulting in the onset of cognitive impairment and AD progression. Collectively, this study provides prospective cues for developing therapeutic strategies to improve cognitive impairment and AD course.
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Affiliation(s)
- Shaochang Wu
- Department of Geriatrics, Lishui Second People’s Hospital, Lishui, China
| | - Fan Yang
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
| | - Shan Chao
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
| | - Bo Wang
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wuqian Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
| | - He Li
- Department of Geriatrics, Lishui Second People’s Hospital, Lishui, China
| | - Limei Yu
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Xingwang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Liya Sun
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
- Shanghai Mental Health Center, Editorial Office, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
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9
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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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10
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Martínez-Iglesias O, Naidoo V, Corzo L, Pego R, Seoane S, Rodríguez S, Alcaraz M, Muñiz A, Cacabelos N, Cacabelos R. DNA Methylation as a Biomarker for Monitoring Disease Outcome in Patients with Hypovitaminosis and Neurological Disorders. Genes (Basel) 2023; 14:genes14020365. [PMID: 36833292 PMCID: PMC9956161 DOI: 10.3390/genes14020365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 02/03/2023] Open
Abstract
DNA methylation remains an under-recognized diagnostic biomarker for several diseases, including neurodegenerative disorders. In this study, we examined differences in global DNA methylation (5mC) levels in serum samples from patients during the initial- and the follow-up visits. Each patient underwent a blood analysis and neuropsychological assessments. The analysis of 5mC levels revealed two categories of patients; Group A who, during the follow-up, had increased 5mC levels, and Group B who had decreased 5mC levels. Patients with low Fe-, folate-, and vitamin B12- levels during the initial visit showed increased levels of 5mC after treatment when assessed during the follow-up. During the follow-up, 5mC levels in Group A patients increased after treatment for hypovitaminosis with the nutraceutical compounds Animon Complex and MineraXin Plus. 5mC levels were maintained during the follow-up in Group A patients treated for neurological disorders with the bioproducts AtreMorine and NeoBrainine. There was a positive correlation between 5mC levels and MMSE scores, and an inverse correlation between 5mC and ADAS-Cog scores. This expected correlation was observed in Group A patients only. Our study appears to indicate that 5mC has a diagnostic value as a biomarker across different pathologies.
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11
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Schäfer Hackenhaar F, Josefsson M, Nordin Adolfsson A, Landfors M, Kauppi K, Porter T, Milicic L, Laws SM, Hultdin M, Adolfsson R, Degerman S, Pudas S. Sixteen-Year Longitudinal Evaluation of Blood-Based DNA Methylation Biomarkers for Early Prediction of Alzheimer's Disease. J Alzheimers Dis 2023; 94:1443-1464. [PMID: 37393498 PMCID: PMC10473121 DOI: 10.3233/jad-230039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2023] [Indexed: 07/03/2023]
Abstract
BACKGROUND DNA methylation (DNAm), an epigenetic mark reflecting both inherited and environmental influences, has shown promise for Alzheimer's disease (AD) prediction. OBJECTIVE Testing long-term predictive ability (>15 years) of existing DNAm-based epigenetic age acceleration (EAA) measures and identifying novel early blood-based DNAm AD-prediction biomarkers. METHODS EAA measures calculated from Illumina EPIC data from blood were tested with linear mixed-effects models (LMMs) in a longitudinal case-control sample (50 late-onset AD cases; 51 matched controls) with prospective data up to 16 years before clinical onset, and post-onset follow-up. Novel DNAm biomarkers were generated with epigenome-wide LMMs, and Sparse Partial Least Squares Discriminant Analysis applied at pre- (10-16 years), and post-AD-onset time-points. RESULTS EAA did not differentiate cases from controls during the follow-up time (p > 0.05). Three new DNA biomarkers showed in-sample predictive ability on average 8 years pre-onset, after adjustment for age, sex, and white blood cell proportions (p-values: 0.022-<0.00001). Our longitudinally-derived panel replicated nominally (p = 0.012) in an external cohort (n = 146 cases, 324 controls). However, its effect size and discriminatory accuracy were limited compared to APOEɛ4-carriership (OR = 1.38 per 1 SD DNAm score increase versus OR = 13.58 for ɛ4-allele carriage; AUCs = 77.2% versus 87.0%). Literature review showed low overlap (n = 4) across 3275 AD-associated CpGs from 8 published studies, and no overlap with our identified CpGs.
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Affiliation(s)
- Fernanda Schäfer Hackenhaar
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
- Umeå Center for Functional Brain Imaging, Umeå University, Umeå, Sweden
| | - Maria Josefsson
- Umeå Center for Functional Brain Imaging, Umeå University, Umeå, Sweden
- Department of Statistics, USBE, Umeå University, Umeå, Sweden
- Center for Ageing and Demographic Research, Umeå University, Umeå, Sweden
| | | | - Mattias Landfors
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Karolina Kauppi
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Tenielle Porter
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Lidija Milicic
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Simon M. Laws
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Magnus Hultdin
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Rolf Adolfsson
- Department of Clinical Sciences, Umeå University, Umeå, Sweden
| | - Sofie Degerman
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Sara Pudas
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
- Umeå Center for Functional Brain Imaging, Umeå University, Umeå, Sweden
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12
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Cao R, Xie J, Zhang L. Abnormal methylation caused by folic acid deficiency in neural tube defects. Open Life Sci 2022; 17:1679-1688. [PMID: 36589786 PMCID: PMC9784971 DOI: 10.1515/biol-2022-0504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/27/2022] [Accepted: 09/01/2022] [Indexed: 12/24/2022] Open
Abstract
Neural tube closure disorders, including anencephaly, spina bifida, and encephalocele, cause neural tube defects (NTDs). This congenital disability remained not only a major contributor to the prevalence of stillbirths and neonatal deaths but also a significant cause of lifelong physical disability in surviving infants. NTDs are complex diseases caused by multiple etiologies, levels, and mechanisms. Currently, the pathogenesis of NTDs is considered to be associated with both genetic and environmental factors. Here, we aimed to review the research progress on the etiology and mechanism of NTDs induced by methylation modification caused by folic acid deficiency. Folic acid supplementation in the diet is reported to be beneficial in preventing NTDs. Methylation modification is one of the most important epigenetic modifications crucial for brain neurodevelopment. Disturbances in folic acid metabolism and decreased S-adenosylmethionine levels lead to reduced methyl donors and methylation modification disorders. In this review, we summarized the relationship between NTDs, folic acid metabolism, and related methylation of DNA, imprinted genes, cytoskeletal protein, histone, RNA, and non-coding RNA, so as to clarify the role of folic acid and methylation in NTDs and to better understand the various pathogenesis mechanisms of NTDs and the effective prevention.
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Affiliation(s)
- Rui Cao
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Key Laboratory for Cellular Physiology of Ministry of Education, Shanxi Medical University, No. 56, Xinjian South Road, Yingze District, Taiyuan, Shanxi Province, China,Shanxi Key Laboratory of Pharmaceutical Biotechnology, Shanxi Biological Research Institute Co., Ltd, Taiyuan, China
| | - Jun Xie
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Key Laboratory for Cellular Physiology of Ministry of Education, Shanxi Medical University, No. 56, Xinjian South Road, Yingze District, Taiyuan, Shanxi Province, China
| | - Li Zhang
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Key Laboratory for Cellular Physiology of Ministry of Education, Shanxi Medical University, No. 56, Xinjian South Road, Yingze District, Taiyuan, Shanxi Province, China,Department of Hepatobiliary and Pancreatic Surgery and Liver Transplant Center, The First Hospital of Shanxi Medical University, No. 56, Xinjian South Road, Yingze District, Taiyuan, Shanxi Province, China
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13
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White Blood Cell and Platelet Counts Are Not Suitable as Biomarkers in the Differential Diagnostics of Dementia. Brain Sci 2022; 12:brainsci12111424. [DOI: 10.3390/brainsci12111424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/06/2022] [Accepted: 10/21/2022] [Indexed: 11/16/2022] Open
Abstract
Apart from Alzheimer’s disease (AD), no biomarkers for the differential diagnosis of dementia have been established to date. Inflammatory processes contribute to the pathogenesis of dementia subtypes, e.g., AD or frontotemporal dementia (FTD). In the context of cancer or cardiovascular diseases, white blood cell (WBC) populations and platelet counts, as well as C-reactive protein (CRP), have emerged as biomarkers. Their clinical relevance in dementia, however, is currently only insufficiently investigated. In the present study, hematological and inflammatory parameters were measured in the peripheral blood of 97 patients admitted to the gerontopsychiatric ward of Hannover Medical School, a university hospital in Germany, for dementia assessment. The study population comprised 20 non-demented, depressed patients (control group) and 77 demented patients who were assigned to five different groups based on their underlying dementia etiology: AD, n = 33; vascular dementia, n = 12; mixed dementia, n = 21; FTD, n = 5; and Korsakoff syndrome, n = 6. We observed neither statistically significant differences regarding total WBC populations, platelet counts, neutrophil-to-lymphocyte ratio and platelet-to-lymphocyte ratio, nor CRP levels between the control group and the five dementia groups. CRP levels tended to be higher in patients with Korsakoff syndrome than in the control group and in AD patients. Thus, CRP could possibly play a role in the differential diagnosis of dementia. This should be investigated further in future prospective studies with larger sample sizes. WBC and platelet counts, by contrast, do not appear to be suitable biomarkers in the differential diagnosis of dementia.
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14
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Huang H, Yang L, Liu Y, Dong GH, Chen L, Li S, Guo Y, Xie B, Chen G. Long-term ambient air pollution exposure and DNA methylation of peripheral brain-derived neurotrophic factor promoter. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 244:114061. [PMID: 36088717 DOI: 10.1016/j.ecoenv.2022.114061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/18/2022] [Accepted: 09/04/2022] [Indexed: 06/15/2023]
Abstract
This study aimed to investigate the association between air pollutants and methylation of peripheral brain-derived neurotrophic factor (BDNF) promoters. A total of 101 individuals were recruited in this panel study. BDNF promoter methylation was detected by bisulfite-PCR amplification and pyrosequencing. Participants' exposure to air pollutants was estimated using a satellite-based random forests approach. A generalized estimated equation model with natural cubic splines was employed to examine the associations between air pollutants and BDNF promoter methylation levels. The associations between air pollution and BDNF promoter methylation showed nonlinear curves with threshold effects. The threshold concentration for the association of nitrogen dioxide (NO2) with average methylation level was 59.7 μg/m3, and that for the association of particulate matter ≤ 1 µm in diameter (PM1) with CpG2 methylation level was 70.9 μg/m3. The percent change of average methylation level at the 95th percentile of NO2 against the threshold concentration was 43.25% (95%CI: 13.10%, 73.40%), and that of CpG2 methylation at the 95th percentile of PM1 was 128.29% (95%CI: 43.27%, 213.31%). Overall, long-term exposures of PM1, PM2.5, PM10, and NO2 were associated with significant changes in BDNF promoter methylation levels with threshold effects.
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Affiliation(s)
- Haoyu Huang
- Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Lei Yang
- Department of Epidemiology and Statistics, School of Public Health, Hebei Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang 050017, China
| | - Yuewei Liu
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Guang-Hui Dong
- Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Lijun Chen
- College of Information Engineering, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Shanshan Li
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne 3004, Australia
| | - Yuming Guo
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne 3004, Australia
| | - Bing Xie
- College of Forensic Medicine, Hebei Medical University, Shijiazhuang 050017, China; Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, China.
| | - Gongbo Chen
- Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China.
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15
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Lin J, Yang S, Wang C, Yu E, Zhu Z, Shi J, Li X, Xin J, Chen X, Pan X. Prediction of Alzheimer’s Disease Using Patterns of Methylation Levels in Key Immunologic-Related Genes. J Alzheimers Dis 2022; 90:783-794. [DOI: 10.3233/jad-220701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background: DNA methylation is expected to become a kind of new diagnosis and treatment method of Alzheimer’s disease (AD). Neuroinflammation- and immune-related pathways represent one of the major genetic risk factors for AD. Objective: We aimed to investigate DNA methylation levels of 7 key immunologic-related genes in peripheral blood and appraise their applicability in the diagnosis of AD. Methods: Methylation levels were obtained from 222 participants (101 AD, 72 MC, 49 non-cognitively impaired controls). Logistic regression models for diagnosing AD were established after least absolute shrinkage and selection operator (LASSO) and best subset selection (BSS), evaluated by respondent working curve and decision curve analysis for sensitivity. Results: Six differentially methylated positions (DMPs) in the MCI group and 64 in the AD group were found, respectively. Among them, there were 2 DMPs in the MCI group and 30 DMPs in the AD group independent of age, gender, and APOE4 carriers (p < 0.05). AD diagnostic prediction models differentiated AD from normal controls both in a training dataset (LASSO: 8 markers, including methylation levels at ABCA7_1040077, CNR1_88166293, CX3CR1_39322324, LRRK2_40618505, LRRK2_40618493, NGFR_49496745, TARDBP_11070956, TARDBP_11070840, area under the curve [AUC] = 0.81; BSS: 2 markers, including methylation levels at ABCA7_1040077 and CX3CR1_39322324, AUC = 0.80) and a testing dataset (AUC = 0.84, AUC = 0.82, respectively). Conclusion: Our work indicated that methylation levels of 7 key immunologic-related genes (ABCA7, CNR1, CX3CR1, CSF1 R, LRRK2, NGFR, and TARDBP) in peripheral blood was altered in AD and the models including methylation of immunologic-related genes biomarkers improved prediction of AD.
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Affiliation(s)
- Junhan Lin
- Department of Neurology, Center for Cognitive Neurology, Institute of Clinical Neurology, Fujian Institute of Geriatrics, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Siyu Yang
- Department of Neurology, Center for Cognitive Neurology, Institute of Clinical Neurology, Fujian Institute of Geriatrics, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Chao Wang
- Department of Neurology, Center for Cognitive Neurology, Institute of Clinical Neurology, Fujian Institute of Geriatrics, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Erhan Yu
- Department of Neurology, Center for Cognitive Neurology, Institute of Clinical Neurology, Fujian Institute of Geriatrics, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Zhibao Zhu
- Department of Neurology, Center for Cognitive Neurology, Institute of Clinical Neurology, Fujian Institute of Geriatrics, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Jinying Shi
- Department of Neurology, Center for Cognitive Neurology, Institute of Clinical Neurology, Fujian Institute of Geriatrics, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Xiang Li
- Department of Neurology, Center for Cognitive Neurology, Institute of Clinical Neurology, Fujian Institute of Geriatrics, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Jiawei Xin
- Department of Neurology, Center for Cognitive Neurology, Institute of Clinical Neurology, Fujian Institute of Geriatrics, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Xiaochun Chen
- Department of Neurology, Center for Cognitive Neurology, Institute of Clinical Neurology, Fujian Institute of Geriatrics, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Xiaodong Pan
- Department of Neurology, Center for Cognitive Neurology, Institute of Clinical Neurology, Fujian Institute of Geriatrics, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
- Key Laboratory of Brain Aging and Neurodegenerative Diseases, Fujian Medical University, Fuzhou, China
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16
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C. Silva T, Zhang W, Young JI, Gomez L, Schmidt MA, Varma A, Chen XS, Martin ER, Wang L. Distinct sex-specific DNA methylation differences in Alzheimer's disease. Alzheimers Res Ther 2022; 14:133. [PMID: 36109771 PMCID: PMC9479371 DOI: 10.1186/s13195-022-01070-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/30/2022] [Indexed: 01/17/2023]
Abstract
BACKGROUND Sex is increasingly recognized as a significant factor contributing to the biological and clinical heterogeneity in AD. There is also growing evidence for the prominent role of DNA methylation (DNAm) in Alzheimer's disease (AD). METHODS We studied sex-specific DNA methylation differences in the blood samples of AD subjects compared to cognitively normal subjects, by performing sex-specific meta-analyses of two large blood-based epigenome-wide association studies (ADNI and AIBL), which included DNA methylation data for a total of 1284 whole blood samples (632 females and 652 males). Within each dataset, we used two complementary analytical strategies, a sex-stratified analysis that examined methylation to AD associations in male and female samples separately, and a methylation-by-sex interaction analysis that compared the magnitude of these associations between different sexes. After adjusting for age, estimated immune cell type proportions, batch effects, and correcting for inflation, the inverse-variance fixed-effects meta-analysis model was used to identify the most consistent DNAm differences across datasets. In addition, we also evaluated the performance of the sex-specific methylation-based risk prediction models for AD diagnosis using an independent external dataset. RESULTS In the sex-stratified analysis, we identified 2 CpGs, mapped to the PRRC2A and RPS8 genes, significantly associated with AD in females at a 5% false discovery rate, and an additional 25 significant CpGs (21 in females, 4 in males) at P-value < 1×10-5. In methylation-by-sex interaction analysis, we identified 5 significant CpGs at P-value < 10-5. Out-of-sample validations using the AddNeuroMed dataset showed in females, the best logistic prediction model included age, estimated immune cell-type proportions, and methylation risk scores (MRS) computed from 9 of the 23 CpGs identified in AD vs. CN analysis that are also available in AddNeuroMed dataset (AUC = 0.74, 95% CI: 0.65-0.83). In males, the best logistic prediction model included only age and MRS computed from 2 of the 5 CpGs identified in methylation-by-sex interaction analysis that are also available in the AddNeuroMed dataset (AUC = 0.70, 95% CI: 0.56-0.82). CONCLUSIONS Overall, our results show that the DNA methylation differences in AD are largely distinct between males and females. Our best-performing sex-specific methylation-based prediction model in females performed better than that for males and additionally included estimated cell-type proportions. The significant discriminatory classification of AD samples with our methylation-based prediction models demonstrates that sex-specific DNA methylation could be a predictive biomarker for AD. As sex is a strong factor underlying phenotypic variability in AD, the results of our study are particularly relevant for a better understanding of the epigenetic architecture that underlie AD and for promoting precision medicine in AD.
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Affiliation(s)
- Tiago C. Silva
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA
| | - Wei Zhang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA
| | - Juan I. Young
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lissette Gomez
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Michael A. Schmidt
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Achintya Varma
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - X. Steven Chen
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Eden R. Martin
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lily Wang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
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17
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C. Silva T, Young JI, Zhang L, Gomez L, Schmidt MA, Varma A, Chen XS, Martin ER, Wang L. Cross-tissue analysis of blood and brain epigenome-wide association studies in Alzheimer's disease. Nat Commun 2022; 13:4852. [PMID: 35982059 PMCID: PMC9388493 DOI: 10.1038/s41467-022-32475-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/01/2022] [Indexed: 01/17/2023] Open
Abstract
To better understand DNA methylation in Alzheimer's disease (AD) from both mechanistic and biomarker perspectives, we performed an epigenome-wide meta-analysis of blood DNA methylation in two large independent blood-based studies in AD, the ADNI and AIBL studies, and identified 5 CpGs, mapped to the SPIDR, CDH6 genes, and intergenic regions, that are significantly associated with AD diagnosis. A cross-tissue analysis that combined these blood DNA methylation datasets with four brain methylation datasets prioritized 97 CpGs and 10 genomic regions that are significantly associated with both AD neuropathology and AD diagnosis. An out-of-sample validation using the AddNeuroMed dataset showed the best performing logistic regression model includes age, sex, immune cell type proportions, and methylation risk score based on prioritized CpGs in cross-tissue analysis (AUC = 0.696, 95% CI: 0.616 - 0.770, P-value = 2.78 × 10-5). Our study offers new insights into epigenetics in AD and provides a valuable resource for future AD biomarker discovery.
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Affiliation(s)
- Tiago C. Silva
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Juan I. Young
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lanyu Zhang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Lissette Gomez
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Michael A. Schmidt
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Achintya Varma
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - X. Steven Chen
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Eden R. Martin
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lily Wang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
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18
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Berger TC, Taubøll E, Heuser K. The potential role of DNA methylation as preventive treatment target of epileptogenesis. Front Cell Neurosci 2022; 16:931356. [PMID: 35936496 PMCID: PMC9353008 DOI: 10.3389/fncel.2022.931356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/27/2022] [Indexed: 11/23/2022] Open
Abstract
Pharmacological therapy of epilepsy has so far been limited to symptomatic treatment aimed at neuronal targets, with the result of an unchanged high proportion of patients lacking seizure control. The dissection of the intricate pathological mechanisms that transform normal brain matter to a focus for epileptic seizures—the process of epileptogenesis—could yield targets for novel treatment strategies preventing the development or progression of epilepsy. While many pathological features of epileptogenesis have been identified, obvious shortcomings in drug development are now believed to be based on the lack of knowledge of molecular upstream mechanisms, such as DNA methylation (DNAm), and as well as a failure to recognize glial cell involvement in epileptogenesis. This article highlights the potential role of DNAm and related gene expression (GE) as a treatment target in epileptogenesis.
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Affiliation(s)
- Toni Christoph Berger
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- *Correspondence: Toni Christoph Berger
| | - Erik Taubøll
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kjell Heuser
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Kjell Heuser
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19
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Milicic L, Vacher M, Porter T, Doré V, Burnham SC, Bourgeat P, Shishegar R, Doecke J, Armstrong NJ, Tankard R, Maruff P, Masters CL, Rowe CC, Villemagne VL, Laws SM. Comprehensive analysis of epigenetic clocks reveals associations between disproportionate biological ageing and hippocampal volume. GeroScience 2022; 44:1807-1823. [PMID: 35445885 PMCID: PMC9213584 DOI: 10.1007/s11357-022-00558-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/30/2022] [Indexed: 12/21/2022] Open
Abstract
The concept of age acceleration, the difference between biological age and chronological age, is of growing interest, particularly with respect to age-related disorders, such as Alzheimer's Disease (AD). Whilst studies have reported associations with AD risk and related phenotypes, there remains a lack of consensus on these associations. Here we aimed to comprehensively investigate the relationship between five recognised measures of age acceleration, based on DNA methylation patterns (DNAm age), and cross-sectional and longitudinal cognition and AD-related neuroimaging phenotypes (volumetric MRI and Amyloid-β PET) in the Australian Imaging, Biomarkers and Lifestyle (AIBL) and the Alzheimer's Disease Neuroimaging Initiative (ADNI). Significant associations were observed between age acceleration using the Hannum epigenetic clock and cross-sectional hippocampal volume in AIBL and replicated in ADNI. In AIBL, several other findings were observed cross-sectionally, including a significant association between hippocampal volume and the Hannum and Phenoage epigenetic clocks. Further, significant associations were also observed between hippocampal volume and the Zhang and Phenoage epigenetic clocks within Amyloid-β positive individuals. However, these were not validated within the ADNI cohort. No associations between age acceleration and other Alzheimer's disease-related phenotypes, including measures of cognition or brain Amyloid-β burden, were observed, and there was no association with longitudinal change in any phenotype. This study presents a link between age acceleration, as determined using DNA methylation, and hippocampal volume that was statistically significant across two highly characterised cohorts. The results presented in this study contribute to a growing literature that supports the role of epigenetic modifications in ageing and AD-related phenotypes.
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Affiliation(s)
- Lidija Milicic
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, 6027, Australia
| | - Michael Vacher
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, 6027, Australia
- CSIRO Health and Biosecurity, Australian E-Health Research Centre, Floreat, Western Australia, 6014, Australia
| | - Tenielle Porter
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, 6027, Australia
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, 6102, Australia
| | - Vincent Doré
- Australian E-Health Research Centre, CSIRO, Parkville, Victoria, 3052, Australia
- Department of Molecular Imaging and Therapy and Centre for PET, Austin Health, Heidelberg, Victoria, Australia
| | - Samantha C Burnham
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia
- Australian E-Health Research Centre, CSIRO, Parkville, Victoria, 3052, Australia
| | - Pierrick Bourgeat
- Australian E-Health Research Centre, CSIRO, Herston, Queensland, 4029, Australia
| | - Rosita Shishegar
- Australian E-Health Research Centre, CSIRO, Parkville, Victoria, 3052, Australia
- School of Psychological Sciences and Turner Institute for Brain and Mental Health, Monash University, Melbourne, VIC, Australia
| | - James Doecke
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia
- Australian E-Health Research Centre, CSIRO, Herston, Queensland, 4029, Australia
| | - Nicola J Armstrong
- Department of Mathematics and Statistics, Curtin University, Bentley, Western Australia, Australia
| | - Rick Tankard
- School of Mathematics and Statistics, Murdoch University, Perth, Western Australia, Australia
| | - Paul Maruff
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3052, Australia
- Cogstate Ltd, Melbourne, VIC, Australia
| | - Colin L Masters
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Christopher C Rowe
- Department of Molecular Imaging and Therapy and Centre for PET, Austin Health, Heidelberg, Victoria, Australia
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Victor L Villemagne
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia
- Department of Molecular Imaging and Therapy and Centre for PET, Austin Health, Heidelberg, Victoria, Australia
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Simon M Laws
- Centre for Precision Health, Edith Cowan University, 270 Joondalup Drive, Joondalup, Western Australia, 6027, Australia.
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, 6027, Australia.
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia, 6102, Australia.
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20
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Schaffner SL, Wassouf Z, Lazaro DF, Xylaki M, Gladish N, Lin DTS, MacIsaac J, Ramadori K, Hentrich T, Schulze-Hentrich JM, Outeiro TF, Kobor MS. Alpha-synuclein overexpression induces epigenomic dysregulation of glutamate signaling and locomotor pathways. Hum Mol Genet 2022; 31:3694-3714. [PMID: 35567546 PMCID: PMC9616577 DOI: 10.1093/hmg/ddac104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 04/15/2022] [Accepted: 05/03/2022] [Indexed: 11/26/2022] Open
Abstract
Parkinson’s disease (PD) is a neurological disorder with complex interindividual etiology that is becoming increasingly prevalent worldwide. Elevated alpha-synuclein levels can increase risk of PD and may influence epigenetic regulation of PD pathways. Here, we report genome-wide DNA methylation and hydroxymethylation alterations associated with overexpression of two PD-linked alpha-synuclein variants (wild-type and A30P) in LUHMES cells differentiated to dopaminergic neurons. Alpha-synuclein altered DNA methylation at thousands of CpGs and DNA hydroxymethylation at hundreds of CpGs in both genotypes, primarily in locomotor behavior and glutamate signaling pathway genes. In some cases, epigenetic changes were associated with transcription. SMITE network analysis incorporating H3K4me1 ChIP-seq to score DNA methylation and hydroxymethylation changes across promoters, enhancers, and gene bodies confirmed epigenetic and transcriptional deregulation of glutamate signaling modules in both genotypes. Our results identify distinct and shared impacts of alpha-synuclein variants on the epigenome, and associate alpha-synuclein with the epigenetic etiology of PD.
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Affiliation(s)
- Samantha L Schaffner
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Zinah Wassouf
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37073 Göttingen, Germany.,German Centre for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany
| | - Diana F Lazaro
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Mary Xylaki
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Nicole Gladish
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - David T S Lin
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Julia MacIsaac
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Katia Ramadori
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Thomas Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Julia M Schulze-Hentrich
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Nanoscale Microscopy and Molecular Physiology of the Brain, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, 37073 Göttingen, Germany.,German Centre for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany.,Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
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21
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Wu H, Liu H, Liu H, Chen Y, Liu T, Shen X, Liu L. Genome-wide DNA methylation profiling in differentiating Crohn's disease from intestinal tuberculosis. Genes Genomics 2022; 44:603-615. [PMID: 35305241 DOI: 10.1007/s13258-022-01224-1] [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: 08/23/2021] [Accepted: 01/20/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Differential diagnosis of Crohn's disease (CD) and intestinal tuberculosis (ITB) is still difficult in clinical pratice. DNA methylation has been considered as a favorable area for biomarker exploration and identification. OBJECTIVE The purpose of the current study was to evaluate DNA methylation changes between CD and ITB. METHODS We performed a genome-wide association study to identify differentially methylated positions (DMPs), including 8 CD patients (before the initial of biologics or immunomodulators), 6 ITB patients, and 8 healthy controls (HCs), in whole blood DNA using the Infinium HumanMethylation850 BeadChip. RESULTS Patients in the CD group and ITB group were all observed with hypo-methylated changes compared with HCs. However, the CD group overlaps with the ITB group in DNA methylation, suggesting a stable epigenetic profile between the two diseases. The pathway enrichment analysis showed the alternation in inflammation-related pathway, immune system, and signal transduction. Focused on the DMPs located in the promoter region, further analysis indicated hypermethylation of cg03122532 (5'UTR of KCNJ15) could be a potential CD-specific biomarker. CONCLUSIONS We identified specific differential methylation loci related to CD and ITB in blood DNA. DNA metylation as a important epigenetic modification could contribute to the pathogenesis study and biomarker exploration of the diseases.
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Affiliation(s)
- Hao Wu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China
| | - Hongchun Liu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China
| | - Haining Liu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China
| | - Yanjie Chen
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China
| | - Taotao Liu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China
| | - Xizhong Shen
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China.
| | - Lili Liu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China.
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22
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Zhang T, Wei W, Chang S, Liu N, Li H. Integrated Network Pharmacology and Comprehensive Bioinformatics Identifying the Mechanisms and Molecular Targets of Yizhiqingxin Formula for Treatment of Comorbidity With Alzheimer’s Disease and Depression. Front Pharmacol 2022; 13:853375. [PMID: 35548356 PMCID: PMC9081443 DOI: 10.3389/fphar.2022.853375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The Yizhiqinxin formula (YZQX) has been used to treat Alzheimer’s disease (AD) or major depression disorder (MDD). However, its specific underlying mechanisms and therapeutic targets remain unclear.Methods: The ingredients and putative targets of YZQX were screened using the TCMSP and Drugbank databases. Next, the GEO database was used to retrieve relevant differentially expressed genes (DEGs) in AD or MDD and normal tissues. The PPI network was established, merged, and further screened to identify the main ingredients and core targets of YZQX against AD and MDD comorbidities. We performed enrichment analysis of core targets to identify biological processes and pathways. Finally, AutoDock software was used to validate the binding affinity between the crucial targets of direct action and their corresponding ingredients.Results: A total of 43 ingredients were identified from YZQX, of which 43 were screened to yield 504 targets. By establishing the PPI network, 92 targets were regarded as targets of YZQX against AD and MDD comorbidities in the core network. Promising targets (HSP90AA1, ESR1, AKT1, VCAM1, EGFR, CDK1, MAPK1, CDK2, MYC, HSPB1, and HSPA5) and signaling pathways (PI3K-Akt signaling pathway, ubiquitin-mediated proteolysis, MAPK signaling pathway, etc.) were filtered and refined to elucidate the underlying mechanism of YZQX against AD and MDD comorbidities. Molecular docking confirmed the ingredients of YZQX (quercetin and kaempferol) could bind well to multiple crucial targets.Conclusion: The ingredients of YZQX, such as quercetin and kaempferol, might treat AD and MDD comorbidities by acting on multiple targets and pathways.
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Affiliation(s)
- Tingting Zhang
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Wei Wei
- Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Surui Chang
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Nanyang Liu
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Nanyang Liu, ; Hao Li,
| | - Hao Li
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- Wangjing Hospital, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Nanyang Liu, ; Hao Li,
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23
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Pérez RF, Alba-Linares JJ, Tejedor JR, Fernández AF, Calero M, Román-Domínguez A, Borrás C, Viña J, Ávila J, Medina M, Fraga MF. Blood DNA methylation patterns in older adults with evolving dementia. J Gerontol A Biol Sci Med Sci 2022; 77:1743-1749. [PMID: 35299244 PMCID: PMC9434456 DOI: 10.1093/gerona/glac068] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Indexed: 11/14/2022] Open
Abstract
Dementia and cognitive disorders are major aging-associated pathologies. The prevalence and severity of these conditions are influenced by both genetic and environmental factors. Reflecting this, epigenetic alterations have been associated with each of these processes, especially at the level of DNA methylation, and such changes may help explain the observed interindividual variability in the development of the 2 pathologies. However, the importance of epigenetic alterations in explaining their etiology is unclear because little is known about the timing of when they appear. Here, using Illumina MethylationEPIC arrays, we have longitudinally analyzed the peripheral blood methylomes of cognitively healthy older adults (>70 year), some of whom went on to develop dementia while others stayed healthy. We have characterized 34 individuals at the prediagnosis stage and at a 4-year follow-up in the postdiagnosis stage (total n = 68). Our results show multiple DNA methylation alterations linked to dementia status, particularly at the level of differentially methylated regions. These loci are associated with several dementia-related genes, including PON1, AP2A2, MAGI2, POT1, ITGAX, PACSIN1, SLC2A8, and EIF4E. We also provide validation of the previously reported epigenetic alteration of HOXB6 and PM20D1. Importantly, we show that most of these regions are already altered in the prediagnosis stage of individuals who go on to develop dementia. In conclusion, our observations suggest that dementia-associated epigenetic patterns that have specific biological features are already present before diagnosis, and thus may be important in the design of epigenetic biomarkers for disease detection based on peripheral tissues.
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Affiliation(s)
- Raúl Fernández Pérez
- Cancer Epigenetics and Nanomedicine Laboratory. Nanomaterials and Nanotechnology Research Center (CINN-CSIC). Health Research Institute of Asturias (ISPA-FINBA). Institute of Oncology of Asturias (IUOPA) and Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain. Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII)
| | - Juan José Alba-Linares
- Cancer Epigenetics and Nanomedicine Laboratory. Nanomaterials and Nanotechnology Research Center (CINN-CSIC). Health Research Institute of Asturias (ISPA-FINBA). Institute of Oncology of Asturias (IUOPA) and Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain. Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII)
| | - Juan Ramón Tejedor
- Cancer Epigenetics and Nanomedicine Laboratory. Nanomaterials and Nanotechnology Research Center (CINN-CSIC). Health Research Institute of Asturias (ISPA-FINBA). Institute of Oncology of Asturias (IUOPA) and Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain. Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII)
| | - Agustín Fernández Fernández
- Cancer Epigenetics and Nanomedicine Laboratory. Nanomaterials and Nanotechnology Research Center (CINN-CSIC). Health Research Institute of Asturias (ISPA-FINBA). Institute of Oncology of Asturias (IUOPA) and Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain. Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII)
| | - Miguel Calero
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain.,Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Madrid, Spain.,CIEN Foundation, Queen Sofia Foundation Alzheimer Center, Madrid, Spain
| | - Aurora Román-Domínguez
- Freshage Research Group, Department of Physiology, Faculty of Medicine, University of Valencia and CIBERFES-ISCIII, Fundación Investigación Hospital Clínico Universitario/INCLIVA, Valencia, Spain
| | - Consuelo Borrás
- Freshage Research Group, Department of Physiology, Faculty of Medicine, University of Valencia and CIBERFES-ISCIII, Fundación Investigación Hospital Clínico Universitario/INCLIVA, Valencia, Spain
| | - José Viña
- Freshage Research Group, Department of Physiology, Faculty of Medicine, University of Valencia and CIBERFES-ISCIII, Fundación Investigación Hospital Clínico Universitario/INCLIVA, Valencia, Spain
| | - Jesús Ávila
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain.,Centro de Biología Molecular Severo Ochoa (CBMSO) CSIC-UAM, Madrid, Spain
| | - Miguel Medina
- Network Center for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain.,CIEN Foundation, Queen Sofia Foundation Alzheimer Center, Madrid, Spain
| | - Mario Fernández Fraga
- Cancer Epigenetics and Nanomedicine Laboratory. Nanomaterials and Nanotechnology Research Center (CINN-CSIC). Health Research Institute of Asturias (ISPA-FINBA). Institute of Oncology of Asturias (IUOPA) and Department of Organisms and Systems Biology (B.O.S.), University of Oviedo, Oviedo, Spain. Rare Diseases CIBER (CIBERER) of the Carlos III Health Institute (ISCIII)
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24
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Chen L, Shen Q, Xu S, Yu H, Pei S, Zhang Y, He X, Wang Q, Li D. 5-Hydroxymethylcytosine Signatures in Circulating Cell-Free DNA as Diagnostic Biomarkers for Late-Onset Alzheimer's Disease. J Alzheimers Dis 2021; 85:573-585. [PMID: 34864677 DOI: 10.3233/jad-215217] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND 5-Hydroxymethylcytosine (5hmC) is an epigenetic DNA modification that is highly abundant in central nervous system. It has been reported that DNA 5hmC dysregulation play a critical role in Alzheimer's disease (AD) pathology. Changes in 5hmC signatures can be detected in circulating cell-free DNA (cfDNA), which has shown potential as a non-invasive liquid biopsy material. OBJECTIVE However, the genome-wide profiling of 5hmC in cfDNA and its potential for the diagnosis of AD has not been reported to date. METHODS We carried out a case-control study and used a genome-wide chemical capture followed by high-throughput sequencing to detect the genome-wide profiles of 5hmC in human cfDNA and identified differentially hydroxymethylated regions (DhMRs) in late-onset AD patients and the control. RESULTS We discovered significant differences of 5hmC enrichment in gene bodies which were linked to multiple AD pathogenesis-associated signaling pathways in AD patients compared with cognitively normal controls, indicating they can be well distinguished from normal controls by DhMRs in cfDNA. Specially, we identified 7 distinct genes (RABEP1, CPNE4, DNAJC15, REEP3, ROR1, CAMK1D, and RBFOX1) with predicting diagnostic potential based on their significant correlations with MMSE and MoCA scores of subjects. CONCLUSION The present results suggest that 5hmC markers derived from plasma cfDNA can served as an effective, minimally invasive biomarkers for clinical auxiliary diagnosis of late-onset AD.
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Affiliation(s)
- Lei Chen
- Institute of Nutrition & Health, Qingdao University, Qingdao, China.,School of Public health, Qingdao University, Qingdao, China
| | - Qianqian Shen
- Institute of Nutrition & Health, Qingdao University, Qingdao, China.,School of Public health, Qingdao University, Qingdao, China
| | - Shunliang Xu
- Department of Neurology, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hongzhuan Yu
- Weifang Hospital of Traditional Chinese Medicine, Weifang, China
| | - Shengjie Pei
- Institute of Nutrition & Health, Qingdao University, Qingdao, China.,School of Public health, Qingdao University, Qingdao, China
| | - Yangting Zhang
- Institute of Nutrition & Health, Qingdao University, Qingdao, China.,School of Public health, Qingdao University, Qingdao, China
| | - Xin He
- Institute of Nutrition & Health, Qingdao University, Qingdao, China.,School of Public health, Qingdao University, Qingdao, China
| | - QiuZhen Wang
- Institute of Nutrition & Health, Qingdao University, Qingdao, China.,School of Public health, Qingdao University, Qingdao, China
| | - Duo Li
- Institute of Nutrition & Health, Qingdao University, Qingdao, China.,School of Public health, Qingdao University, Qingdao, China
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25
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Liu X, Song N, Qian D, Gu S, Pu J, Huang L, Liu J, Qian K. Porous Inorganic Materials for Bioanalysis and Diagnostic Applications. ACS Biomater Sci Eng 2021; 8:4092-4109. [PMID: 34494831 DOI: 10.1021/acsbiomaterials.1c00733] [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: 12/22/2022]
Abstract
Porous inorganic materials play an important role in adsorbing targeted analytes and supporting efficient reactions in analytical science. The detection performance relies on the structural properties of porous materials, considering the tunable pore size, shape, connectivity, etc. Herein, we first clarify the enhancement mechanisms of porous materials for bioanalysis, concerning the detection sensitivity and selectivity. The diagnostic applications of porous material-assisted platforms by coupling with various analytical techniques, including electrochemical sensing, optical spectrometry, and mass spectrometry, etc., are then reviewed. We foresee that advanced porous materials will bring far-reaching implications in bioanalysis toward real-case applications, especially as diagnostic assays in clinical settings.
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Affiliation(s)
- Xun Liu
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Naikun Song
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Dahong Qian
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
| | - Sai Gu
- School of Engineering, University of Warwick, Coventry CV4 7AL, W Midlands, England.,Department of Chemical and Process Engineering, University of Surrey, Guildford, Surrey GU27XH, United Kingdom
| | - Jun Pu
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200127, P. R. China
| | - Lin Huang
- Stem Cell Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200127, P. R. China
| | - Jian Liu
- Department of Chemical and Process Engineering, University of Surrey, Guildford, Surrey GU27XH, United Kingdom.,Chinese Academy of Sciences, Dalian Institute of Chemical Physics, CAS State Key Laboratory of Catalysis, 568 Zhongshan Road, Dalian 116023, P. R. China
| | - Kun Qian
- School of Biomedical Engineering, Institute of Medical Robotics and Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, P. R. China.,Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200127, P. R. China
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26
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Wu D, Li Y, Ren Q, Pei S, Wang L, Yang L, Chong Y, Sun S, Hao J, Feng F. TANC1 methylation as a novel biomarker for the diagnosis of patients with anti-tuberculosis drug-induced liver injury. Sci Rep 2021; 11:17423. [PMID: 34465797 PMCID: PMC8408132 DOI: 10.1038/s41598-021-96869-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/11/2021] [Indexed: 01/02/2023] Open
Abstract
We aimed to elucidate the differences in genomic methylation patterns between ADLI and non-ADLI patients to identify DNA methylation-based biomarkers. Genome-wide DNA methylation patterns were obtained using Infinium MethylationEPIC (EPIC) BeadChip array to analyze 14 peripheral blood samples (7 ADLI cases, 7 non-ADLI controls). Changes in the mRNA and DNA methylation in the target genes of another 120 peripheral blood samples (60 ADLI cases, 60 non-ADLI controls) were analyzed by real-time polymerase chain reaction and pyrosequencing, respectively. A total of 308 hypermethylated CpG sites and 498 hypomethylated CpG sites were identified. Significantly, hypermethylated CpG sites cg06961147 and cg24666046 in TANC1 associated with ADLI was identified by genome-wide DNA methylation profiling. The mRNA expression of TANC1 was lower in the cases compared to the controls. Pyrosequencing validated these two differentially methylated loci, which was consistent with the results from the EPIC BeadChip array. Receiver operating characteristic analysis indicated that the area under the curve of TANC1 (cg06961147, cg24666046, and their combinations) was 0.812, 0.842, and 0.857, respectively. These results indicate that patients with ADLI have different genomic methylation patterns than patients without ADLI. The hypermethylated differentially methylated site cg06961147 combined with cg24666046 in TANC1 provides evidence for the diagnosis of ADLI.
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Affiliation(s)
- Dongxue Wu
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China
| | - Yuhong Li
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China
| | - Qi Ren
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China
| | - Shengfei Pei
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China
| | - Lin Wang
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China
| | - Luming Yang
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China
| | - Yingzhi Chong
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China
| | - Shufeng Sun
- College of Nursing and Rehabilitation, North China University of Science and Technology, Tangshan, 063210, China
| | - Jinqi Hao
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China.,School of Public Health, Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou City, 014040, Inner Mongolia, China
| | - Fumin Feng
- School of Public Health, North China University of Science and Technology, Tangshan, 063210, China. .,School of Life Science, North China University of Science and Technology, Tangshan, 063210, China.
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27
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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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28
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Sharma VK, Mehta V, Singh TG. Alzheimer's Disorder: Epigenetic Connection and Associated Risk Factors. Curr Neuropharmacol 2021; 18:740-753. [PMID: 31989902 PMCID: PMC7536832 DOI: 10.2174/1570159x18666200128125641] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 11/26/2019] [Accepted: 01/27/2020] [Indexed: 12/13/2022] Open
Abstract
The gene based therapeutics and drug targets have shown incredible and appreciable advances in alleviating human sufferings and complexities. Epigenetics simply means above genetics or which controls the organism beyond genetics. At present it is very clear that all characteristics of an individual are not determined by DNA alone, rather the environment, stress, life style and nutrition play a vital part in determining the response of an organism. Thus, nature (genetic makeup) and nurture (exposure) play equally important roles in the responses observed, both at the cellular and organism levels. Epigenetics influence plethora of complications at cellular and molecular levels that includes cancer, metabolic and cardiovascular complications including neurological (psychosis) and neurodegenerative disorders (Alzheimer’s disease, Parkinson disease etc.). The epigenetic mechanisms include DNA methylation, histone modification and non coding RNA which have substantial impact on progression and pathways linked to Alzheimer’s disease. The epigenetic mechanism gets deregulated in Alzheimer’s disease and is characterized by DNA hyper methylation, deacetylation of histones and general repressed chromatin state which alter gene expression at the transcription level by upregulation, downregulation or silencing of genes. Thus, the processes or modulators of these epigenetic processes have shown vast potential as a therapeutic target in Alzheimer’s disease.
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Affiliation(s)
| | - Vineet Mehta
- Govt. College of Pharmacy, Rohru, District Shimla, Himachal Pradesh-171207, India
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29
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Balnis J, Madrid A, Hogan KJ, Drake LA, Chieng HC, Tiwari A, Vincent CE, Chopra A, Vincent PA, Robek MD, Singer HA, Alisch RS, Jaitovich A. Blood DNA methylation and COVID-19 outcomes. Clin Epigenetics 2021; 13:118. [PMID: 34034806 PMCID: PMC8148415 DOI: 10.1186/s13148-021-01102-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/11/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND There are no prior reports that compare differentially methylated regions of DNA in blood samples from COVID-19 patients to samples collected before the SARS-CoV-2 pandemic using a shared epigenotyping platform. We performed a genome-wide analysis of circulating blood DNA CpG methylation using the Infinium Human MethylationEPIC BeadChip on 124 blood samples from hospitalized COVID-19-positive and COVID-19-negative patients and compared these data with previously reported data from 39 healthy individuals collected before the pandemic. Prospective outcome measures such as COVID-19-GRAM risk-score and mortality were combined with methylation data. RESULTS Global mean methylation levels did not differ between COVID-19 patients and healthy pre-pandemic controls. About 75% of acute illness-associated differentially methylated regions were located near gene promoter regions and were hypo-methylated in comparison with healthy pre-pandemic controls. Gene ontology analyses revealed terms associated with the immune response to viral infections and leukocyte activation; and disease ontology analyses revealed a predominance of autoimmune disorders. Among COVID-19-positive patients, worse outcomes were associated with a prevailing hyper-methylated status. Recursive feature elimination identified 77 differentially methylated positions predictive of COVID-19 severity measured by the GRAM-risk score. CONCLUSION Our data contribute to the awareness that DNA methylation may influence the expression of genes that regulate COVID-19 progression and represent a targetable process in that setting.
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Affiliation(s)
- Joseph Balnis
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Andy Madrid
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA
| | - Kirk J Hogan
- Department of Anesthesiology, University of Wisconsin, Madison, WI, USA
| | - Lisa A Drake
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Hau C Chieng
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Anupama Tiwari
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Catherine E Vincent
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Amit Chopra
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA
| | - Peter A Vincent
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Michael D Robek
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, USA
| | - Harold A Singer
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Reid S Alisch
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, USA.
| | - Ariel Jaitovich
- Division of Pulmonary and Critical Care Medicine, Albany Medical Center, Albany, NY, USA.
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA.
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30
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Kobayashi N, Shinagawa S, Nagata T, Tagai K, Shimada K, Ishii A, Oka N, Shigeta M, Kondo K. Blood DNA Methylation Levels in the WNT5A Gene Promoter Region: A Potential Biomarker for Agitation in Subjects with Dementia. J Alzheimers Dis 2021; 81:1601-1611. [PMID: 33967051 PMCID: PMC8293647 DOI: 10.3233/jad-210078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Background: Behavioral and psychological symptoms of dementia (BPSD) cause a heavy burden for both patient and caregivers. These symptoms are diverse, and their mechanism is still unclear. Agitation is the most common and difficult to treat among BPSD. In recent years, while changes in DNA methylation levels have been receiving attention as a biomarker of aging and dementia, associations with BPSD have not been examined. Objective: Focusing on agitation, the objective of the present study was to identify a region where changes in DNA methylation levels are associated with agitation. Methods: Using genome-wide DNA methylation analysis data for 7 dementia subjects with agitation, 5 dementia subjects without agitation, and 4 normal elderly controls, we determined a signaling pathway in the WNT5A gene promoter region to be associated with agitation. Based on this result, we measured DNA methylation levels in this region for 26 dementia subjects with agitation and 82 dementia subjects without agitation by means of methylation-sensitive high-resolution melting (MS-HRM) analysis. Results: The WNT5A DNA methylation level in dementia subjects with agitation was significantly lower than in those without agitation (p = 0.001). Changes in WNT5A DNA methylation levels were not influenced by age, sex, body mass index, APOE ɛ4, medication, or inflammatory cytokines. Conclusion: Our results suggested an association of agitation with Wnt signaling, in particular with changes in WNT5A DNA methylation levels, which could be a potentially useful biomarker for predicting the appearance of agitation. It may contribute to the elucidation of the mechanism of BPSD.
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Affiliation(s)
- Nobuyuki Kobayashi
- Department of Virology, The Jikei University School of Medicine, Tokyo, Japan.,Department of Psychiatry, The Jikei University School of Medicine, Tokyo, Japan
| | | | - Tomoyuki Nagata
- Department of Psychiatry, The Jikei University School of Medicine, Tokyo, Japan
| | - Kenji Tagai
- Department of Psychiatry, The Jikei University School of Medicine, Tokyo, Japan
| | - Kazuya Shimada
- Department of Virology, The Jikei University School of Medicine, Tokyo, Japan
| | - Azusa Ishii
- Department of Virology, The Jikei University School of Medicine, Tokyo, Japan
| | - Naomi Oka
- Department of Virology, The Jikei University School of Medicine, Tokyo, Japan
| | - Masahiro Shigeta
- Department of Psychiatry, The Jikei University School of Medicine, Tokyo, Japan
| | - Kazuhiro Kondo
- Department of Virology, The Jikei University School of Medicine, Tokyo, Japan
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31
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Wang W, Li W, Jiang W, Lin H, Wu Y, Wen Y, Xu C, Tian X, Li S, Tan Q, Zhang D. Genome-wide DNA methylation analysis of cognitive function in middle and old-aged Chinese monozygotic twins. J Psychiatr Res 2021; 136:571-580. [PMID: 33131831 DOI: 10.1016/j.jpsychires.2020.10.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 08/13/2020] [Accepted: 10/25/2020] [Indexed: 12/13/2022]
Abstract
Cognitive ability plays an important role in mental and physical well-beings in the increasingly ageing populations. Here, based on a sample of 30 cognitive function-discordant monozygotic twin pairs, we aimed to detect specific epigenetic variants potentially related to cognitive function by conducting an epigenome-wide association study (EWAS). Association between methylation level of single CpG site with cognitive function score was tested by linear mixed effect model. Functions of cis-regulatory regions and ontology enrichments were predicted by Genomic Regions Enrichment of Annotations Tool (GREAT). Differentially methylated regions (DMRs) were detected by comb-p python library. A list of 28 CpG sites were identified to reach the level of P < 1 × 10-4, and the strongest association (cor = 0.138, P = 2.549 × 10-6) was detected for DNA CpG site (Chr17: 40,700,490 bp) located at HSD17B1P1. The identified 14,065 genomic CpG sites (P < 0.05) were mapped to 2646 genes, especially HSD17B1P1, CUL4A, INTS8, GFI1B, ZNF467, CDH15, and PSMA1. GREAT ontology enrichments mainly highlighted nicotine pharmacodynamics pathway, GABA-B receptor II/nicotinic acetylcholine receptor/hedgehog/endothelin/Wnt signaling pathways, Parkinson disease, Huntington disease, glycolysis, neuronal system, and toll-like receptor binding. We detected 15 DMRs located at/near 16 genes, especially LINC01551, LINC02282, and FAM32A. And 32 cognitive function-associated differentially methylated genes could be replicated, such as SHANK2, ABCA2, PRDM16, NCOR2, and INPP5A. Our EWAS in monozygotic twins identify specific epigenetic variations which are significantly involved in functional genes, biological function and pathways that mediate cognitive function. The findings provide clues to further identify new diagnostic biomarkers and therapeutic targets for cognitive dysfunction.
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Affiliation(s)
- Weijing Wang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, 266021, Shandong Province, China.
| | - Weilong Li
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, DK-5000, Odense C, Denmark.
| | - Wenjie Jiang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, 266021, Shandong Province, China.
| | - Haijun Lin
- Biomarker Technologies orporation, Beijing, 100000, China.
| | - Yili Wu
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, 266021, Shandong Province, China.
| | - Yanhua Wen
- Biomarker Technologies orporation, Beijing, 100000, China.
| | - Chunsheng Xu
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, 266033, Shandong Province, China; Qingdao Institute of Preventive Medicine, Qingdao, 266033, Shandong Province, China.
| | - Xiaocao Tian
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, 266033, Shandong Province, China; Qingdao Institute of Preventive Medicine, Qingdao, 266033, Shandong Province, China.
| | - Shuxia Li
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, DK-5000, Odense C, Denmark.
| | - Qihua Tan
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, DK-5000, Odense C, Denmark; Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, DK-5000, Odense C, Denmark.
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, 266021, Shandong Province, China.
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32
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Wang K, Wang L, Chen L, Peng C, Luo B, Mo J, Chen W. Intranasal administration of dauricine loaded on graphene oxide: multi-target therapy for Alzheimer's disease. Drug Deliv 2021; 28:580-593. [PMID: 33729067 PMCID: PMC7971267 DOI: 10.1080/10717544.2021.1895909] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is a degenerative disease of the central nervous system characterized by progressive cognitive and memory-related impairment. However, current therapeutic treatments have not proved sufficiently effective, mainly due to the complicated pathogenesis of the disease. In this study, a nano-formulation of graphene oxide (GO) loaded with dauricine (Dau) was investigated in terms of the combined anti-inflammatory and anti-oxidative stress effects of Dau and the inhibition of misfolding and aggregation of the amyloid-β (Aβ) protein by GO. Both in vivo and in vitro models were induced using Aβ1-42, and the formulation was administered nasally in mice. The results showed that GO loaded with Dau greatly reduced oxidative stress through increasing superoxide dismutase levels and decreasing reactive oxygen species and malondialdehyde levels in vitro; it also alleviated the cognitive memory deficits and brain glial cell activation in mice with Aβ1-42-induced AD. This proved that GO loaded with Dau could protect against Aβ1-42-induced oxidative damage and apoptosis in both in vitro and in vivo AD models; therefore, GO loaded with Dau has the potential to be an effective and agent for the rapid treatment of AD.
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Affiliation(s)
- Kaixuan Wang
- School of Pharmacy, Guilin Medical University, Guilin, China
| | - Lingfeng Wang
- School of Pharmacy, Zhejiang Chinese Medical University, Zhejiang, China
| | - Ling Chen
- School of Pharmacy, Guilin Medical University, Guilin, China
| | - Chiwei Peng
- School of Pharmacy, Guilin Medical University, Guilin, China
| | - Beijiao Luo
- School of Pharmacy, Guilin Medical University, Guilin, China
| | - Jingxin Mo
- Department of Pharmacy, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Wei Chen
- Department of Pharmacy, Affiliated Hospital of Guilin Medical University, Guilin, China
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33
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Chen Y, Li TR, Hao SW, Wang XN, Cai YN, Han Y. Blood NCAPH2 Methylation Is Associated With Hippocampal Volume in Subjective Cognitive Decline With Apolipoprotein E ε4 Non-carriers. Front Aging Neurosci 2021; 13:632382. [PMID: 33603659 PMCID: PMC7884760 DOI: 10.3389/fnagi.2021.632382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/06/2021] [Indexed: 11/13/2022] Open
Abstract
Objective: This study assessed the methylation of peripheral NCAPH2 in individuals with subjective cognitive decline (SCD), identified its correlation with the hippocampal volume, and explored whether the correlation is influenced by apolipoprotein E ε4 (APOE ε4) status. Methods: Cognitively normal controls (NCs, n = 56), individuals with SCD (n = 81), and patients with objective cognitive impairment (OCI, n = 51) were included from the Sino Longitudinal Study on Cognitive Decline (NCT03370744). All participants completed neuropsychological assessments, blood tests, and structural MRI. NCAPH2 methylation was compared according to the diagnostic and APOE ε4 status. Partial correlation analysis was conducted to assess the correlations between the hippocampal volume, cognitive tests, and the NCAPH2 methylation levels. Results: Individuals with SCD and patients with OCI showed significantly lower levels of NCAPH2 methylation than NCs, which were independent of the APOE ε4 status. The NCAPH2 methylation levels and the hippocampal volumes were positively correlated in the SCD APOE ε4 non-carriers but not in the OCI group. No association was found between the NCAPH2 methylation levels and the cognitive function. Conclusion: Abnormal changes in blood NCAPH2 methylation were found to occur in SCD, indicating its potential to be used as a useful peripheral biomarker in the early stage of Alzheimer's disease screening.
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Affiliation(s)
- Ying Chen
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China.,Department of Neurology, Zhejiang Taizhou Municipal Hospital, Taizhou, Zhejiang, China
| | - Tao-Ran Li
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Shu-Wen Hao
- Department of Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Xiao-Ni Wang
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Yan-Ning Cai
- Department of Neurobiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Ying Han
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China.,Center of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing, China.,National Clinical Research Center for Geriatric Disorders, Beijing, China
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Wang Q, Chen Y, Readhead B, Chen K, Su Y, Reiman EM, Dudley JT. Longitudinal data in peripheral blood confirm that PM20D1 is a quantitative trait locus (QTL) for Alzheimer's disease and implicate its dynamic role in disease progression. Clin Epigenetics 2020; 12:189. [PMID: 33298155 PMCID: PMC7724832 DOI: 10.1186/s13148-020-00984-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/18/2020] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND While Alzheimer's disease (AD) remains one of the most challenging diseases to tackle, genome-wide genetic/epigenetic studies reveal many disease-associated risk loci, which sheds new light onto disease heritability, provides novel insights to understand its underlying mechanism and potentially offers easily measurable biomarkers for early diagnosis and intervention. METHODS We analyzed whole-genome DNA methylation data collected from peripheral blood in a cohort (n = 649) from the Alzheimer's Disease Neuroimaging Initiative (ADNI) and compared the DNA methylation level at baseline among participants diagnosed with AD (n = 87), mild cognitive impairment (MCI, n = 175) and normal controls (n = 162), to identify differentially methylated regions (DMRs). We also leveraged up to 4 years of longitudinal DNA methylation data, sampled at approximately 1 year intervals to model alterations in methylation levels at DMRs to delineate methylation changes associated with aging and disease progression, by linear mixed-effects (LME) modeling for the unchanged diagnosis groups (AD, MCI and control, respectively) and U-shape testing for those with changed diagnosis (converters). RESULTS When compared with controls, patients with MCI consistently displayed promoter hypomethylation at methylation QTL (mQTL) gene locus PM20D1. This promoter hypomethylation was even more prominent in patients with mild to moderate AD. This is in stark contrast with previously reported hypermethylation in hippocampal and frontal cortex brain tissues in patients with advanced-stage AD at this locus. From longitudinal data, we show that initial promoter hypomethylation of PM20D1 during MCI and early stage AD is reversed to eventual promoter hypermethylation in late stage AD, which helps to complete a fuller picture of methylation dynamics. We also confirm this observation in an independent cohort from the Religious Orders Study and Memory and Aging Project (ROSMAP) Study using DNA methylation and gene expression data from brain tissues as neuropathological staging (Braak score) advances. CONCLUSIONS Our results confirm that PM20D1 is an mQTL in AD and demonstrate that it plays a dynamic role at different stages of the disease. Further in-depth study is thus warranted to fully decipher its role in the evolution of AD and potentially explore its utility as a blood-based biomarker for AD.
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Affiliation(s)
- Qi Wang
- grid.215654.10000 0001 2151 2636ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ USA
| | - Yinghua Chen
- grid.418204.b0000 0004 0406 4925Banner Alzheimer’s Institute, Phoenix, AZ USA
| | - Benjamin Readhead
- grid.215654.10000 0001 2151 2636ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ USA
| | - Kewei Chen
- grid.418204.b0000 0004 0406 4925Banner Alzheimer’s Institute, Phoenix, AZ USA
| | - Yi Su
- grid.418204.b0000 0004 0406 4925Banner Alzheimer’s Institute, Phoenix, AZ USA
| | - Eric M. Reiman
- grid.215654.10000 0001 2151 2636ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ USA ,grid.418204.b0000 0004 0406 4925Banner Alzheimer’s Institute, Phoenix, AZ USA
| | - Joel T. Dudley
- grid.215654.10000 0001 2151 2636ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ USA ,grid.59734.3c0000 0001 0670 2351Icahn School of Medicine at Mount Sinai, New York, NY USA
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Dabin LC, Guntoro F, Campbell T, Bélicard T, Smith AR, Smith RG, Raybould R, Schott JM, Lunnon K, Sarkies P, Collinge J, Mead S, Viré E. Altered DNA methylation profiles in blood from patients with sporadic Creutzfeldt-Jakob disease. Acta Neuropathol 2020; 140:863-879. [PMID: 32918118 PMCID: PMC7666287 DOI: 10.1007/s00401-020-02224-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/13/2020] [Accepted: 08/31/2020] [Indexed: 12/13/2022]
Abstract
Prion diseases are fatal and transmissible neurodegenerative disorders caused by the misfolding and aggregation of prion protein. Although recent studies have implicated epigenetic variation in common neurodegenerative disorders, no study has yet explored their role in human prion diseases. Here we profiled genome-wide blood DNA methylation in the most common human prion disease, sporadic Creutzfeldt–Jakob disease (sCJD). Our case–control study (n = 219), when accounting for differences in cell type composition between individuals, identified 38 probes at genome-wide significance (p < 1.24 × 10–7). Nine of these sites were taken forward in a replication study, performed in an independent case–control (n = 186) cohort using pyrosequencing. Sites in or close to FKBP5, AIM2 (2 probes), UHRF1, KCNAB2 successfully replicated. The blood-based DNA methylation signal was tissue- and disease-specific, in that the replicated probe signals were unchanged in case–control studies using sCJD frontal-cortex (n = 84), blood samples from patients with Alzheimer’s disease, and from inherited and acquired prion diseases. Machine learning algorithms using blood DNA methylation array profiles accurately distinguished sCJD patients and controls. Finally, we identified sites whose methylation levels associated with prolonged survival in sCJD patients. Altogether, this study has identified a peripheral DNA methylation signature of sCJD with a variety of potential biomarker applications.
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Affiliation(s)
- Luke C Dabin
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, Courtauld Building, 33 Cleveland Street, London, W1W 7FF, UK
| | - Fernando Guntoro
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, Courtauld Building, 33 Cleveland Street, London, W1W 7FF, UK
| | - Tracy Campbell
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, Courtauld Building, 33 Cleveland Street, London, W1W 7FF, UK
| | - Tony Bélicard
- MRC London Institute of Medical Sciences Du Cane Road London W12 0NN and Institute of Clinical Sciences, Imperial College London Du Cane Road London W12 0NN, Imperial College London, London, W12 0NN, UK
| | - Adam R Smith
- College of Medicine and Health, University of Exeter Medical School, Exeter University, RILD Building Level 4, Royal Devon and Exeter Hospital, Barrack Rd, Exeter, EX2 5DW, UK
| | - Rebecca G Smith
- College of Medicine and Health, University of Exeter Medical School, Exeter University, RILD Building Level 4, Royal Devon and Exeter Hospital, Barrack Rd, Exeter, EX2 5DW, UK
| | - Rachel Raybould
- Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, UHW Main Building, Heath Park, Cardiff, CF14 4XN, UK
| | - Jonathan M Schott
- Dementia Research Centre, UCL Institute of Neurology, 8-11 Queen Square, London, WC1N 3AR, UK
| | - Katie Lunnon
- College of Medicine and Health, University of Exeter Medical School, Exeter University, RILD Building Level 4, Royal Devon and Exeter Hospital, Barrack Rd, Exeter, EX2 5DW, UK
| | - Peter Sarkies
- MRC London Institute of Medical Sciences Du Cane Road London W12 0NN and Institute of Clinical Sciences, Imperial College London Du Cane Road London W12 0NN, Imperial College London, London, W12 0NN, UK
| | - John Collinge
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, Courtauld Building, 33 Cleveland Street, London, W1W 7FF, UK
| | - Simon Mead
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, Courtauld Building, 33 Cleveland Street, London, W1W 7FF, UK.
| | - Emmanuelle Viré
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, Courtauld Building, 33 Cleveland Street, London, W1W 7FF, UK
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Fransquet PD, Ritchie K, Januar V, Saffery R, Ancelin ML, Ryan J. Is Peripheral BDNF Promoter Methylation a Preclinical Biomarker of Dementia? J Alzheimers Dis 2020; 73:645-655. [PMID: 31839607 DOI: 10.3233/jad-190738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Brain-derived neurotrophic factor (BDNF) has been implicated in dementia. Preliminary evidence suggests that BDNF DNA methylation may be a diagnostic biomarker of dementia, but the potential pre-clinical utility remains unclear. Participants in the ESPRIT study were assessed for cognitive function and dementia (DSM-IV criteria) over 14 years. BDNF exon 1 promoter methylation was measured in blood at baseline (n = 769) and buccal samples during follow-up (n = 1062). Genotyping was carried out for several common BDNF SNPs, including Val66Met (rs6265) and APOE ɛ4. Multivariable logistic regression analyses determined the association between BDNF methylation and both prevalent and incident dementia. Adjustment for gender, age, education, APOEɛ4 genotype, body mass index, depression, and type 2 diabetes, as well as possible effect modification by gender and genetic variation were also investigated. Weak evidence of an association between lower blood methylation and dementia was observed at one of 11 sites investigated (Δ-0.5%, 95% CI:-0.9,-0.04, p = 0.03, p = 0.22 adjusted for multiple comparisons). Buccal methylation at two other sites was associated with 14-year incident dementia cases prior to adjustment for multiple comparisons only, and the effect sizes were small (Δ+0.3%, OR:1.57, SE:0.30, p = 0.02, p = 0.14 adjusted and Δ-1.5%, OR:0.85, SE:0.06, p = 0.03, p = 0.14 adjusted). Genetic variation in the BDNF gene did not modify these associations, and no gender-specific effects were observed. There was only a weak correlation between blood and buccal BDNF log-methylation at two sites (both r=-0.11). There was no strong evidence that blood or buccal BDNF exon 1 promoter DNA methylation is associated with prevalent or incident dementia, and reported associations would not remain after adjustment for multiple testing.
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Affiliation(s)
- Peter D Fransquet
- Biological Neuropsychiatry and Dementia Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia.,Epigenetics Group, Murdoch Childrens Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia
| | - Karen Ritchie
- Inserm U1061, Hospital La Colombiere & University Montpellier, Montpellier, France.,Center for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Vania Januar
- Epigenetics Group, Murdoch Childrens Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia
| | - Richard Saffery
- Epigenetics Group, Murdoch Childrens Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia
| | - Marie-Laure Ancelin
- Inserm U1061, Hospital La Colombiere & University Montpellier, Montpellier, France
| | - Joanne Ryan
- Biological Neuropsychiatry and Dementia Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia.,Epigenetics Group, Murdoch Childrens Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia.,Inserm U1061, Hospital La Colombiere & University Montpellier, Montpellier, France
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Atlante A, Amadoro G, Bobba A, Latina V. Functional Foods: An Approach to Modulate Molecular Mechanisms of Alzheimer's Disease. Cells 2020; 9:E2347. [PMID: 33114170 PMCID: PMC7690784 DOI: 10.3390/cells9112347] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/15/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
A new epoch is emerging with intense research on nutraceuticals, i.e., "food or food product that provides medical or health benefits including the prevention and treatment of diseases", such as Alzheimer's disease. Nutraceuticals act at different biochemical and metabolic levels and much evidence shows their neuroprotective effects; in particular, they are able to provide protection against mitochondrial damage, oxidative stress, toxicity of β-amyloid and Tau and cell death. They have been shown to influence the composition of the intestinal microbiota significantly contributing to the discovery that differential microorganisms composition is associated with the formation and aggregation of cerebral toxic proteins. Further, the routes of interaction between epigenetic mechanisms and the microbiota-gut-brain axis have been elucidated, thus establishing a modulatory role of diet-induced epigenetic changes of gut microbiota in shaping the brain. This review examines recent scientific literature addressing the beneficial effects of some natural products for which mechanistic evidence to prevent or slowdown AD are available. Even if the road is still long, the results are already exceptional.
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Affiliation(s)
- Anna Atlante
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM)-CNR, Via G. Amendola 122/O, 70126 Bari, Italy;
| | - Giuseppina Amadoro
- Institute of Translational Pharmacology (IFT)-CNR, Via Fosso del Cavaliere 100, 00133 Rome, Italy;
- European Brain Research Institute (EBRI), Viale Regina Elena 295, 00161 Rome, Italy;
| | - Antonella Bobba
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM)-CNR, Via G. Amendola 122/O, 70126 Bari, Italy;
| | - Valentina Latina
- European Brain Research Institute (EBRI), Viale Regina Elena 295, 00161 Rome, Italy;
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Walker RM, Bermingham ML, Vaher K, Morris SW, Clarke T, Bretherick AD, Zeng Y, Amador C, Rawlik K, Pandya K, Hayward C, Campbell A, Porteous DJ, McIntosh AM, Marioni RE, Evans KL. Epigenome-wide analyses identify DNA methylation signatures of dementia risk. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2020; 12:e12078. [PMID: 32789163 PMCID: PMC7416667 DOI: 10.1002/dad2.12078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 01/04/2023]
Abstract
INTRODUCTION Dementia pathogenesis begins years before clinical symptom onset, necessitating the understanding of premorbid risk mechanisms. Here we investigated potential pathogenic mechanisms by assessing DNA methylation associations with dementia risk factors in Alzheimer's disease (AD)-free participants. METHODS Associations between dementia risk measures (family history, AD genetic risk score [GRS], and dementia risk scores [combining lifestyle, demographic, and genetic factors]) and whole-blood DNA methylation were assessed in discovery and replication samples (n = ~400 to ~5000) from Generation Scotland. RESULTS AD genetic risk and two dementia risk scores were associated with differential methylation. The GRS associated predominantly with methylation differences in cis but also identified a genomic region implicated in Parkinson disease. Loci associated with dementia risk scores were enriched for those previously associated with body mass index and alcohol consumption. DISCUSSION Dementia risk measures show widespread association with blood-based methylation, generating several hypotheses for assessment by future studies.
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Affiliation(s)
- Rosie M. Walker
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Mairead L. Bermingham
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Kadi Vaher
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Stewart W. Morris
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Toni‐Kim Clarke
- Division of PsychiatryUniversity of EdinburghRoyal Edinburgh HospitalEdinburghUK
| | - Andrew D. Bretherick
- MRC Human Genetics UnitInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Yanni Zeng
- Faculty of Forensic MedicineZhongshan School of MedicineSun Yat‐Sen University74 Zhongshan 2nd RoadGuangzhou510080China
| | - Carmen Amador
- MRC Human Genetics UnitInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Konrad Rawlik
- Division of Genetics and GenomicsThe Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of Edinburgh, Easter Bush, RoslinEdinburghUK
| | - Kalyani Pandya
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Caroline Hayward
- MRC Human Genetics UnitInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Archie Campbell
- Generation ScotlandCentre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - David J. Porteous
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
- Generation ScotlandCentre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Andrew M. McIntosh
- MRC Centre for Reproductive HealthThe Queen's Medical Research InstituteEdinburgh Bioquarter47 Little France CrescentEdinburghEH16 4TJUK
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Kathryn L. Evans
- Centre for Genomic and Experimental MedicineInstitute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
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Exploring Beyond the DNA Sequence: A Review of Epigenomic Studies of DNA and Histone Modifications in Dementia. CURRENT GENETIC MEDICINE REPORTS 2020. [DOI: 10.1007/s40142-020-00190-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Abstract
Purpose of Review
Although genome-scale studies have identified many genetic variants associated with dementia, these do not account for all of disease incidence and so recently attention has turned to studying mechanisms of genome regulation. Epigenetic processes such as modifications to the DNA and histones alter transcriptional activity and have been hypothesized to be involved in the etiology of dementia. Here, we review the growing body of literature on dementia epigenomics, with a focus on novel discoveries, current limitations, and future directions for the field.
Recent Findings
It is through advances in genomic technology that large-scale quantification of epigenetic modifications is now possible in dementia. Most of the literature in the field has primarily focussed on exploring DNA modifications, namely DNA methylation, in postmortem brain samples from individuals with Alzheimer’s disease. However, recent studies have now begun to explore other epigenetic marks, such as histone modifications, investigating these signatures in both the brain and blood, and in a range of other dementias.
Summary
There is still a demand for more epigenomic studies to be conducted in the dementia field, particularly those assessing chromatin dynamics and a broader range of histone modifications. The field faces limitations in sample accessibility with many studies lacking power. Furthermore, the frequent use of heterogeneous bulk tissue containing multiple cell types further hinders data interpretation. Looking to the future, multi-omic studies, integrating many different epigenetic marks, with matched genetic, transcriptomic, and proteomic data, will be vital, particularly when undertaken in isolated cell populations, or ideally at the level of the single cell. Ultimately these studies could identify novel dysfunctional pathways and biomarkers for disease, which could lead to new therapeutic avenues.
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Differential Methylation Levels in CpGs of the BIN1 Gene in Individuals With Alzheimer Disease. Alzheimer Dis Assoc Disord 2020; 33:321-326. [PMID: 31335457 DOI: 10.1097/wad.0000000000000329] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Late-onset Alzheimer disease (LOAD) is the most common dementia worldwide. APOE-[Latin Small Letter Open E]4 and BIN1 (Bridging Integrator 1) have been implicated in the pathogenesis of this disease, but, although DNA methylation of dinucleotide CpGs in the BIN1 gene influences alterations, it has not been studied in Hispanics. OBJECTIVE The objective of this study was to evaluate the BIN1 3' intergenic region DNA methylation patterns in a Colombian sample of LOAD patients. METHODS A case-control study was conducted in 50 individuals with LOAD and 50 age-sex matched controls to determine associations of LOAD with DNA methylation. DNA was isolated from peripheral blood, and methylation levels of 8 CpGs were estimated by bisulfite conversion followed by Sanger sequencing with direct PCR analysis. Logistic regression models adjusted by age, sex, and APOE were used to calculate risk associations between methylation levels and LOAD. RESULTS Overall, participants with LOAD had significantly lower methylation levels on CpG26 (0.86±0.11 vs. 0.95±0.05; P>0.001), CpG44 (0.84±0.09 vs. 0.94±0.06; P=0.001), and CpG87 (0.64±0.12 vs. 0.82±0.10; P>0.001). Adjusted regression models showed that decreased methylation levels of these CpGs remained as risk factors for LOAD (P<0.05). CONCLUSIONS Hypomethylation of CpGs in BIN1 might play an important role in the expression of BIN1 and may be a biomarker for identifying individuals at high risk of developing LOAD.
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Sato K, Mano T, Suzuki K, Toda T, Iwatsubo T, Iwata A. Attempt to Predict A/T/N-Based Alzheimer's Disease Cerebrospinal Fluid Biomarkers Using a Peripheral Blood DNA Methylation Clock. J Alzheimers Dis Rep 2020; 4:287-296. [PMID: 32904719 PMCID: PMC7458568 DOI: 10.3233/adr-200205] [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] [Indexed: 11/25/2022] Open
Abstract
Background: Although aging is the strongest risk factor for the development of Alzheimer’s disease (AD), it remains uncertain if the blood DNA methylation clock, which reflects the effect of biological aging on DNA methylation (DNAme) status of blood cells, may be used as a surrogate biomarker for AD pathology in the central nervous system (CNS). Objective: We aimed to develop a practical model to predict for A/T/N-based AD biomarkers as the prediction targets using the aging acceleration of blood cells. Methods: We obtained data of North American ADNI study participants (n = 317) whose blood DNA methylation microarray (Illumina HumanMethylation EPIC Beadchips) and cerebrospinal fluid (CSF) AD biomarkers (Aβ, t-tau, and p-tau) were recorded simultaneously. Methylation clock was calculated to conduct machine learning, in order to predict binary statuses (+ or –) for A (corresponding to the lowered CSF Aβ), T (the elevated CSF p-tau), or N (the elevated CSF t-tau). The predictive performance of the models was evaluated by area under curve (AUC) in the test subset within ADNI. Results: Among the 317 included samples, 194 (61.2%) were A+, 247 (77.9%) were T+, and 104 (32.8%) were N+. The degree of blood aging acceleration showed weak positive correlation with the CSF Aβ levels, even after adjustment with APOE genotype and other covariates. However, the contribution of aging acceleration to improve the predictive performance of models was not significant for any of A+, T+, or N+. Conclusion: Our exploratory attempts could not demonstrate the substantial utility of the peripheral blood cells’ methylation clock as a predictor for A/T/N-based CSF biomarkers of AD, and further additional work should be conducted to determine whether the blood DNAme signatures including methylation clock have substantial utility in detecting underlying amyloid, tau or neurodegeneration pathology of AD.
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Affiliation(s)
- Kenichiro Sato
- Department of Neurology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Tatsuo Mano
- Department of Neurology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Kazushi Suzuki
- Unit for Early and Exploratory Clinical Development, The University of Tokyo Hospital, Tokyo, Japan
| | - Tatsushi Toda
- Department of Neurology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Takeshi Iwatsubo
- Department of Neuropathology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Atsushi Iwata
- Department of Neurology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan.,Department of Neurology, Tokyo Metropolitan Geriatric Medical Center Hospital, Tokyo, Japan
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Kobayashi N, Shinagawa S, Niimura H, Kida H, Nagata T, Tagai K, Shimada K, Oka N, Shikimoto R, Noda Y, Nakajima S, Mimura M, Shigeta M, Kondo K. Increased blood COASY DNA methylation levels a potential biomarker for early pathology of Alzheimer's disease. Sci Rep 2020; 10:12217. [PMID: 32699290 PMCID: PMC7376092 DOI: 10.1038/s41598-020-69248-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/07/2020] [Indexed: 01/12/2023] Open
Abstract
Early diagnosis of dementia including Alzheimer's disease (AD) is an urgent medical and welfare issue. However, to date, no simple biometrics have been available. We reported that blood DNA methylation levels of the COASY gene, which encodes coenzyme A synthase, were increased in individuals with AD and amnestic mild cognitive impairment (aMCI). The present study sought to replicate these findings with larger numbers of samples. Another objective was to clarify whether COASY methylation is associated with neurodegeneration through a comparison of AD, AD with cardiovascular disease (CVD), and vascular dementia (VaD). We measured blood COASY methylation levels in normal controls (NCs) (n = 200), and individuals with aMCI (n = 22), AD (n = 151), and VaD (n = 21). Compared with NCs, they were significantly higher in individuals with aMCI and AD. Further, they were significantly higher in AD patients without cardiovascular diseases compared to AD patients with them. These findings suggest that COASY methylation levels may be related to neurodegeneration in AD.
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Affiliation(s)
- Nobuyuki Kobayashi
- Department of Virology, The Jikei University School of Medicine, Tokyo, Japan. .,Department of Psychiatry, The Jikei University School of Medicine, Tokyo, Japan.
| | | | - Hidehito Niimura
- Department of Neuropsychiatry, Keio University School of Medicine, Tokyo, Japan
| | - Hisashi Kida
- Department of Neuropsychiatry, Keio University School of Medicine, Tokyo, Japan
| | - Tomoyuki Nagata
- Department of Psychiatry, The Jikei University School of Medicine, Tokyo, Japan
| | - Kenji Tagai
- Department of Psychiatry, The Jikei University School of Medicine, Tokyo, Japan
| | - Kazuya Shimada
- Department of Virology, The Jikei University School of Medicine, Tokyo, Japan
| | - Naomi Oka
- Department of Virology, The Jikei University School of Medicine, Tokyo, Japan
| | - Ryo Shikimoto
- Department of Neuropsychiatry, Keio University School of Medicine, Tokyo, Japan
| | - Yoshihiro Noda
- Department of Neuropsychiatry, Keio University School of Medicine, Tokyo, Japan
| | - Shinichiro Nakajima
- Department of Neuropsychiatry, Keio University School of Medicine, Tokyo, Japan
| | - Masaru Mimura
- Department of Neuropsychiatry, Keio University School of Medicine, Tokyo, Japan
| | - Masahiro Shigeta
- Department of Psychiatry, The Jikei University School of Medicine, Tokyo, Japan
| | - Kazuhiro Kondo
- Department of Virology, The Jikei University School of Medicine, Tokyo, Japan
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Fransquet PD, Lacaze P, Saffery R, Phung J, Parker E, Shah R, Murray A, Woods RL, Ryan J. Blood DNA methylation signatures to detect dementia prior to overt clinical symptoms. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2020; 12:e12056. [PMID: 32671182 PMCID: PMC7346866 DOI: 10.1002/dad2.12056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/27/2020] [Accepted: 05/27/2020] [Indexed: 12/13/2022]
Abstract
INTRODUCTION This study determined whether blood DNA methylation (DNAm) patterns differentiate individuals with presymptomatic dementia compared to controls. METHODS DNAm was measured in 73 individuals prior to dementia diagnosis and 87 cognitively healthy controls matched for age, sex, smoking, education, and baseline cognition. DNAm was also measured at 3 years follow-up in 25 dementia cases, and 24 controls. RESULTS Cases and controls differed in DNAm (unadjusted P < .01) at the time of diagnosis (n = 28,787 probes), and pre-diagnosis (n = 15,111 probes), with cg01404610 (General transcription factor IIA subunit 1 gene) significant after correction for multiple testing. Overall, 1150 probes overlapped between analyses (methylation differences from -10.6% to +11.0%), and effect sizes increased from pre-diagnosis to diagnosis. DISCUSSION Discernible blood DNAm signatures are in dementia cases before the appearance of overt clinical symptoms. Blood-based methylation may serve as a potential biomarker of dementia, but further investigation is needed to determine their true clinical utility.
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Affiliation(s)
- Peter Daniel Fransquet
- School of Public Health and Preventive MedicineMonash UniversityMelbourneVictoriaAustralia
| | - Paul Lacaze
- School of Public Health and Preventive MedicineMonash UniversityMelbourneVictoriaAustralia
| | - Richard Saffery
- Department of PaediatricsMurdoch Children's Research InstituteThe University of MelbourneParkvilleVictoriaAustralia
| | - James Phung
- School of Public Health and Preventive MedicineMonash UniversityMelbourneVictoriaAustralia
| | - Emily Parker
- School of Public Health and Preventive MedicineMonash UniversityMelbourneVictoriaAustralia
| | - Raj Shah
- Department of Family Medicine and Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
| | - Anne Murray
- Berman Center for Outcomes and Clinical ResearchHennepin Healthcare, Division of GeriatricsDepartment of MedicineHennepin Healthcare Research InstituteUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Robyn L. Woods
- School of Public Health and Preventive MedicineMonash UniversityMelbourneVictoriaAustralia
| | - Joanne Ryan
- School of Public Health and Preventive MedicineMonash UniversityMelbourneVictoriaAustralia
- PSNRECUniversité de MontpellierINSERMMontpellierFrance
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Vasanthakumar A, Davis JW, Idler K, Waring JF, Asque E, Riley-Gillis B, Grosskurth S, Srivastava G, Kim S, Nho K, Nudelman KNH, Faber K, Sun Y, Foroud TM, Estrada K, Apostolova LG, Li QS, Saykin AJ. Harnessing peripheral DNA methylation differences in the Alzheimer's Disease Neuroimaging Initiative (ADNI) to reveal novel biomarkers of disease. Clin Epigenetics 2020; 12:84. [PMID: 32539856 PMCID: PMC7294637 DOI: 10.1186/s13148-020-00864-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 05/14/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a chronic progressive neurodegenerative disease impacting an estimated 44 million adults worldwide. The causal pathology of AD (accumulation of amyloid-beta and tau), precedes hallmark symptoms of dementia by more than a decade, necessitating development of early diagnostic markers of disease onset, particularly for new drugs that aim to modify disease processes. To evaluate differentially methylated positions (DMPs) as novel blood-based biomarkers of AD, we used a subset of 653 individuals with peripheral blood (PB) samples in the Alzheimer's disease Neuroimaging Initiative (ADNI) consortium. The selected cohort of AD, mild cognitive impairment (MCI), and age-matched healthy controls (CN) all had imaging, genetics, transcriptomics, cerebrospinal protein markers, and comprehensive clinical records, providing a rich resource of concurrent multi-omics and phenotypic information on a well-phenotyped subset of ADNI participants. RESULTS In this manuscript, we report cross-diagnosis differential peripheral DNA methylation in a cohort of AD, MCI, and age-matched CN individuals with longitudinal DNA methylation measurements. Epigenome-wide association studies (EWAS) were performed using a mixed model with repeated measures over time with a P value cutoff of 1 × 10-5 to test contrasts of pairwise differential peripheral methylation in AD vs CN, AD vs MCI, and MCI vs CN. The most highly significant differentially methylated loci also tracked with Mini Mental State Examination (MMSE) scores. Differentially methylated loci were enriched near brain and neurodegeneration-related genes (e.g., BDNF, BIN1, APOC1) validated using the genotype tissue expression project portal (GTex). CONCLUSIONS Our work shows that peripheral differential methylation between age-matched subjects with AD relative to healthy controls will provide opportunities to further investigate and validate differential methylation as a surrogate of disease. Given the inaccessibility of brain tissue, the PB-associated methylation marks may help identify the stage of disease and progression phenotype, information that would be central to bringing forward successful drugs for AD.
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Affiliation(s)
| | - Justin W Davis
- Genomics Research Center, AbbVie, North Chicago, IL, USA
| | - Kenneth Idler
- Genomics Research Center, AbbVie, North Chicago, IL, USA
| | | | | | | | | | | | - Sungeun Kim
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
- Electrical and Computer Engineering, State University of New York, Oswego, NY, 13126, USA
| | - Kwangsik Nho
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kelly N H Nudelman
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
- National Centralized Repository for Alzheimer's Disease and Related Dementias, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kelley Faber
- National Centralized Repository for Alzheimer's Disease and Related Dementias, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yu Sun
- Neuroscience Therapeutic Area, Janssen Research & Development, Pennington, NJ, 08534, USA
- Research Information Technology, Janssen Research & Development, Pennington, NJ, 08534, USA
| | - Tatiana M Foroud
- National Centralized Repository for Alzheimer's Disease and Related Dementias, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Karol Estrada
- Biogen, Cambridge, MA, 02142, USA
- Currently at Biomarin Pharmaceuticals, Novato, CA, 94949, USA
| | - Liana G Apostolova
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Qingqin S Li
- Neuroscience Therapeutic Area, Janssen Research & Development, Pennington, NJ, 08534, USA
- Research Information Technology, Janssen Research & Development, Pennington, NJ, 08534, USA
| | - Andrew J Saykin
- Center for Neuroimaging, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
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DNA methylation patterns of LINE-1 and Alu for pre-symptomatic dementia in type 2 diabetes. PLoS One 2020; 15:e0234578. [PMID: 32525932 PMCID: PMC7289438 DOI: 10.1371/journal.pone.0234578] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/28/2020] [Indexed: 12/13/2022] Open
Abstract
The identification of early markers of dementia is important for higher-risk populations such as those with type 2 diabetes (T2D). Retrotransposons, including long interspersed nuclear element 1 (LINE-1) and Alu, comprise ~40% of the human genome. Although dysregulation of these retrotransposons can induce aberrant gene regulation and genomic instability, their role in the development of pre-symptomatic dementia (PSD) among T2D patients is unknown. Here, we examined locus-specific changes in LINE-1 and Alu methylation in PSD and the potential to offset these changes via supplementation with folate and vitamin B12. We interrogated DNA methylation patterns corresponding to 22,352 probes for LINE-1 and Alu elements using publicly-available Illumina Infinium 450K methylation datasets from i) an 18-month prospective study in 28 T2D patients (GSE62003) and ii) an intervention study in which 44 individuals were supplemented with folic acid (400 μg/day) and vitamin B12 (500 μg/day) over two years (GSE74548). We identified 714 differentially methylated positions (DMP) mapping to retrotransposons in T2D patients who developed PSD in comparison to those who did not (PFDR < 0.05), comprised of 2.4% (228 probes) of all LINE-1 probes and 3.8% (486 probes) of all Alu probes. These loci were enriched in genes with functions related to Alzheimer's disease and cognitive decline, including GNB5, GNG7 and PKN3 (p < 0.05). In older individuals supplemented with folate/vitamin B12, 85 (11.9%) PSD retrotransposon loci showed significant changes in methylation (p < 0.05): participants with the MTHFR CC genotype predominantly showed hypermethylation at these loci, while hypomethylation was observed more frequently in those with the TT genotype. In T2D patients, LINE-1 and Alu elements are differentially methylated in PSD in a locus-specific manner and may offer clinical utility in monitoring risk of dementia. Further work is required to examine the potential for dietary supplementation in lowering the risk of PSD.
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Sibbett RA, Altschul DM, Marioni RE, Deary IJ, Starr JM, Russ TC. DNA methylation-based measures of accelerated biological ageing and the risk of dementia in the oldest-old: a study of the Lothian Birth Cohort 1921. BMC Psychiatry 2020; 20:91. [PMID: 32111184 PMCID: PMC7048023 DOI: 10.1186/s12888-020-2469-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/30/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Previous studies have demonstrated an association between DNA methylation-based measures of accelerated ageing and age-related health outcomes and mortality. As a disease closely associated with advancing age, we hypothesized that DNA methylation-based measures of accelerated ageing might be associated with risk for dementia. This study therefore aimed to examine the association between four recognised measures of age acceleration and subsequent dementia. METHODS Study subjects (n = 488) were members of the Lothian Birth Cohort 1921. Dementia case ascertainment used data from death certificates, electronic hospital records, and clinical reviews. Venous blood samples were taken at baseline, at age 79 years. DNA methylation and measures of epigenetic age were calculated in accordance with Horvath's epigenetic clock tutorial, using the online calculator (https://dnamage.genetics.ucla.edu/). From these values, four measures of accelerated ageing were calculated: extrinsic epigenetic age acceleration (EEAA), intrinsic epigenetic age acceleration (IEAA), AgeAccelPheno and AgeAccelGrim. Competing risk regression models - with death as a competing risk - were performed to examine the association between each measure of accelerated ageing and incident dementia. APOE ɛ4 status, sex, age, smoking status, history of cardiovascular disease, cerebrovascular disease, hypertension, and diabetes were included as covariates. RESULTS None of the multivariate models revealed a positive association between increased epigenetic age acceleration and dementia risk. Across all included models, never-smoking increased risk for dementia (HR 1.69 [1.06, 2.71], p = 0.03), and having no APOE ɛ4 alleles reduced risk for dementia (HR 0.44 [0.29, 0.67], p < 0.001). CONCLUSIONS The present study did not demonstrate any consistent association between DNA methylation-based measures of accelerated ageing and dementia in subjects aged over 79 years. Further, larger studies - including separate analyses of dementia subtypes - are required to further investigate the potential association between DNA methylation-based measures of accelerated ageing and dementia.
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Affiliation(s)
- Ruth A Sibbett
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK.
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.
| | - Drew M Altschul
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Riccardo E Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - John M Starr
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Tom C Russ
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Edinburgh Dementia Prevention Research Group, University of Edinburgh, Edinburgh, UK
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Yan Y, Zhao A, Qui Y, Li Y, Yan R, Wang Y, Xu W, Deng Y. Genetic Association of FERMT2, HLA-DRB1, CD2AP, and PTK2B Polymorphisms With Alzheimer's Disease Risk in the Southern Chinese Population. Front Aging Neurosci 2020; 12:16. [PMID: 32116649 PMCID: PMC7010721 DOI: 10.3389/fnagi.2020.00016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 01/17/2020] [Indexed: 12/13/2022] Open
Abstract
Objectives This study aimed to explore the relationship between 18 single nucleotide polymorphisms (SNPs) and Alzheimer’s disease (AD) within the southern Chinese population. Methods A total of 420 participants, consisting of 215 AD patients and 205 sex- and age-matched controls, were recruited. The SNaPshot technique and polymer chain reaction (PCR) were used to detect the 18 SNPs. Combined with the apolipoprotein E (APOE) ε4 allele and age at onset, we performed an association analysis between these SNPs and AD susceptibility. Furthermore, we analyzed SNP-associated gene expression using the expression quantitative trait loci analysis. Results Our study found that rs17125924 of FERMT2 was associated with the risk of developing AD in the dominant (P = 0.022, odds ratio [OR] = 1.57, 95% confidence interval [CI]: 1.07–2.32) and overdominant (P = 0.005, OR = 1.76, 95% CI: 1.18–2.61) models. Moreover, compared with APOE ε4 non-carriers, the frequency of the G-allele at rs17125924 was significantly higher among AD patients in APOE ε4 allele carriers (P = 0.029). The rs9271058 of HLA-DRB1 (dominant, overdominant, and additive models), rs9473117 of CD2AP (dominant and additive models), and rs73223431 of PTK2B (dominant, overdominant, and additive models) were associated with early onset AD (EOAD). Using the genotype-tissue expression (GTEx) and Braineac database, we found a significant association between rs9271058 genotypes and HLA-DRB1 expression levels, while the CC genotype at rs9473117 and the TT genotype of rs73223431 increased CD2AP and PTK2B gene expression, respectively. Conclusion Our study identifies the G-allele at rs17125924 as a risk factor for developing AD, especially in APOE ε4 carriers. In addition, we found that rs9271058 of HLA-DRB1, rs9473117 of CD2AP, and rs73223431 of PTK2B were associated with EOAD. Further studies with larger sample sizes are needed to confirm our results.
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Affiliation(s)
- Yi Yan
- Department of Neurology, Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Aonan Zhao
- Department of Neurology, Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yinghui Qui
- Department of Neurology, Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuanyuan Li
- Department of Neurology, Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ran Yan
- Department of Neurology, Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Wang
- Department of Neurology, Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Xu
- Department of Neurology, Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yulei Deng
- Department of Neurology, Institute of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Neurology, Ruijin Hospital, Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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48
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Zeng M, Zhen J, Zheng X, Qiu H, Xu X, Wu J, Lin Z, Hu J. The Role of DNA Methylation in Ischemic Stroke: A Systematic Review. Front Neurol 2020; 11:566124. [PMID: 33193003 PMCID: PMC7652818 DOI: 10.3389/fneur.2020.566124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/28/2020] [Indexed: 02/05/2023] Open
Abstract
Background: Knowledge about the classic risk and protective factors of ischemic stroke is accumulating, but the underlying pathogenesis has not yet been fully understood. As emerging evidence indicates that DNA methylation plays a role in the pathological process of cerebral ischemia, this study aims to summarize the evidence of the association between DNA methylation and ischemic stroke. Methods: MEDLINE, EMBASE, PubMed, and Cochrane Central Register of Controlled Trials were searched for eligible studies. The results reported by each study were summarized narratively. Results: A total of 20 studies with 7,014 individuals finally met the inclusion criteria. Three studies focused on global methylation, 11 studies on candidate-gene methylation, and six on epigenome-wide methylation analysis. Long-interspersed nuclear element 1 was found to be hypomethylated in stroke cases in two studies. Another 16 studies reported 37 genes that were differentially methylated between stroke cases and controls. Individuals with ischemic stroke were also reported to have higher acceleration in Hanuum 's epigenetic age compared to controls. Conclusion: DNA methylation might be associated with ischemic stroke and play a role in several pathological pathways. It is potentially a promising biomarker for stroke prevention, diagnosis and treatment, but the current evidence is limited by sample size and cross-sectional or retrospective design. Therefore, studies on large asymptomatic populations with the prospective design are needed to validate the current evidence, explore new pathways and identify novel risk/protective loci.
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Affiliation(s)
- Minyan Zeng
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Juanying Zhen
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
- Department of Clinical Medicine, Shantou University Medical College, Shantou, China
| | - Xiaodan Zheng
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
- Department of Clinical Medicine, Shantou University Medical College, Shantou, China
| | - Hongyan Qiu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Xiaonan Xu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Jun Wu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Zhijian Lin
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
- *Correspondence: Zhijian Lin
| | - Jun Hu
- Department of Neurology, Peking University Shenzhen Hospital, Shenzhen, China
- Jun Hu
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Ludwig N, Fehlmann T, Kern F, Gogol M, Maetzler W, Deutscher S, Gurlit S, Schulte C, von Thaler AK, Deuschle C, Metzger F, Berg D, Suenkel U, Keller V, Backes C, Lenhof HP, Meese E, Keller A. Machine Learning to Detect Alzheimer's Disease from Circulating Non-coding RNAs. GENOMICS PROTEOMICS & BIOINFORMATICS 2019; 17:430-440. [PMID: 31809862 PMCID: PMC6943763 DOI: 10.1016/j.gpb.2019.09.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/26/2019] [Accepted: 10/07/2019] [Indexed: 12/11/2022]
Abstract
Blood-borne small non-coding (sncRNAs) are among the prominent candidates for blood-based diagnostic tests. Often, high-throughput approaches are applied to discover biomarker signatures. These have to be validated in larger cohorts and evaluated by adequate statistical learning approaches. Previously, we published high-throughput sequencing based microRNA (miRNA) signatures in Alzheimer’s disease (AD) patients in the United States (US) and Germany. Here, we determined abundance levels of 21 known circulating miRNAs in 465 individuals encompassing AD patients and controls by RT-qPCR. We computed models to assess the relation between miRNA expression and phenotypes, gender, age, or disease severity (Mini-Mental State Examination; MMSE). Of the 21 miRNAs, expression levels of 20 miRNAs were consistently de-regulated in the US and German cohorts. 18 miRNAs were significantly correlated with neurodegeneration (Benjamini-Hochberg adjusted P < 0.05) with highest significance for miR-532-5p (Benjamini-Hochberg adjusted P = 4.8 × 10−30). Machine learning models reached an area under the curve (AUC) value of 87.6% in differentiating AD patients from controls. Further, ten miRNAs were significantly correlated with MMSE, in particular miR-26a/26b-5p (adjusted P = 0.0002). Interestingly, the miRNAs with lower abundance in AD were enriched in monocytes and T-helper cells, while those up-regulated in AD were enriched in serum, exosomes, cytotoxic t-cells, and B-cells. Our study represents the next important step in translational research for a miRNA-based AD test.
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Affiliation(s)
- Nicole Ludwig
- Department of Human Genetics, Saarland University, 66421 Homburg/Saar, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Manfred Gogol
- Institut für Gerontologie, Universität Heidelberg, 69047 Heidelberg, Germany
| | - Walter Maetzler
- Department of Neurology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany; Center for Neurology and Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen, 72074 Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Stephanie Deutscher
- Department of Human Genetics, Saarland University, 66421 Homburg/Saar, Germany
| | - Simone Gurlit
- Department of Anesthesiology and Intensive Care, St. Franziskus Hospital Muenster, 48145 Muenster, Germany
| | - Claudia Schulte
- Center for Neurology and Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen, 72074 Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Anna-Katharina von Thaler
- Center for Neurology and Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen, 72074 Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Christian Deuschle
- Center for Neurology and Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen, 72074 Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Florian Metzger
- Department of Psychiatry and Psychotherapy, University Hospital Tuebingen, 72016 Tuebingen, Germany
| | - Daniela Berg
- Department of Neurology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany; Center for Neurology and Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen, 72074 Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Ulrike Suenkel
- Center for Neurology and Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen, 72074 Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Verena Keller
- Department of Medicine II, Saarland University Medical Center, 66421 Homburg/Saar, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg/Saar, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany.
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50
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Madrid A, Hogan KJ, Papale LA, Clark LR, Asthana S, Johnson SC, Alisch RS. DNA Hypomethylation in Blood Links B3GALT4 and ZADH2 to Alzheimer's Disease. J Alzheimers Dis 2019; 66:927-934. [PMID: 30372681 DOI: 10.3233/jad-180592] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Differentially methylated positions (DMPs) between persons with and without late-onset Alzheimer's disease (LOAD) were observed at 477 of 769,190 loci in a plurality of genes. Of these, 17 were shared with DMPs identified using clinical LOAD markers analyzed independently as continuous variables comprising Rey Auditory Verbal Learning Test scores, cerebrospinal fluid total tau (t-tau) and phosphorylated tau 181 (p-tau181) levels, and t-tau/Aβ1-42 (Aβ42), p-tau181/Aβ42, and Aβ42/Aβ1-40 (Aβ40) ratios. In patients with LOAD, 12 of the shared 17 DMPs were hypomethylated in B3GALT4 (Beta-1,3-galatcosyltransferase 4) (EC 2.4.1.62), and 5 were hypomethylated in ZADH2 (Prostaglandin reductase 3) (EC 1.3.1.48).
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Affiliation(s)
- Andy Madrid
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Neuroscience Training Program, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Kirk J Hogan
- Department of Anesthesiology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Wisconsin Alzheimer's Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Ligia A Papale
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Lindsay R Clark
- Wisconsin Alzheimer's Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Sanjay Asthana
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Sterling C Johnson
- Wisconsin Alzheimer's Institute, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Reid S Alisch
- Department of Psychiatry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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