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Ramos-Campoy O, Comas-Albertí A, Hervás D, Borrego-Écija S, Bosch B, Sandoval J, Fort-Aznar L, Moreno-Izco F, Fernández-Villullas G, Molina-Porcel L, Balasa M, Lladó A, Sánchez-Valle R, Antonell A. Genome-Wide DNA Methylation in Early-Onset-Dementia Patients Brain Tissue and Lymphoblastoid Cell Lines. Int J Mol Sci 2024; 25:5445. [PMID: 38791483 PMCID: PMC11121630 DOI: 10.3390/ijms25105445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Epigenetics, a potential underlying pathogenic mechanism of neurodegenerative diseases, has been in the scope of several studies performed so far. However, there is a gap in regard to analyzing different forms of early-onset dementia and the use of Lymphoblastoid cell lines (LCLs). We performed a genome-wide DNA methylation analysis on sixty-four samples (from the prefrontal cortex and LCLs) including those taken from patients with early-onset forms of Alzheimer's disease (AD) and frontotemporal dementia (FTD) and healthy controls. A beta regression model and adjusted p-values were used to obtain differentially methylated positions (DMPs) via pairwise comparisons. A correlation analysis of DMP levels with Clariom D array gene expression data from the same cohort was also performed. The results showed hypermethylation as the most frequent finding in both tissues studied in the patient groups. Biological significance analysis revealed common pathways altered in AD and FTD patients, affecting neuron development, metabolism, signal transduction, and immune system pathways. These alterations were also found in LCL samples, suggesting the epigenetic changes might not be limited to the central nervous system. In the brain, CpG methylation presented an inverse correlation with gene expression, while in LCLs, we observed mainly a positive correlation. This study enhances our understanding of the biological pathways that are associated with neurodegeneration, describes differential methylation patterns, and suggests LCLs are a potential cell model for studying neurodegenerative diseases in earlier clinical phases than brain tissue.
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Affiliation(s)
- Oscar Ramos-Campoy
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Aina Comas-Albertí
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - David Hervás
- Department of Applied Statistics and Operations Research and Quality, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Sergi Borrego-Écija
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Beatriz Bosch
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Juan Sandoval
- Epigenomics Core Facility, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Laura Fort-Aznar
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Fermín Moreno-Izco
- Cognitive Disorders Unit, Department of Neurology, Hospital Universitario Donostia, 20014 San Sebastian, Spain
- Instituto de Investigación Sanitaria Biogipuzkoa, Neurosciences Area, Group of Neurodegenerative Diseases, 20014 San Sebastian, Spain
| | - Guadalupe Fernández-Villullas
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Laura Molina-Porcel
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
- Neurological Tissue Bank, Biobank-Hospital Clinic-IDIBAPS, 08036 Barcelona, Spain
| | - Mircea Balasa
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Albert Lladó
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Raquel Sánchez-Valle
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
- Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Anna Antonell
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, FRCB-IDIBAPS, Universitat de Barcelona (UB), 08036 Barcelona, Spain
- Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona (UB), 08036 Barcelona, Spain
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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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Younesian S, Yousefi AM, Momeny M, Ghaffari SH, Bashash D. The DNA Methylation in Neurological Diseases. Cells 2022; 11:3439. [PMID: 36359835 PMCID: PMC9657829 DOI: 10.3390/cells11213439] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 10/25/2022] [Indexed: 07/30/2023] Open
Abstract
DNA methylation is critical for the normal development and functioning of the human brain, such as the proliferation and differentiation of neural stem cells, synaptic plasticity, neuronal reparation, learning, and memory. Despite the physical stability of DNA and methylated DNA compared to other epigenetic modifications, some DNA methylation-based biomarkers have translated into clinical practice. Increasing reports indicate a strong association between DNA methylation profiles and various clinical outcomes in neurological diseases, making DNA methylation profiles valuable as novel clinical markers. In this review, we aim to discuss the latest evidence concerning DNA methylation alterations in the development of neurodegenerative, neurodevelopmental, and neuropsychiatric diseases. We also highlighted the relationship of DNA methylation alterations with the disease progression and outcome in many neurological diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, frontotemporal dementia, and autism.
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Affiliation(s)
- Samareh Younesian
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1971653313, Iran
| | - Amir-Mohammad Yousefi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1971653313, Iran
| | - Majid Momeny
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Seyed H. Ghaffari
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1971653313, Iran
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Ma SL, Tang NLS, Lam LCW. Promoter Methylation and Gene Expression of Pin1 Associated with the Risk of Alzheimer's Disease in Southern Chinese. Curr Alzheimer Res 2021; 17:1232-1237. [PMID: 33557736 DOI: 10.2174/1567205018666210208163946] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 11/18/2020] [Accepted: 12/21/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Pin1 is a propyl cis-trans isomerase and it has been associated with age-atonset of Alzheimer's disease (AD) and other pathological characteristics of AD. DNA methylation is one of the gene regulation mechanisms and it might affect the gene expression. OBJECTIVE This study was aimed to examine the correlation between DNA methylation and gene expression of Pin1 and its effect on the risk of AD in a Chinese population. METHODS 80 AD patients and 180 normal controls were recruited in this study and their cognitive functions were assessed. Pin1 gene expression and methylation were quantified by real-time RT-PCR and Melting Curve Analysis-Methylation assay (MCA-Meth), respectively. RESULTS Our finding revealed a positive correlation between methylation and gene expression of Pin1 (p=0.001) and increased Pin1 methylation was predisposed to the risk of AD (p<0.001). CG genotype of Pin1 SNP rs2287839 was associated with higher gene expression of Pin1 (p=0.036) and the effect was only prominent in normal controls as AD patients were already methylated at Pin1 promoter. Furthermore, methylation of Pin1 was associated with better performance in cognition (p=0.018). CONCLUSION Our result further supported the involvement of Pin1 in AD and the increased level of Pin1 might be a protective factor for AD.
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Affiliation(s)
- Suk L Ma
- Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, China
| | - Nelson L S Tang
- Department of Chemical Pathology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Linda C Wa Lam
- Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, China
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5
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He C, Huang ZS, Yu CC, Wang HH, Zhou H, Kong LH. Epigenetic Regulation of Amyloid-beta Metabolism in Alzheimer's Disease. Curr Med Sci 2021; 40:1022-1030. [PMID: 33428129 DOI: 10.1007/s11596-020-2283-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 10/05/2020] [Indexed: 11/28/2022]
Abstract
Senile plaques (SPs) are one of the pathological features of Alzheimer's disease (AD) and they are formed by the overproduction and aggregation of amyloid-beta (Aβ) peptides derived from the abnormal cleavage of amyloid precursor protein (APP). Thus, understanding the regulatory mechanisms during Aβ metabolism is of great importance to elucidate AD pathogenesis. Recent studies have shown that epigenetic modulation-including DNA methylation, non-coding RNA alterations, and histone modifications-is of great significance in regulating Aβ metabolism. In this article, we review the aberrant epigenetic regulation of Aβ metabolism.
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Affiliation(s)
- Chuan He
- Hubei University of Chinese Medicine, Wuhan, 430060, China
| | | | - Chao-Chao Yu
- Department of Tuina, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518000, China.,The 4th Clinical College of Guangzhou University of Chinese Medicine, Shenzhen, 518000, China
| | - Hai-Hua Wang
- Hospital of Traditional Chinese Medicine of Fengrun District, Tangshan, 064000, China
| | - Hua Zhou
- Hubei University of Chinese Medicine, Wuhan, 430060, China.
| | - Li-Hong Kong
- Hubei University of Chinese Medicine, Wuhan, 430060, China.
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6
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Fransquet PD, Lacaze P, Saffery R, Phung J, Parker E, Shah RC, Murray A, Woods RL, Ryan J. DNA methylation analysis of candidate genes associated with dementia in peripheral blood. Epigenomics 2020; 12:2109-2123. [PMID: 33300824 DOI: 10.2217/epi-2020-0236] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aim: To investigate whether genes implicated in dementia pathogenesis are differently methylated in peripheral blood. Materials & methods: Participants included 160 cognitively healthy individuals aged 70+ years: 73 who were subsequently diagnosed with dementia and 87 controls matched on age, gender, education, smoking and baseline cognition. A total of 49 participants also provided blood samples at diagnosis. Blood DNA methylation of APOE, APP, BDNF, PIN1, SNCA and TOMM40 was examined. Results: A total of 56 of 299 probes were differentially methylated in dementia compared with controls and 39 probes prior to diagnosis. The greatest effect size was in APP (cg19423170, Δ-8.32%, adjusted p = 0.009 at diagnosis; cg19933173, Δ-4.18%, adjusted p < 0.0001 prediagnosis). Conclusion: Genes implicated in dementia pathogenesis show differential blood methylation in dementia, even prior to diagnosis.
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Affiliation(s)
- Peter D Fransquet
- School of Public Health & Preventive Medicine, Monash University, Melbourne, 3004 Victoria, Australia
| | - Paul Lacaze
- School of Public Health & Preventive Medicine, Monash University, Melbourne, 3004 Victoria, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute & Department of Paediatrics, The University of Melbourne, Parkville, 3052 Victoria, Australia
| | - James Phung
- School of Public Health & Preventive Medicine, Monash University, Melbourne, 3004 Victoria, Australia
| | - Emily Parker
- School of Public Health & Preventive Medicine, Monash University, Melbourne, 3004 Victoria, Australia
| | - Raj C Shah
- Department of Family Medicine & Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Anne Murray
- Berman Center for Outcomes & Clinical Research, Hennepin Healthcare Research Institute, Hennepin Healthcare; Division of Geriatrics, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Robyn L Woods
- School of Public Health & Preventive Medicine, Monash University, Melbourne, 3004 Victoria, Australia
| | - Joanne Ryan
- School of Public Health & Preventive Medicine, Monash University, Melbourne, 3004 Victoria, Australia.,PSNREC, University of Montpellier, INSERM, Montpellier, France
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7
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Fagiani F, Govoni S, Racchi M, Lanni C. The Peptidyl-prolyl Isomerase Pin1 in Neuronal Signaling: from Neurodevelopment to Neurodegeneration. Mol Neurobiol 2020; 58:1062-1073. [PMID: 33083964 PMCID: PMC7878263 DOI: 10.1007/s12035-020-02179-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/14/2020] [Indexed: 12/11/2022]
Abstract
The peptidyl-prolyl isomerase Pin1 is a unique enzyme catalyzing the isomerization of the peptide bond between phosphorylated serine-proline or threonine-proline motifs in proteins, thereby regulating a wide spectrum of protein functions, including folding, intracellular signaling, transcription, cell cycle progression, and apoptosis. Pin1 has been reported to act as a key molecular switch inducing cell-type-specific effects, critically depending on the different phosphorylation patterns of its targets within different biological contexts. While its implication in proliferating cells, and, in particular, in the field of cancer, has been widely characterized, less is known about Pin1 biological functions in terminally differentiated and post-mitotic neurons. Notably, Pin1 is widely expressed in the central and peripheral nervous system, where it regulates a variety of neuronal processes, including neuronal development, apoptosis, and synaptic activity. However, despite studies reporting the interaction of Pin1 with neuronal substrates or its involvement in specific signaling pathways, a more comprehensive understanding of its biological functions at neuronal level is still lacking. Besides its implication in physiological processes, a growing body of evidence suggests the crucial involvement of Pin1 in aging and age-related and neurodegenerative diseases, including Alzheimer's disease, Parkinson disease, frontotemporal dementias, Huntington disease, and amyotrophic lateral sclerosis, where it mediates profoundly different effects, ranging from neuroprotective to neurotoxic. Therefore, a more detailed understanding of Pin1 neuronal functions may provide relevant information on the consequences of Pin1 deregulation in age-related and neurodegenerative disorders.
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Affiliation(s)
- Francesca Fagiani
- Department of Drug Sciences, Pharmacology Section, University of Pavia, Viale Taramelli 14, 27100, Pavia, Italy.,Scuola Universitaria Superiore IUSS Pavia, P.zza Vittoria, 15, 27100, Pavia, Italy
| | - Stefano Govoni
- Department of Drug Sciences, Pharmacology Section, University of Pavia, Viale Taramelli 14, 27100, Pavia, Italy
| | - Marco Racchi
- Department of Drug Sciences, Pharmacology Section, University of Pavia, Viale Taramelli 14, 27100, Pavia, Italy
| | - Cristina Lanni
- Department of Drug Sciences, Pharmacology Section, University of Pavia, Viale Taramelli 14, 27100, Pavia, Italy.
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8
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Liu Y, Wang M, Marcora EM, Zhang B, Goate AM. Promoter DNA hypermethylation - Implications for Alzheimer's disease. Neurosci Lett 2019; 711:134403. [PMID: 31351091 PMCID: PMC6759378 DOI: 10.1016/j.neulet.2019.134403] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 07/12/2019] [Accepted: 07/23/2019] [Indexed: 12/31/2022]
Abstract
Recent methylome-wide association studies (MWAS) in humans have solidified the concept that aberrant DNA methylation is associated with Alzheimer's disease (AD). We summarize these findings to improve the understanding of mechanisms governing DNA methylation pertinent to transcriptional regulation, with an emphasis of AD-associated promoter DNA hypermethylation, which establishes an epigenetic barrier for transcriptional activation. By considering brain cell type specific expression profiles that have been published only for non-demented individuals, we detail functional activities of selected neuron, microglia, and astrocyte-enriched genes (AGAP2, DUSP6 and GPR37L1, respectively), which are DNA hypermethylated at promoters in AD. We highlight future directions in MWAS including experimental confirmation, functional relevance to AD, cell type-specific temporal characterization, and mechanism investigation.
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Affiliation(s)
- Yiyuan Liu
- Department of Neuroscience and Department of Genetics and Genomic Sciences, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA.
| | - Edoardo M Marcora
- Department of Neuroscience and Department of Genetics and Genomic Sciences, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Alison M Goate
- Department of Neuroscience and Department of Genetics and Genomic Sciences, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
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9
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Abstract
Biomarker discovery and validation are necessary for improving the prediction of clinical outcomes and patient monitoring. Despite considerable interest in biomarker discovery and development, improvements in the range and quality of biomarkers are still needed. The main challenge is how to integrate preclinical data to obtain a reliable biomarker that can be measured with acceptable costs in routine clinical practice. Epigenetic alterations are already being incorporated as valuable candidates in the biomarker field. Furthermore, their reversible nature offers a promising opportunity to ameliorate disease symptoms by using epigenetic-based therapy. Thus, beyond helping to understand disease biology, clinical epigenetics is being incorporated into patient management in oncology, as well as being explored for clinical applicability for other human pathologies such as neurological and infectious diseases and immune system disorders.
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10
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Fenoglio C, Scarpini E, Galimberti D. Epigenetic regulatory modifications in genetic and sporadic frontotemporal dementia. Expert Rev Neurother 2018; 18:469-475. [PMID: 29799291 DOI: 10.1080/14737175.2018.1481389] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Epigenetic modifications have recently been linked to neurodegenerative diseases, such as frontotemporal dementia (FTD), which represents the second most common form of dementia in adulthood after Alzheimer's disease (AD). Epigenetic regulation occurs at different cellular levels and serve as a way to alter genetic information not only in aging but also following environmental signals. Thus, epigenetics mechanisms could exert their function at early stage of the disease, especially in sporadic cases. Areas covered: Herein, the available evidence supporting the concept that epigenetic-driven changes might shed the light into the pathogenic mechanisms of FTD will be summarized, with particular regard to their influence in underlying sporadic/familiar FTD onset and/or severity, and to the possibility to open a new scenario to facilitate early diagnosis and the identification of novel therapeutic targets. Bibliographic search through PubMed was used to find the studies included in this review. Expert commentary: Although epigenetic investigation in neurodegenerative disorders is in its infancy, recent advances in the technology of epigenetic change determination has led to novel, challenging findings. In particular, the knowledge and the characterization of epigenetic events could result in novel therapeutic strategies.
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Affiliation(s)
- Chiara Fenoglio
- a Neurodegenerative Disease Unit , University of Milan, Dino Ferrari Center, Fondazione Cà Granda, IRCCS Ospedale Maggiore Policlinico , Milan , Italy
| | - Elio Scarpini
- a Neurodegenerative Disease Unit , University of Milan, Dino Ferrari Center, Fondazione Cà Granda, IRCCS Ospedale Maggiore Policlinico , Milan , Italy
| | - Daniela Galimberti
- a Neurodegenerative Disease Unit , University of Milan, Dino Ferrari Center, Fondazione Cà Granda, IRCCS Ospedale Maggiore Policlinico , Milan , Italy
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11
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Hypermethylation of TRIM59 and KLF14 Influences Cell Death Signaling in Familial Alzheimer's Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:6918797. [PMID: 29849909 PMCID: PMC5904768 DOI: 10.1155/2018/6918797] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/14/2018] [Accepted: 02/04/2018] [Indexed: 12/11/2022]
Abstract
Epigenetic mechanisms play an important role in the development and progression of various neurodegenerative diseases. Abnormal methylation of numerous genes responsible for regulation of transcription, DNA replication, and apoptosis has been linked to Alzheimer's disease (AD) pathology. We have recently performed whole transcriptome profiling of familial early-onset Alzheimer's disease (fEOAD) patient-derived fibroblasts. On this basis, we demonstrated a strong dysregulation of cell cycle checkpoints and DNA damage response (DDR) in both fibroblasts and reprogrammed neurons. Here, we show that the aging-correlated hypermethylation of KLF14 and TRIM59 genes associates with abnormalities in DNA repair and cell cycle control in fEOAD. Based on the resulting transcriptome networks, we found that the hypermethylation of KLF14 might be associated with epigenetic regulation of the chromatin organization and mRNA processing followed by hypermethylation of TRIM59 likely associated with the G2/M cell cycle phase and p53 role in DNA repair with BRCA1 protein as the key player. We propose that the hypermethylation of KLF14 could constitute a superior epigenetic mechanism for TRIM59 hypermethylation. The methylation status of both genes affects genome stability and might contribute to proapoptotic signaling in AD. Since this study combines data obtained from various tissues from AD patients, it reinforces the view that the genetic methylation status in the blood may be a valuable predictor of molecular processes occurring in affected tissues. Further research is necessary to define a detailed role of TRIM59 and KLF4 in neurodegeneration of neurons.
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12
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Casati M, Ferri E, Gussago C, Mazzola P, Abbate C, Bellelli G, Mari D, Cesari M, Arosio B. Increased expression of TREM2 in peripheral cells from mild cognitive impairment patients who progress into Alzheimer's disease. Eur J Neurol 2018; 25:805-810. [PMID: 29377401 DOI: 10.1111/ene.13583] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/19/2018] [Indexed: 01/06/2023]
Abstract
BACKGROUND AND PURPOSE Neuroinflammation plays a role in the aetiopathogenesis of Alzheimer's disease (AD). Triggering receptor expressed on myeloid cells 2 (TREM2), a cell surface receptor of the immunoglobulin superfamily, seems to have protective anti-inflammatory activity in AD. METHODS Triggering receptor expressed on myeloid cells 2 expression was analysed in peripheral blood mononuclear cells from healthy subjects (CT) and from patients with either AD or mild cognitive impairment (MCI). MCI patients were re-evaluated at a 2-year follow-up to investigate their progression to AD (MCI-AD) or lack thereof (MCI-MCI). RESULTS Triggering receptor expressed on myeloid cells 2 gene expression was higher in AD than CT patients, but was highest in MCI. At recruitment TREM2 levels were higher in MCI-AD than in MCI-MCI, and in MCI-AD were higher initially than at follow-up. TREM2 displayed a moderate degree of sensitivity and specificity for identifying MCI-AD in all MCI patients. Our data showed higher TREM2 levels in allele ε4 of apolipoprotein E (ApoE ε4) carriers than non-carriers in MCI and particularly in MCI-AD. CONCLUSIONS These data seem to confirm the protective role of TREM2 in the pre-clinical stage of AD. Upregulation of TREM2 in MCI-AD could be a mechanism to counteract the activation of neuroinflammatory processes. It is possible that TREM2 and ApoE ε4 interact synergistically in the pre-clinical stage of AD. Therefore, TREM2 may be useful as an early peripheral biomarker for the development of AD.
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Affiliation(s)
- M Casati
- Geriatric Unit, Department of Medical Sciences and Community Health, University of Milan, Milan, Italy.,Nutritional Sciences, University of Milan, Milan, Italy
| | - E Ferri
- Geriatric Unit, Fondazione Ca' Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - C Gussago
- Geriatric Unit, Department of Medical Sciences and Community Health, University of Milan, Milan, Italy
| | - P Mazzola
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.,Acute Geriatrics Unit, San Gerardo Hospital ASST Monza, Monza, Italy.,NeuroMI Milan Center for Neuroscience, Clinical Neurosciences research area, Milano, Italy
| | - C Abbate
- Geriatric Unit, Fondazione Ca' Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - G Bellelli
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy.,Acute Geriatrics Unit, San Gerardo Hospital ASST Monza, Monza, Italy.,NeuroMI Milan Center for Neuroscience, Clinical Neurosciences research area, Milano, Italy
| | - D Mari
- Geriatric Unit, Department of Medical Sciences and Community Health, University of Milan, Milan, Italy.,Geriatric Unit, Fondazione Ca' Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - M Cesari
- Geriatric Unit, Department of Medical Sciences and Community Health, University of Milan, Milan, Italy.,Geriatric Unit, Fondazione Ca' Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - B Arosio
- Geriatric Unit, Department of Medical Sciences and Community Health, University of Milan, Milan, Italy.,Geriatric Unit, Fondazione Ca' Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
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13
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Matena A, Rehic E, Hönig D, Kamba B, Bayer P. Structure and function of the human parvulins Pin1 and Par14/17. Biol Chem 2018; 399:101-125. [PMID: 29040060 DOI: 10.1515/hsz-2017-0137] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 09/29/2017] [Indexed: 12/16/2022]
Abstract
Parvulins belong to the family of peptidyl-prolyl cis/trans isomerases (PPIases) assisting in protein folding and in regulating the function of a broad variety of proteins in all branches of life. The human representatives Pin1 and Par14/17 are directly involved in processes influencing cellular maintenance and cell fate decisions such as cell-cycle progression, metabolic pathways and ribosome biogenesis. This review on human parvulins summarizes the current knowledge of these enzymes and intends to oppose the well-studied Pin1 to its less well-examined homolog human Par14/17 with respect to structure, catalytic and cellular function.
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Affiliation(s)
- Anja Matena
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Edisa Rehic
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Dana Hönig
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Bianca Kamba
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
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14
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Fransquet PD, Lacaze P, Saffery R, McNeil J, Woods R, Ryan J. Blood DNA methylation as a potential biomarker of dementia: A systematic review. Alzheimers Dement 2017; 14:81-103. [PMID: 29127806 DOI: 10.1016/j.jalz.2017.10.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/27/2017] [Accepted: 10/07/2017] [Indexed: 01/22/2023]
Abstract
Dementia is a major public health issue with rising prevalence rates, but many individuals remain undiagnosed. Accurate and timely diagnosis is key for the optimal targeting of interventions. A noninvasive, easily measurable peripheral biomarker would have greatest utility in population-wide diagnostic screening. Epigenetics, including DNA methylation, is implicated in dementia; however, it is unclear whether epigenetic changes can be detected in peripheral tissue. This study aimed to systematically review the evidence for an association between dementia and peripheral DNA methylation. Forty-eight studies that measured DNA methylation in peripheral blood were identified, and 67% reported significant associations with dementia. However, most studies were underpowered and limited by their case-control design. We emphasize the need for future longitudinal studies on large well-characterized populations, measuring epigenetic patterns in asymptomatic individuals. A biomarker detectable in the preclinical stages of the disease would have the greatest utility in future intervention and treatment trials.
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Affiliation(s)
- Peter D Fransquet
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia; Disease Epigenetics, Murdoch Children's Research Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Paul Lacaze
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Richard Saffery
- Disease Epigenetics, Murdoch Children's Research Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - John McNeil
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Robyn Woods
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Joanne Ryan
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia; Disease Epigenetics, Murdoch Children's Research Institute, The University of Melbourne, Parkville, Victoria, Australia; INSERM, Neuropsychiatry: Epidemiological and Clinical Research, University of Montpellier, Montpellier, France.
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15
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Investigation of gene expression and serum levels of PIN1 and eNOS with high blood pressure in patients with Alzheimer disease. J Clin Neurosci 2017; 43:77-81. [DOI: 10.1016/j.jocn.2017.04.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 04/22/2017] [Indexed: 11/17/2022]
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16
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Epigenetics in Alzheimer's Disease: Perspective of DNA Methylation. Mol Neurobiol 2017; 55:1026-1044. [PMID: 28092081 DOI: 10.1007/s12035-016-0357-6] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 12/28/2016] [Indexed: 12/12/2022]
Abstract
Research over the years has shown that causes of Alzheimer's disease are not well understood, but over the past years, the involvement of epigenetic mechanisms in the developing memory formation either under pathological or physiological conditions has become clear. The term epigenetics represents the heredity of changes in phenotype that are independent of altered DNA sequences. Different studies validated that cytosine methylation of genomic DNA decreases with age in different tissues of mammals, and therefore, the role of epigenetic factors in developing neurological disorders in aging has been under focus. In this review, we summarized and reviewed the involvement of different epigenetic mechanisms especially the DNA methylation in Alzheimer's disease (AD), late-onset Alzheimer's disease (LOAD), familial Alzheimer's disease (FAD), and autosomal dominant Alzheimer's disease (ADAD). Down to the minutest of details, we tried to discuss the methylation patterns like mitochondrial DNA methylation and ribosomal DNA (rDNA) methylation. Additionally, we mentioned some therapeutic approaches related to epigenetics, which could provide a potential cure for AD. Moreover, we reviewed some recent studies that validate DNA methylation as a potential biomarker and its role in AD. We hope that this review will provide new insights into the understanding of AD pathogenesis from the epigenetic perspective especially from the perspective of DNA methylation.
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17
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Wen KX, Miliç J, El-Khodor B, Dhana K, Nano J, Pulido T, Kraja B, Zaciragic A, Bramer WM, Troup J, Chowdhury R, Ikram MA, Dehghan A, Muka T, Franco OH. The Role of DNA Methylation and Histone Modifications in Neurodegenerative Diseases: A Systematic Review. PLoS One 2016; 11:e0167201. [PMID: 27973581 PMCID: PMC5156363 DOI: 10.1371/journal.pone.0167201] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 11/10/2016] [Indexed: 12/11/2022] Open
Abstract
IMPORTANCE Epigenetic modifications of the genome, such as DNA methylation and histone modifications, have been reported to play a role in neurodegenerative diseases (ND) such as Alzheimer's disease (AD) and Parkinson's disease (PD). OBJECTIVE To systematically review studies investigating epigenetic marks in AD or PD. METHODS Eleven bibliographic databases (Embase.com, Medline (Ovid), Web-of-Science, Scopus, PubMed, Cinahl (EBSCOhost), Cochrane Central, ProQuest, Lilacs, Scielo and Google Scholar) were searched until July 11th 2016 to identify relevant articles. We included all randomized controlled trials, cohort, case-control and cross-sectional studies in humans that examined associations between epigenetic marks and ND. Two independent reviewers, with a third reviewer available for disagreements, performed the abstract and full text selection. Data was extracted using a pre-designed data collection form. RESULTS Of 6,927 searched references, 73 unique case-control studies met our inclusion criteria. Overall, 11,453 individuals were included in this systematic review (2,640 AD and 2,368 PD outcomes). There was no consistent association between global DNA methylation pattern and any ND. Studies reported epigenetic regulation of 31 genes (including cell communication, apoptosis, and neurogenesis genes in blood and brain tissue) in relation to AD and PD. Methylation at the BDNF, SORBS3 and APP genes in AD were the most consistently reported associations. Methylation of α-synuclein gene (SNCA) was also found to be associated with PD. Seven studies reported histone protein alterations in AD and PD. CONCLUSION Many studies have investigated epigenetics and ND. Further research should include larger cohort or longitudinal studies, in order to identify clinically significant epigenetic changes. Identifying relevant epigenetic changes could lead to interventional strategies in ND.
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Affiliation(s)
- Ke-xin Wen
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Jelena Miliç
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Bassem El-Khodor
- Research and Development, Metagenics, Inc, United States of America
| | - Klodian Dhana
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Jana Nano
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Tammy Pulido
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Bledar Kraja
- Department of Biomedical Sciences, Faculty of Medicine, University of Medicine, Tirana, Albania
- University Clinic of Gastrohepatology, University Hospital Center Mother Teresa, Tirana, Albania
| | - Asija Zaciragic
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | | | - John Troup
- Research and Development, Metagenics, Inc, United States of America
| | - Rajiv Chowdhury
- Department of Public Health & Primary Care, Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, CB1 8RN, United Kingdom
| | - M. Arfam Ikram
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Taulant Muka
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Oscar H. Franco
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
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