1
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Hossain MK, Kim HR, Chae HJ. Aging phenotype in AD brain organoids: Track to success and challenges. Ageing Res Rev 2024; 96:102256. [PMID: 38460555 DOI: 10.1016/j.arr.2024.102256] [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: 10/01/2023] [Revised: 02/19/2024] [Accepted: 02/27/2024] [Indexed: 03/11/2024]
Abstract
Alzheimer's disease (AD) poses a complex challenge, with abnormal protein accumulation in the brain causing memory loss and cognitive decline. Traditional models fall short in AD research, prompting interest in 3D brain organoids (BOs) from human stem cells. These findings hold promise for unveiling the mechanisms of AD, especially in relation to aging. However, an understanding of the aging impact of AD remains elusive. BOs offer insight but face challenges. This review delves into the role of BOs in deciphering aging-related AD and acknowledges limitations. Strategies to enhance BOs for accurate aging modeling in AD brains are suggested. Strengthened by molecular advancements, BOs have the potential to uncover the aging phenotype, advancing AD research.
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Affiliation(s)
| | - Hyung-Ryong Kim
- Department of Pharmacology, College of Dentistry, Jeonbuk National University, Jeonju 54896, Republic of Korea.
| | - Han Jung Chae
- School of Pharmacy, Jeonbuk National University, Jeonju 54896, Republic of Korea.
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2
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Daily KP, Badr A, Eltobgy M, Estfanous S, Whitham O, Tan MH, Carafice C, Krause K, McNamara A, Hamilton K, Houle S, Gupta S, Gupta GA, Madhu S, Fitzgerald J, Saadey AA, Laster B, Yan P, Webb A, Zhang X, Pietrzak M, Kokiko-Cochran ON, Ghoneim HE, Amer AO. DNA hypomethylation promotes the expression of CASPASE-4 which exacerbates inflammation and amyloid-β deposition in Alzheimer's disease. Alzheimers Res Ther 2024; 16:29. [PMID: 38326859 PMCID: PMC10851453 DOI: 10.1186/s13195-024-01390-2] [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: 07/06/2023] [Accepted: 01/09/2024] [Indexed: 02/09/2024]
Abstract
Alzheimer's disease (AD) is the sixth leading cause of death in the USA. It is established that neuroinflammation contributes to the synaptic loss, neuronal death, and symptomatic decline of AD patients. Accumulating evidence suggests a critical role for microglia, innate immune phagocytes of the brain. For instance, microglia release pro-inflammatory products such as IL-1β which is highly implicated in AD pathobiology. The mechanisms underlying the transition of microglia to proinflammatory promoters of AD remain largely unknown. To address this gap, we performed reduced representation bisulfite sequencing (RRBS) to profile global DNA methylation changes in human AD brains compared to no disease controls. We identified differential DNA methylation of CASPASE-4 (CASP4), which when expressed promotes the generation of IL-1β and is predominantly expressed in immune cells. DNA upstream of the CASP4 transcription start site was hypomethylated in human AD brains, which was correlated with increased expression of CASP4. Furthermore, microglia from a mouse model of AD (5xFAD) express increased levels of CASP4 compared to wild-type (WT) mice. To study the role of CASP4 in AD, we developed a novel mouse model of AD lacking the mouse ortholog of CASP4 and CASP11, which is encoded by mouse Caspase-4 (5xFAD/Casp4-/-). The expression of CASP11 was associated with increased accumulation of pathologic protein aggregate amyloid-β (Aβ) and increased microglial production of IL-1β in 5xFAD mice. Utilizing RNA-sequencing, we determined that CASP11 promotes unique transcriptomic phenotypes in 5xFAD mouse brains, including alterations of neuroinflammatory and chemokine signaling pathways. Notably, in vitro, CASP11 promoted generation of IL-1β from macrophages in response to cytosolic Aβ through cleavage of downstream effector Gasdermin D (GSDMD). Therefore, here we unravel the role for CASP11 and GSDMD in the generation of IL-1β in response to Aβ and the progression of pathologic inflammation in AD. Overall, our results demonstrate that overexpression of CASP4 due to differential DNA methylation in AD microglia contributes to the progression of AD pathobiology. Thus, we identify CASP4 as a potential target for immunotherapies for the treatment and prevention of AD.
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Affiliation(s)
- Kylene P Daily
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Asmaa Badr
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
- Clinical Pathology Department, College of Medicine, Mansoura University, Mansoura, Egypt
| | - Mostafa Eltobgy
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Shady Estfanous
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Owen Whitham
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Michelle H Tan
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Cierra Carafice
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Kathrin Krause
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Andrew McNamara
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Kaitlin Hamilton
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Samuel Houle
- Department of Neuroscience, The Ohio State University, Columbus, OH, 43210, USA
| | - Spandan Gupta
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Gauruv A Gupta
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Shruthi Madhu
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Julie Fitzgerald
- Department of Neuroscience, The Ohio State University, Columbus, OH, 43210, USA
| | - Abbey A Saadey
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Brooke Laster
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Pearlly Yan
- Genomics Shared Resource, Department of Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Amy Webb
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Xiaoli Zhang
- Center for Biostatistics, Ohio State University, Columbus, OH, USA
| | - Maciej Pietrzak
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | | | - Hazem E Ghoneim
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA.
- Pelotonia Institute for Immuno-Oncology, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
| | - Amal O Amer
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA.
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3
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Ma Y, Wang W, Liu S, Qiao X, Xing Y, Zhou Q, Zhang Z. Epigenetic Regulation of Neuroinflammation in Alzheimer's Disease. Cells 2023; 13:79. [PMID: 38201283 PMCID: PMC10778497 DOI: 10.3390/cells13010079] [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: 11/28/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Alzheimer's disease (AD) is a chronic and progressive neurodegenerative disease and clinically manifests with cognitive decline and behavioral disabilities. Over the past years, mounting studies have demonstrated that the inflammatory response plays a key role in the onset and development of AD, and neuroinflammation has been proposed as the third major pathological driving factor of AD, ranking after the two well-known core pathologies, amyloid β (Aβ) deposits and neurofibrillary tangles (NFTs). Epigenetic mechanisms, referring to heritable changes in gene expression independent of DNA sequence alterations, are crucial regulators of neuroinflammation which have emerged as potential therapeutic targets for AD. Upon regulation of transcriptional repression or activation, epigenetic modification profiles are closely involved in inflammatory gene expression and signaling pathways of neuronal differentiation and cognitive function in central nervous system disorders. In this review, we summarize the current knowledge about epigenetic control mechanisms with a focus on DNA and histone modifications involved in the regulation of inflammatory genes and signaling pathways in AD, and the inhibitors under clinical assessment are also discussed.
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Affiliation(s)
- Yajing Ma
- College of Biology and Food, Shangqiu Normal University, Shangqiu 476000, China;
| | - Wang Wang
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China; (W.W.); (Y.X.)
| | - Sufang Liu
- Department of Biomedical Sciences, College of Dentistry, Texas A&M University, Dallas, TX 75246, USA;
| | - Xiaomeng Qiao
- Department of Pathology and Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China;
| | - Ying Xing
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China; (W.W.); (Y.X.)
| | - Qingfeng Zhou
- College of Biology and Food, Shangqiu Normal University, Shangqiu 476000, China;
| | - Zhijian Zhang
- College of Biology and Food, Shangqiu Normal University, Shangqiu 476000, China;
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4
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Adiga D, Eswaran S, Sriharikrishnaa S, Khan NG, Prasada Kabekkodu S, Kumar D. Epigenetics of Alzheimer’s Disease: Past, Present and Future. ENZYMATIC TARGETS FOR DRUG DISCOVERY AGAINST ALZHEIMER'S DISEASE 2023:27-72. [DOI: 10.2174/9789815136142123010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Alzheimer’s disease (AD) exemplifies a looming epidemic lacking effective
treatment and manifests with the accumulation of neurofibrillary tangles, amyloid-β
plaques, neuroinflammation, behavioral changes, and acute cognitive impairments. It is
a complex, multifactorial disorder that arises from the intricate interaction between
environment and genetic factors, restrained via epigenetic machinery. Though the
research progress has improved the understanding of clinical manifestations and
disease advancement, the causal mechanism of detrimental consequences remains
undefined. Despite the substantial improvement in recent diagnostic modalities, it is
challenging to distinguish AD from other forms of dementia. Accurate diagnosis is a
major glitch in AD as it banks on the symptoms and clinical criteria. Several studies are
underway in exploring novel and reliable biomarkers for AD. In this direction,
epigenetic alterations have transpired as key modulators in AD pathogenesis with the
impeding inferences for the management of this neurological disorder. The present
chapter aims to discuss the significance of epigenetic modifications reported in the
pathophysiology of AD such as DNA methylation, hydroxy-methylation, methylation
of mtDNA, histone modifications, and noncoding RNAs. Additionally, the chapter also
describes the possible therapeutic avenues that target epigenetic modifications in AD.
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Affiliation(s)
- Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy
of Higher Education (MAHE), Manipal – 576104, Karnataka, India
| | - Sangavi Eswaran
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy
of Higher Education (MAHE), Manipal – 576104, Karnataka, India
| | - S. Sriharikrishnaa
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy
of Higher Education (MAHE), Manipal – 576104, Karnataka, India
| | - Nadeem G. Khan
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy
of Higher Education (MAHE), Manipal – 576104, Karnataka, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy
of Higher Education (MAHE), Manipal – 576104, Karnataka, India
| | - Dileep Kumar
- Department of Pharmaceutical Chemistry, Poona College of Pharmacy, Bharati Vidyapeeth
(Deemed to be University), Erandwane, Pune – 411038, Maharashtra, India
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5
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Gamache J, Gingerich D, Shwab EK, Barrera J, Garrett ME, Hume C, Crawford GE, Ashley-Koch AE, Chiba-Falek O. Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer's disease brains. Cell Biosci 2023; 13:185. [PMID: 37789374 PMCID: PMC10546724 DOI: 10.1186/s13578-023-01120-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/30/2023] [Indexed: 10/05/2023] Open
Abstract
BACKGROUND The genetic underpinnings of late-onset Alzheimer's disease (LOAD) are yet to be fully elucidated. Although numerous LOAD-associated loci have been discovered, the causal variants and their target genes remain largely unknown. Since the brain is composed of heterogenous cell subtypes, it is imperative to study the brain on a cell subtype specific level to explore the biological processes underlying LOAD. METHODS Here, we present the largest parallel single-nucleus (sn) multi-omics study to simultaneously profile gene expression (snRNA-seq) and chromatin accessibility (snATAC-seq) to date, using nuclei from 12 normal and 12 LOAD brains. We identified cell subtype clusters based on gene expression and chromatin accessibility profiles and characterized cell subtype-specific LOAD-associated differentially expressed genes (DEGs), differentially accessible peaks (DAPs) and cis co-accessibility networks (CCANs). RESULTS Integrative analysis defined disease-relevant CCANs in multiple cell subtypes and discovered LOAD-associated cell subtype-specific candidate cis regulatory elements (cCREs), their candidate target genes, and trans-interacting transcription factors (TFs), some of which, including ELK1, JUN, and SMAD4 in excitatory neurons, were also LOAD-DEGs. Finally, we focused on a subset of cell subtype-specific CCANs that overlap known LOAD-GWAS regions and catalogued putative functional SNPs changing the affinities of TF motifs within LOAD-cCREs linked to LOAD-DEGs, including APOE and MYO1E in a specific subtype of microglia and BIN1 in a subpopulation of oligodendrocytes. CONCLUSIONS To our knowledge, this study represents the most comprehensive systematic interrogation to date of regulatory networks and the impact of genetic variants on gene dysregulation in LOAD at a cell subtype resolution. Our findings reveal crosstalk between epigenetic, genomic, and transcriptomic determinants of LOAD pathogenesis and define catalogues of candidate genes, cCREs, and variants involved in LOAD genetic etiology and the cell subtypes in which they act to exert their pathogenic effects. Overall, these results suggest that cell subtype-specific cis-trans interactions between regulatory elements and TFs, and the genes dysregulated by these networks contribute to the development of LOAD.
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Affiliation(s)
- Julia Gamache
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Daniel Gingerich
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - E Keats Shwab
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Julio Barrera
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Melanie E Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, DUMC Box 104775, Durham, NC, 27701, USA
| | - Cordelia Hume
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA.
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, DUMC Box 3382, Durham, NC, 27708, USA.
- Center for Advanced Genomic Technologies, Duke University Medical Center, Durham, NC, 27708, USA.
| | - Allison E Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, DUMC Box 104775, Durham, NC, 27701, USA.
- Department of Medicine, Duke University Medical Center, Durham, NC, 27708, USA.
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University Medical Center, DUMC Box 2900, Durham, NC, 27710, USA.
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, 27708, USA.
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6
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Daily KP, Badr A, Eltobgy M, Estfanous S, Whitham O, Tan MH, Carafice C, Krause K, McNamara A, Hamilton K, Houle S, Gupta S, Gupta GA, Madhu S, Fitzgerald J, Saadey AA, Laster B, Yan P, Webb A, Zhang X, Pietrzak M, Kokiko-Cochran ON, Ghoneim HE, Amer AO. DNA hypomethylation promotes the expression of CASPASE-4 which exacerbates neuroinflammation and amyloid-β deposition in Alzheimer's disease The Ohio State University College of Medicine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.555526. [PMID: 37693600 PMCID: PMC10491177 DOI: 10.1101/2023.08.30.555526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Alzheimer's Disease (AD) is the 6th leading cause of death in the US. It is established that neuroinflammation contributes to the synaptic loss, neuronal death, and symptomatic decline of AD patients. Accumulating evidence suggests a critical role for microglia, innate immune phagocytes of the brain. For instance, microglia release proinflammatory products such as IL-1β which is highly implicated in AD pathobiology. The mechanisms underlying the transition of microglia to proinflammatory promoters of AD remain largely unknown. To address this gap, we performed Reduced Representation Bisulfite Sequencing (RRBS) to profile global DNA methylation changes in human AD brains compared to no disease controls. We identified differential DNA methylation of CASPASE-4 (CASP4), which when expressed, can be involved in generation of IL-1β and is predominantly expressed in immune cells. DNA upstream of the CASP4 transcription start site was hypomethylated in human AD brains, which was correlated with increased expression of CASP4. Furthermore, microglia from a mouse model of AD (5xFAD) express increased levels of CASP4 compared to wild-type (WT) mice. To study the role of CASP4 in AD, we developed a novel mouse model of AD lacking the mouse ortholog of CASP4, CASP11, which is encoded by mouse Caspase-4 (5xFAD/Casp4-/-). The expression of CASP11 was associated with increased accumulation of pathologic protein aggregate amyloid-β (Aβ) and increased microglial production of IL-1β in 5xFAD mice. Utilizing RNA sequencing, we determined that CASP11 promotes unique transcriptomic phenotypes in 5xFAD mouse brains, including alterations of neuroinflammatory and chemokine signaling pathways. Notably, in vitro, CASP11 promoted generation of IL-1β from macrophages in response to cytosolic Aβ through cleavage of downstream effector Gasdermin D (G SDMD). We describe a role for CASP11 and GSDMD in the generation of IL-1β in response to Aβ and the progression of pathologic inflammation in AD. Overall, our results demonstrate that overexpression of CASP4 due to differential methylation in AD microglia contributes to the progression of AD pathobiology, thus identifying CASP4 as a potential target for immunotherapies for the treatment of AD.
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Affiliation(s)
- Kylene P. Daily
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Asmaa Badr
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Mostafa Eltobgy
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Shady Estfanous
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Owen Whitham
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Michelle H. Tan
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Cierra Carafice
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Kathrin Krause
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Andrew McNamara
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Kaitlin Hamilton
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Samuel Houle
- Department of Neuroscience, The Ohio State University, Columbus, Ohio 43210
| | - Spandan Gupta
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Gauruv A. Gupta
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Shruthi Madhu
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Julie Fitzgerald
- Department of Neuroscience, The Ohio State University, Columbus, Ohio 43210
| | - Abbey A. Saadey
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Brooke Laster
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Pearlly Yan
- Genomics Shared Resource, Comprehensive Cancer Center, USA; Department of Internal Medicine, The Ohio State University, USA; The Ohio State University, Columbus, OH 43210, USA
| | - Amy Webb
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Xiaoli Zhang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Maciej Pietrzak
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | | | - Hazem E. Ghoneim
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
| | - Amal O. Amer
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA
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7
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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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Beadell AV, Zhang Z, Capuano AW, Bennett DA, He C, Zhang W, Arvanitakis Z. Genome-Wide Mapping Implicates 5-Hydroxymethylcytosines in Diabetes Mellitus and Alzheimer's Disease. J Alzheimers Dis 2023; 93:1135-1151. [PMID: 37182870 PMCID: PMC10490934 DOI: 10.3233/jad-221113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
BACKGROUND Diabetes mellitus (DM) is a recognized risk factor for dementia. Because DM is a potentially modifiable condition, greater understanding of the mechanisms linking DM to the clinical expression of Alzheimer's disease dementia may provide insights into much needed dementia therapeutics. OBJECTIVE In this feasibility study, we investigated DM as a dementia risk factor by examining genome-wide distributions of the epigenetic DNA modification 5-hydroxymethylcytosine (5hmC). METHODS We obtained biologic samples from the Rush Memory and Aging Project and used the highly sensitive 5hmC-Seal technique to perform genome-wide profiling of 5hmC in circulating cell-free DNA (cfDNA) from antemortem serum samples and in genomic DNA from postmortem prefrontal cortex brain tissue from 80 individuals across four groups: Alzheimer's disease neuropathologically defined (AD), DM clinically defined, AD with DM, and individuals with neither disease (controls). RESULTS Distinct 5hmC signatures and biological pathways were enriched in persons with both AD and DM versus AD alone, DM alone, or controls, including genes inhibited by EGFR signaling in oligodendroglia and those activated by constitutive RHOA. We also demonstrate the potential diagnostic value of 5hmC profiling in circulating cfDNA. Specifically, an 11-gene weighted model distinguished AD from non-AD/non-DM controls (AUC = 91.8%; 95% CI, 82.9-100.0%), while a 4-gene model distinguished DM-associated AD from AD alone (AUC = 87.9%; 95% CI, 77.5-98.3%). CONCLUSION We demonstrate in this small sample, the feasibility of detecting and characterizing 5hmC in DM-associated AD and of using 5hmC information contained in circulating cfDNA to detect AD in high-risk individuals, such as those with diabetes.
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Affiliation(s)
- Alana V Beadell
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Zhou Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ana W Capuano
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Zoe Arvanitakis
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
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Hajjo R, Sabbah DA, Abusara OH, Al Bawab AQ. A Review of the Recent Advances in Alzheimer's Disease Research and the Utilization of Network Biology Approaches for Prioritizing Diagnostics and Therapeutics. Diagnostics (Basel) 2022; 12:diagnostics12122975. [PMID: 36552984 PMCID: PMC9777434 DOI: 10.3390/diagnostics12122975] [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: 10/16/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
Alzheimer's disease (AD) is a polygenic multifactorial neurodegenerative disease that, after decades of research and development, is still without a cure. There are some symptomatic treatments to manage the psychological symptoms but none of these drugs can halt disease progression. Additionally, over the last few years, many anti-AD drugs failed in late stages of clinical trials and many hypotheses surfaced to explain these failures, including the lack of clear understanding of disease pathways and processes. Recently, different epigenetic factors have been implicated in AD pathogenesis; thus, they could serve as promising AD diagnostic biomarkers. Additionally, network biology approaches have been suggested as effective tools to study AD on the systems level and discover multi-target-directed ligands as novel treatments for AD. Herein, we provide a comprehensive review on Alzheimer's disease pathophysiology to provide a better understanding of disease pathogenesis hypotheses and decipher the role of genetic and epigenetic factors in disease development and progression. We also provide an overview of disease biomarkers and drug targets and suggest network biology approaches as new tools for identifying novel biomarkers and drugs. We also posit that the application of machine learning and artificial intelligence to mining Alzheimer's disease multi-omics data will facilitate drug and biomarker discovery efforts and lead to effective individualized anti-Alzheimer treatments.
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Affiliation(s)
- Rima Hajjo
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carlina at Chapel Hill, Chapel Hill, NC 27599, USA
- National Center for Epidemics and Communicable Disease Control, Amman 11118, Jordan
- Correspondence:
| | - Dima A. Sabbah
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan
| | - Osama H. Abusara
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan
| | - Abdel Qader Al Bawab
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman 11733, Jordan
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Epigenetic Changes in Prion and Prion-like Neurodegenerative Diseases: Recent Advances, Potential as Biomarkers, and Future Perspectives. Int J Mol Sci 2022; 23:ijms232012609. [PMID: 36293477 PMCID: PMC9604074 DOI: 10.3390/ijms232012609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/09/2022] [Accepted: 10/18/2022] [Indexed: 12/01/2022] Open
Abstract
Prion diseases are transmissible spongiform encephalopathies (TSEs) caused by a conformational conversion of the native cellular prion protein (PrPC) to an abnormal, infectious isoform called PrPSc. Amyotrophic lateral sclerosis, Alzheimer’s, Parkinson’s, and Huntington’s diseases are also known as prion-like diseases because they share common features with prion diseases, including protein misfolding and aggregation, as well as the spread of these misfolded proteins into different brain regions. Increasing evidence proposes the involvement of epigenetic mechanisms, namely DNA methylation, post-translational modifications of histones, and microRNA-mediated post-transcriptional gene regulation in the pathogenesis of prion-like diseases. Little is known about the role of epigenetic modifications in prion diseases, but recent findings also point to a potential regulatory role of epigenetic mechanisms in the pathology of these diseases. This review highlights recent findings on epigenetic modifications in TSEs and prion-like diseases and discusses the potential role of such mechanisms in disease pathology and their use as potential biomarkers.
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11
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Li C, Ren J, Zhang M, Wang H, Yi F, Wu J, Tang Y. The heterogeneity of microglial activation and its epigenetic and non-coding RNA regulations in the immunopathogenesis of neurodegenerative diseases. Cell Mol Life Sci 2022; 79:511. [PMID: 36066650 DOI: 10.1007/s00018-022-04536-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 12/15/2022]
Abstract
Microglia are resident immune cells in the brain and play a central role in the development and surveillance of the nervous system. Extensive gliosis is a common pathological feature of several neurodegenerative diseases, such as Alzheimer's disease (AD), the most common cause of dementia. Microglia can respond to multiple inflammatory insults and later transform into different phenotypes, such as pro- and anti-inflammatory phenotypes, thereby exerting different functions. In recent years, an increasing number of studies based on both traditional bulk sequencing and novel single-cell/nuclear sequencing and multi-omics analysis, have shown that microglial phenotypes are highly heterogeneous and dynamic, depending on the severity and stage of the disease as well as the particular inflammatory milieu. Thus, redirecting microglial activation to beneficial and neuroprotective phenotypes promises to halt the progression of neurodegenerative diseases. To this end, an increasing number of studies have focused on unraveling heterogeneous microglial phenotypes and their underlying molecular mechanisms, including those due to epigenetic and non-coding RNA modulations. In this review, we summarize the epigenetic mechanisms in the form of DNA and histone modifications, as well as the general non-coding RNA regulations that modulate microglial activation during immunopathogenesis of neurodegenerative diseases and discuss promising research approaches in the microglial era.
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Affiliation(s)
- Chaoyi Li
- Aging Research Center, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Jie Ren
- Aging Research Center, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Mengfei Zhang
- Aging Research Center, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Huakun Wang
- Aging Research Center, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Fang Yi
- Aging Research Center, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Junjiao Wu
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, 410008, China
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Yu Tang
- Aging Research Center, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, 410008, Hunan, China.
- The Biobank of Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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12
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Min S, Xu Q, Qin L, Li Y, Li Z, Chen C, Wu H, Han J, Zhu X, Jin P, Tang B. Altered hydroxymethylome in the substantia nigra of Parkinson's disease. Hum Mol Genet 2022; 31:3494-3503. [PMID: 35661211 PMCID: PMC9558850 DOI: 10.1093/hmg/ddac122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/05/2022] [Accepted: 05/21/2022] [Indexed: 01/26/2023] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder, and aging and genetic and environmental exposure can contribute to its pathogenesis. DNA methylation has been suggested to play a pivotal role in neurodevelopment and neurodegenerative diseases. 5-hydroxymethylcytosine (5hmC) is generated through 5-methylcytosine (5mC) oxidization by ten-eleven translocation proteins and is particularly enriched in the brain. Although 5hmC has been linked to multiple neurological disorders, little is known about 5hmC alterations in the substantia nigra of patients with PD. To determine the specific alterations in DNA methylation and hydroxymethylation in PD brain samples, we examined the genome-wide profiles of 5mC and 5hmC in the substantia nigra of patients with PD and Alzheimer's disease (ad). We identified 4119 differentially hydroxymethylated regions (DhMRs) and no differentially methylated regions (DMRs) in the postmortem brains of patients with PD compared with those of controls. These DhMRs were PD-specific when compared with the results of AD. Gene ontology analysis revealed that several signaling pathways, such as neurogenesis and neuronal differentiation, were significantly enriched in PD DhMRs. KEGG enrichment analysis revealed substantial alterations in multiple signaling pathways, including phospholipase D (PLD), cAMP and Rap1. In addition, using a PD Drosophila model, we found that one of the 5hmC-modulated genes, PLD1, modulated α-synuclein toxicity. Our analysis suggested that 5hmC may act as an independent epigenetic marker and contribute to the pathogenesis of PD.
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Affiliation(s)
| | | | | | - Yujing Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ziyi Li
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA 30322, USA
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA 30322, USA
| | - Junhai Han
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu 210096, China
| | - Xiongwei Zhu
- To whom correspondence should be addressed at: Department of Neurology, Xiangya Hospital, Central South University, #87 Xiangya Road, Changsha, Hunan 410008, China. Tel: +86-731-84327398; ; Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA. Tel: +1 404-727-3729; ; Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA. Tel: +1-216-368-5903,
| | - Peng Jin
- To whom correspondence should be addressed at: Department of Neurology, Xiangya Hospital, Central South University, #87 Xiangya Road, Changsha, Hunan 410008, China. Tel: +86-731-84327398; ; Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA. Tel: +1 404-727-3729; ; Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA. Tel: +1-216-368-5903,
| | - Beisha Tang
- To whom correspondence should be addressed at: Department of Neurology, Xiangya Hospital, Central South University, #87 Xiangya Road, Changsha, Hunan 410008, China. Tel: +86-731-84327398; ; Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA. Tel: +1 404-727-3729; ; Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA. Tel: +1-216-368-5903,
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13
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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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Analysis of recent shared ancestry in a familial cohort identifies coding and noncoding autism spectrum disorder variants. NPJ Genom Med 2022; 7:13. [PMID: 35190550 PMCID: PMC8861044 DOI: 10.1038/s41525-022-00284-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 01/21/2022] [Indexed: 12/02/2022] Open
Abstract
Autism spectrum disorder (ASD) is a collection of neurodevelopmental disorders characterized by deficits in social communication and restricted, repetitive patterns of behavior or interests. ASD is highly heritable, but genetically and phenotypically heterogeneous, reducing the power to identify causative genes. We performed whole genome sequencing (WGS) in an ASD cohort of 68 individuals from 22 families enriched for recent shared ancestry. We identified an average of 3.07 million variants per genome, of which an average of 112,512 were rare. We mapped runs of homozygosity (ROHs) in affected individuals and found an average genomic homozygosity of 9.65%, consistent with expectations for multiple generations of consanguineous unions. We identified potentially pathogenic rare exonic or splice site variants in 12 known (including KMT2C, SCN1A, SPTBN1, SYNE1, ZNF292) and 12 candidate (including CHD5, GRB10, PPP1R13B) ASD genes. Furthermore, we annotated noncoding variants in ROHs with brain-specific regulatory elements and identified putative disease-causing variants within brain-specific promoters and enhancers for 5 known ASD and neurodevelopmental disease genes (ACTG1, AUTS2, CTNND2, CNTNAP4, SPTBN4). We also identified copy number variants in two known ASD and neurodevelopmental disease loci in two affected individuals. In total we identified potentially etiological variants in known ASD or neurodevelopmental disease genes for ~61% (14/23) of affected individuals. We combined WGS with homozygosity mapping and regulatory element annotations to identify candidate ASD variants. Our analyses add to the growing number of ASD genes and variants and emphasize the importance of leveraging recent shared ancestry to map disease variants in complex neurodevelopmental disorders.
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Kaur G, Rathod SSS, Ghoneim MM, Alshehri S, Ahmad J, Mishra A, Alhakamy NA. DNA Methylation: A Promising Approach in Management of Alzheimer's Disease and Other Neurodegenerative Disorders. BIOLOGY 2022; 11:biology11010090. [PMID: 35053088 PMCID: PMC8773419 DOI: 10.3390/biology11010090] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/13/2022]
Abstract
Simple Summary DNA methylation is an epigenetic modification of genes which affects corresponding gene expression. During the developmental stage, embryonic stem cells undergo various epigenetic modifications to produce different specialized cells. DNA methylation appears as one of the important epigenetic modifications which not only potentiate neuronal development but also have been sought in various neurodegenerative diseases, such as Alzheimer’s disease. The present work focuses on the history of DNA methylation, its role in neurodevelopment functions, and how assessment of DNA hypermethylation and hypomethylation can be utilized for the prognosis of AD and other neurodegenerative diseases. This review also paves the way for the development of novel treatment strategies based on targeting DNA methylation in neurodegenerative diseases. Abstract DNA methylation, in the mammalian genome, is an epigenetic modification that involves the transfer of a methyl group on the C5 position of cytosine to derive 5-methylcytosine. The role of DNA methylation in the development of the nervous system and the progression of neurodegenerative diseases such as Alzheimer’s disease has been an interesting research area. Furthermore, mutations altering DNA methylation affect neurodevelopmental functions and may cause the progression of several neurodegenerative diseases. Epigenetic modifications in neurodegenerative diseases are widely studied in different populations to uncover the plausible mechanisms contributing to the development and progression of the disease and detect novel biomarkers for early prognosis and future pharmacotherapeutic targets. In this manuscript, we summarize the association of DNA methylation with the pathogenesis of the most common neurodegenerative diseases, such as, Alzheimer’s disease, Parkinson’s disease, Huntington diseases, and amyotrophic lateral sclerosis, and discuss the potential of DNA methylation as a potential biomarker and therapeutic tool for neurogenerative diseases.
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Affiliation(s)
- Gagandeep Kaur
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, Punjab, India; (G.K.); (S.S.S.R.)
| | - Suraj Singh S. Rathod
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, Punjab, India; (G.K.); (S.S.S.R.)
| | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia;
| | - Sultan Alshehri
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Javed Ahmad
- Department of Pharmaceutics, College of Pharmacy, Najran University, Najran 11001, Saudi Arabia;
| | - Awanish Mishra
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)—Guwahati, Changsari, Kamrup 781101, Assam, India
- Correspondence: or ; Tel.: +91-972-1554-158 or +91-829-976-4600
| | - Nabil A. Alhakamy
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
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Lutz MW, Chiba‐Falek O. Bioinformatics pipeline to guide late‐onset Alzheimer's disease (LOAD) post‐GWAS studies: Prioritizing transcription regulatory variants within LOAD‐associated regions. ALZHEIMER'S & DEMENTIA: TRANSLATIONAL RESEARCH & CLINICAL INTERVENTIONS 2022; 8:e12244. [PMID: 35229021 PMCID: PMC8864953 DOI: 10.1002/trc2.12244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/27/2021] [Accepted: 12/15/2021] [Indexed: 11/30/2022]
Abstract
Introduction As new late‐onset Alzheimer's disease (LOAD) genetic risk loci are identified and brain cell–type specific omics data becomes available, there is an unmet need for a bioinformatics framework to prioritize genes and variants for testing in single‐cell molecular profiling experiments and validation using disease models and gene editing technologies. Prior work has characterized and prioritized active enhancers located in LOAD‐genome‐wide association study (GWAS) regions and their potential interactions with candidate genes. The current study extends this work by focusing on single nucleotide polymorphisms (SNPs) within these LOAD enhancers and their impact on altering transcription factor (TF) binding. The proposed bioinformatics pipeline progresses from SNPs located in LOAD‐GWAS regions to a filtered set of candidate regulatory SNPs that have a predicted strong effect on TF binding. Methods Active enhancers within LOAD‐associated regions were identified and SNPs located in the enhancers were catalogued. SNPs that disrupt TF binding sites were prioritized and the respective TFs were filtered to include only those that were expressed in brain tissues relevant to LOAD. The TFs binding to the corresponding sequence was further confirmed by ChIP‐seq signals. Finally, the high‐priority candidate SNPs were evaluated as expression quantitative trait loci (eQTLs) in disease‐relevant tissues. Results We catalogued 61 strong enhancers in LOAD‐GWAS regions encompassing 326 SNPs and 104 TF binding sites. Seventy‐seven and 78 of the TFs were expressed in brain and monocytes, respectively, out of which 19 TF‐binding sites showed ChIP‐seq signals. Eleven SNPs were found to interrupt with TF binding out of which three SNPs were also significant eQTL. Discussion This study provides a framework to catalogue noncoding variations in enhancers located in LOAD‐GWAS loci and characterize their likelihood to perturb TF binding. The approach integrates multiple data types to characterize and prioritize SNPs for putative regulatory function using single‐cell multi‐omics assays and gene editing.
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Affiliation(s)
- Michael W. Lutz
- Division of Translational Brain Sciences Department of Neurology Duke University Medical Center Durham North Carolina USA
| | - Ornit Chiba‐Falek
- Division of Translational Brain Sciences Department of Neurology Duke University Medical Center Durham North Carolina USA
- Center for Genomic and Computational Biology Duke University Medical Center Durham North Carolina USA
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Grant P, Kumar J, Kar S, Overduin M. Effects of Specific Inhibitors for CaMK1D on a Primary Neuron Model for Alzheimer's Disease. Molecules 2021; 26:7669. [PMID: 34946752 PMCID: PMC8707680 DOI: 10.3390/molecules26247669] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/20/2022] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia worldwide. Despite extensive research and targeting of the main molecular components of the disease, beta-amyloid (Aβ) and tau, there are currently no treatments that alter the progression of the disease. Here, we examine the effects of two specific kinase inhibitors for calcium/calmodulin-dependent protein kinase type 1D (CaMK1D) on Aβ-mediated toxicity, using mouse primary cortical neurons. Tau hyperphosphorylation and cell death were used as AD indicators. These specific inhibitors were found to prevent Aβ induced tau hyperphosphorylation in culture, but were not able to protect cells from Aβ induced toxicity. While inhibitors were able to alter AD pathology in cell culture, they were insufficient to prevent cell death. With further research and development, these inhibitors could contribute to a multi-drug strategy to combat AD.
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Affiliation(s)
- Paige Grant
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada; (P.G.); (J.K.)
| | - Jitendra Kumar
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada; (P.G.); (J.K.)
| | - Satyabrata Kar
- Centre for Prions and Protein Folding Diseases, Department of Medicine (Neurology), University of Alberta, Edmonton, AB T6G 2MB, Canada;
| | - Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada; (P.G.); (J.K.)
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18
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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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19
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Longley MJ, Lee J, Jung J, Lohoff FW. Epigenetics of alcohol use disorder-A review of recent advances in DNA methylation profiling. Addict Biol 2021; 26:e13006. [PMID: 33538087 PMCID: PMC8596445 DOI: 10.1111/adb.13006] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 01/05/2021] [Accepted: 01/09/2021] [Indexed: 12/13/2022]
Abstract
Alcohol use disorder (AUD) is a major contributor to morbidity and mortality worldwide. Although there is a heritable component, the etiology of AUD is complex and can involve environmental exposures like trauma and can be associated with many different patterns of alcohol consumption. Epigenetic modifications, which can mediate the influence of genetic variants and environmental variables on gene expression, have emerged as an important area of AUD research. Over the past decade, the number of studies investigating AUD and DNA methylation, a form of epigenetic modification, has grown rapidly. Yet we are still far from understanding how DNA methylation contributes to or reflects aspects of AUD. In this paper, we reviewed studies of DNA methylation and AUD and discussed how the field has evolved. We found that global DNA and candidate DNA methylation studies did not produce replicable results. To assess whether findings of epigenome-wide association studies (EWAS) were replicated, we aggregated significant findings across studies and identified 184 genes and 15 gene ontological pathways that were differentially methylated in at least two studies and four genes and three gene ontological pathways that were differentially methylated in three studies. These genes and pathways repeatedly found enrichment of immune processes, which is in line with recent developments suggesting that the immune system may be altered in AUD. Finally, we assess the current limitations of studies of DNA methylation and AUD and make recommendations on how to design future studies to resolve outstanding questions.
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Affiliation(s)
- Martha J. Longley
- Section on Clinical Genomics and Experimental TherapeuticsNational Institute on Alcohol Abuse and Alcoholism, National Institutes of HealthBethesdaMarylandUSA
| | - Jisoo Lee
- Section on Clinical Genomics and Experimental TherapeuticsNational Institute on Alcohol Abuse and Alcoholism, National Institutes of HealthBethesdaMarylandUSA
| | - Jeesun Jung
- Section on Clinical Genomics and Experimental TherapeuticsNational Institute on Alcohol Abuse and Alcoholism, National Institutes of HealthBethesdaMarylandUSA
| | - Falk W. Lohoff
- Section on Clinical Genomics and Experimental TherapeuticsNational Institute on Alcohol Abuse and Alcoholism, National Institutes of HealthBethesdaMarylandUSA
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20
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Iatrou A, Clark EM, Wang Y. Nuclear dynamics and stress responses in Alzheimer's disease. Mol Neurodegener 2021; 16:65. [PMID: 34535174 PMCID: PMC8447732 DOI: 10.1186/s13024-021-00489-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 09/01/2021] [Indexed: 02/06/2023] Open
Abstract
In response to extracellular and intracellular stressors, the nucleus and nuclear compartments undergo distinct molecular changes to maintain cell homeostasis. In the context of Alzheimer’s disease, misfolded proteins and various cellular stressors lead to profound structural and molecular changes at the nucleus. This review summarizes recent research on nuclear alterations in AD development, from the nuclear envelope changes to chromatin and epigenetic regulation and then to common nuclear stress responses. Finally, we provide our thoughts on the importance of understanding cell-type-specific changes and identifying upstream causal events in AD pathogenesis and highlight novel sequencing and gene perturbation technologies to address those challenges.
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Affiliation(s)
- Artemis Iatrou
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W. Harrison St., Chicago, IL, 60612, USA
| | - Eric M Clark
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W. Harrison St., Chicago, IL, 60612, USA
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W. Harrison St., Chicago, IL, 60612, USA.
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21
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Barrera J, Song L, Gamache JE, Garrett ME, Safi A, Yun Y, Premasinghe I, Sprague D, Chipman D, Li J, Fradin H, Soldano K, Gordân R, Ashley-Koch AE, Crawford GE, Chiba-Falek O. Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer's disease brains. Mol Neurodegener 2021; 16:58. [PMID: 34429139 PMCID: PMC8383438 DOI: 10.1186/s13024-021-00481-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/11/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In the post-GWAS era, there is an unmet need to decode the underpinning genetic etiologies of late-onset Alzheimer's disease (LOAD) and translate the associations to causation. METHODS We conducted ATAC-seq profiling using NeuN sorted-nuclei from 40 frozen brain tissues to determine LOAD-specific changes in chromatin accessibility landscape in a cell-type specific manner. RESULTS We identified 211 LOAD-specific differential chromatin accessibility sites in neuronal-nuclei, four of which overlapped with LOAD-GWAS regions (±100 kb of SNP). While the non-neuronal nuclei did not show LOAD-specific differences, stratification by sex identified 842 LOAD-specific chromatin accessibility sites in females. Seven of these sex-dependent sites in the non-neuronal samples overlapped LOAD-GWAS regions including APOE. LOAD loci were functionally validated using single-nuclei RNA-seq datasets. CONCLUSIONS Using brain sorted-nuclei enabled the identification of sex-dependent cell type-specific LOAD alterations in chromatin structure. These findings enhance the interpretation of LOAD-GWAS discoveries, provide potential pathomechanisms, and suggest novel LOAD-loci.
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Affiliation(s)
- Julio Barrera
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Lingyun Song
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Julia E. Gamache
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Melanie E. Garrett
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701 USA
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Young Yun
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Ivana Premasinghe
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Daniel Sprague
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Danielle Chipman
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Jeffrey Li
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Hélène Fradin
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
| | - Karen Soldano
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701 USA
| | - Raluca Gordân
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27705 USA
- Department of Computer Science, Duke University, Durham, NC 27705 USA
| | - Allison E. Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701 USA
- Department of Medicine, Duke University Medical Center, DUMC, Box 104775, Durham, NC 27708 USA
| | - Gregory E. Crawford
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, DUMC, Box 3382, Durham, NC 27708 USA
- Center for Advanced Genomic Technologies, Duke University Medical Center, Durham, NC 27708 USA
| | - Ornit Chiba-Falek
- Department of Neurology, Division of Translational Brain Sciences, Duke University Medical Center, DUMC, Box 2900, Durham, NC 27710 USA
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC 27708 USA
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22
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Ma Y, Klein HU, De Jager PL. Considerations for integrative multi-omic approaches to explore Alzheimer's disease mechanisms. Brain Pathol 2021; 30:984-991. [PMID: 32654306 DOI: 10.1111/bpa.12878] [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: 06/10/2020] [Accepted: 07/07/2020] [Indexed: 12/29/2022] Open
Abstract
The past decade has seen the maturation of multiple different forms of high-dimensional molecular profiling to the point that these methods could be deployed in initially hundreds and more recently thousands of human samples. In the field of Alzheimer's disease (AD), these profiles have been applied to the target organ: the aging brain. In a growing number of cases, the same samples were profiled with multiple different approaches, yielding genetic, transcriptomic, epigenomic and proteomic data. Here, we review lessons learned so far as we move beyond quantitative trait locus (QTL) analyses which map the effect of genetic variation on molecular features to integrate multiple levels of "omic" data in an effort to identify the molecular drivers of AD. One thing is clear: no single layer of molecular or "omic" data is sufficient to capture the variance of AD or aging-related cognitive decline. Nonetheless, reproducible findings are emerging from current efforts, and there is evidence of convergence using different approaches. Thus, we are on the cusp of an acceleration of truly integrative studies as the availability of large numbers of well-characterized brain samples profiled in three or more dimensions enables the testing, comparison and refinement of analytic methods with which to dissect the molecular architecture of the aging brain.
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Affiliation(s)
- Yiyi Ma
- Center for Translational and Computational Neuroimmunology, Department of Neurology, the Taub Institute for Research in Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY
| | - Hans-Ulrich Klein
- Center for Translational and Computational Neuroimmunology, Department of Neurology, the Taub Institute for Research in Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, the Taub Institute for Research in Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY
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23
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Li L, Qiu Y, Miao M, Liu Z, Li W, Zhu Y, Wang Q. Reduction of Tet2 exacerbates early stage Alzheimer's pathology and cognitive impairments in 2×Tg-AD mice. Hum Mol Genet 2021; 29:1833-1852. [PMID: 31943063 DOI: 10.1093/hmg/ddz282] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 10/20/2019] [Accepted: 11/19/2019] [Indexed: 12/29/2022] Open
Abstract
Abnormal modification of 5-hydroxymethylcytosine (5hmC) is closely related to the occurrence of Alzheimer's disease (AD). However, the role of 5hmC and its writers, ten-eleven translocation (Tet) proteins, in regulating the pathogenesis of AD remains largely unknown. We detected a significant decrease in 5hmC and Tet2 levels in the hippocampus of aged APPswe/PSEN1 double-transgenic (2×Tg-AD) mice that coincides with abundant amyloid-β (Aβ) plaque accumulation. On this basis, we examined the reduction of Tet2 expression in the hippocampus at early disease stages, which caused a decline of 5hmC levels and led young 2×Tg-AD mice to present with advanced stages of AD-related pathological hallmarks, including Aβ accumulation, GFAP-positive astrogliosis and Iba1-positive microglia overgrowth as well as the overproduction of pro-inflammatory factors. Additionally, the loss of Tet2 in the 2×Tg-AD mice at 5 months of age accelerated hippocampal-dependent learning and memory impairments compared to age-matched control 2×Tg-AD mice. In contrast, restoring Tet2 expression in adult neural stem cells isolated from aged 2×Tg-AD mice hippocampi increased 5hmC levels and increased their regenerative capacity, suggesting that Tet2 might be an exciting target for rejuvenating the brain during aging and AD. Further, hippocampal RNA sequencing data revealed that the expression of altered genes identified in both Tet2 knockdown and control 2×Tg-AD mice was significantly associated with inflammation response. Finally, we demonstrated that Tet2-mediated 5hmC epigenetic modifications regulate AD pathology by interacting with HDAC1. These results suggest a combined approach for the regulation and treatment of AD-related memory impairment and cognitive symptoms by increasing Tet2 via HDAC1 suppression.
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Affiliation(s)
- Liping Li
- Ningbo Key Laboratory of Behavioral Neuroscience, Department of Physiology and Pharmacology, Ningbo University School of Medicine, Ningbo 315211, China.,Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China
| | - Yisha Qiu
- Ningbo Key Laboratory of Behavioral Neuroscience, Department of Physiology and Pharmacology, Ningbo University School of Medicine, Ningbo 315211, China.,Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China
| | - Miao Miao
- Ningbo Key Laboratory of Behavioral Neuroscience, Department of Physiology and Pharmacology, Ningbo University School of Medicine, Ningbo 315211, China.,Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China
| | - Zhitao Liu
- Faculty of Sports Science, Ningbo University, Ningbo 315211, China
| | - Wanyi Li
- Faculty of Sports Science, Ningbo University, Ningbo 315211, China
| | - Yiyi Zhu
- Ningbo Key Laboratory of Behavioral Neuroscience, Department of Physiology and Pharmacology, Ningbo University School of Medicine, Ningbo 315211, China.,Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China
| | - Qinwen Wang
- Ningbo Key Laboratory of Behavioral Neuroscience, Department of Physiology and Pharmacology, Ningbo University School of Medicine, Ningbo 315211, China.,Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China
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24
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Higgins-Chen AT, Thrush KL, Levine ME. Aging biomarkers and the brain. Semin Cell Dev Biol 2021; 116:180-193. [PMID: 33509689 PMCID: PMC8292153 DOI: 10.1016/j.semcdb.2021.01.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/15/2022]
Abstract
Quantifying biological aging is critical for understanding why aging is the primary driver of morbidity and mortality and for assessing novel therapies to counter pathological aging. In the past decade, many biomarkers relevant to brain aging have been developed using various data types and modeling techniques. Aging involves numerous interconnected processes, and thus many complementary biomarkers are needed, each capturing a different slice of aging biology. Here we present a hierarchical framework highlighting how these biomarkers are related to each other and the underlying biological processes. We review those measures most studied in the context of brain aging: epigenetic clocks, proteomic clocks, and neuroimaging age predictors. Many studies have linked these biomarkers to cognition, mental health, brain structure, and pathology during aging. We also delve into the challenges and complexities in interpreting these biomarkers and suggest areas for further innovation. Ultimately, a robust mechanistic understanding of these biomarkers will be needed to effectively intervene in the aging process to prevent and treat age-related disease.
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Affiliation(s)
- Albert T Higgins-Chen
- Department of Psychiatry, Yale University School of Medicine, 300 George St, Suite 901, New Haven, CT 06511, USA.
| | - Kyra L Thrush
- Program in Computational Biology and Bioinformatics, Yale University, 300 George St, Suite 501, New Haven, CT 06511, USA.
| | - Morgan E Levine
- Department of Pathology, Yale University School of Medicine, 310 Cedar Street, Suite LH 315A, New Haven, CT 06520, USA.
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25
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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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26
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Rygiel CA, Goodrich JM, Solano-González M, Mercado-García A, Hu H, Téllez-Rojo MM, Peterson KE, Dolinoy DC. Prenatal Lead (Pb) Exposure and Peripheral Blood DNA Methylation (5mC) and Hydroxymethylation (5hmC) in Mexican Adolescents from the ELEMENT Birth Cohort. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:67002. [PMID: 34152198 PMCID: PMC8216410 DOI: 10.1289/ehp8507] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND Gestational lead (Pb) exposure can adversely affect offspring health through multiple mechanisms, including epigenomic alterations via DNA methylation (5mC) and hydroxymethylation (5hmC), an intermediate in oxidative demethylation. Most current methods do not distinguish between 5mC and 5hmC, limiting insights into their individual roles. OBJECTIVE Our study sought to identify the association of trimester-specific (T1, T2, T3) prenatal Pb exposure with 5mC and 5hmC levels at multiple cytosine-phosphate-guanine sites within gene regions previously associated with prenatal Pb (HCN2, NINJ2, RAB5A, TPPP) in whole blood leukocytes of children ages 11-18 years of age. METHODS Participants from the Early Life Exposure in Mexico to Environmental Toxicants (ELEMENT) birth cohorts were selected (n=144) for pyrosequencing analysis following oxidative or standard sodium bisulfite treatment. This workflow directly quantifies total methylation (5mC+5hmC) and 5mC only; 5hmC is estimated by subtraction. RESULTS Participants were 51% male, and mean maternal blood lead levels (BLL) were 6.43±5.16μg/dL in Trimester 1 (T1), 5.66±5.21μg/dL in Trimester 2 (T2), and 5.86±4.34μg/dL in Trimester 3 (T3). In addition, 5hmC levels were calculated for HCN2 (mean±standard deviation(SD), 2.08±4.18%), NINJ2 (G/C: 2.01±5.95; GG: 0.90±3.97), RAB5A (0.66±0.80%), and TPPP (1.11±6.67%). Furthermore, 5mC levels were measured in HCN2 (81.3±9.63%), NINJ2 (heterozygotes: 38.6±7.39%; GG homozygotes: 67.3±9.83%), RAB5A (1.41±1.21%), and TPPP (92.5±8.03%). Several significant associations between BLLs and 5mC/5hmC were identified: T1 BLLs with 5mC in HCN2 (β=-0.37, p=0.03) and 5hmC in NINJ2 (β=0.49, p=0.003); T2 BLLs with 5mC in HCN2 (β=0.37, p=0.03) and 5hmC in NINJ2 (β=0.27, p=0.008); and T3 BLLs with 5mC in HCN2 (β=0.50, p=0.01) and NINJ2 (β=-0.35, p=0.004) and 5hmC in NINJ2 (β=0.45, p<0.001). NINJ2 5mC was negatively correlated with gene expression (Pearson r=-0.5, p-value=0.005), whereas 5hmC was positively correlated (r=0.4, p-value=0.04). DISCUSSION These findings suggest there is variable 5hmC in human whole blood and that prenatal Pb exposure is associated with gene-specific 5mC and 5hmC levels at adolescence, providing evidence to consider 5hmC as a regulatory mechanism that is responsive to environmental exposures. https://doi.org/10.1289/EHP8507.
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Affiliation(s)
- Christine A. Rygiel
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | | | | | - Howard Hu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | | | - Karen E. Peterson
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
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27
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Kuehner JN, Chen J, Bruggeman EC, Wang F, Li Y, Xu C, McEachin ZT, Li Z, Chen L, Hales CM, Wen Z, Yang J, Yao B. 5-hydroxymethylcytosine is dynamically regulated during forebrain organoid development and aberrantly altered in Alzheimer's disease. Cell Rep 2021; 35:109042. [PMID: 33910000 PMCID: PMC8106871 DOI: 10.1016/j.celrep.2021.109042] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 02/02/2021] [Accepted: 04/06/2021] [Indexed: 12/21/2022] Open
Abstract
5-hydroxymethylcytosine (5hmC) undergoes dynamic changes during mammalian brain development, and its dysregulation is associated with Alzheimer’s disease (AD). The dynamics of 5hmC during early human brain development and how they contribute to AD pathologies remain largely unexplored. We generate 5hmC and transcriptome profiles encompassing several developmental time points of healthy forebrain organoids and organoids derived from several familial AD patients. Stage-specific differentially hydroxymethylated regions demonstrate an acquisition or depletion of 5hmC modifications across developmental stages. Additionally, genes concomitantly increasing or decreasing in 5hmC and gene expression are enriched in neurobiological or early developmental processes, respectively. Importantly, our AD organoids corroborate cellular and molecular phenotypes previously observed in human AD brains. 5hmC is significantly altered in developmentally programmed 5hmC intragenic regions in defined fetal histone marks and enhancers in AD organoids. These data suggest a highly coordinated molecular system that may be dysregulated in these early developing AD organoids. Kuehner et al. use forebrain organoids derived from healthy controls to study the dynamics of 5hmC across early brain development. In addition, organoids derived from several AD patients reveal aberrant 5hmC patterns that could disrupt early neuronal networks and contribute to the onset of AD later in life.
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Affiliation(s)
- Janise N Kuehner
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Junyu Chen
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Emily C Bruggeman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Feng Wang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Yangping Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Chongchong Xu
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA; Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Zachary T McEachin
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Ziyi Li
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Li Chen
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Chadwick M Hales
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA; Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA; Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.
| | - Jingjing Yang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
| | - Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
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28
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De Jager PL. Deconstructing the epigenomic architecture of human neurodegeneration. Neurobiol Dis 2021; 153:105331. [PMID: 33711493 DOI: 10.1016/j.nbd.2021.105331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 10/21/2022] Open
Abstract
The past 10 years have seen a rapid advance in our ability to profile the epigenome from human pathologic material, opening up new study designs to investigate the role of epigenomic features in human disease. Moderate to large scale studies have now been conducted in the target tissue of neurodegenerative diseases, the brain, and, through the use of rigorous statistical methodologies, have laid a foundation of validated observations and successful study designs that inform our perspective on the role of the epigenome in these diseases, generate new hypotheses, and guide our path forward for a second generation of studies. It is clear that sampling the epigenome is not redundant with other "omic" profiling of the same tissue and that it can serve as an important vehicle for the integration of the effect of multiple environmental exposures on risk of disease. In some cases, change in the epigenome may thus have a causal impact on disease, but we now have evidence that such changes may also mediate some of the effect of tau proteinopathy and that other changes may moderate the impact of genetic risk factors. Thus, the epigenome may be involved at multiple different stages of the sequence of events that leads to human neurodegeneration, and we review the study designs that may begin to guide the development of a more comprehensive perspective on the aging brain's epigenome.
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Affiliation(s)
- Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, NY, United States of America; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, United States of America; Department of Neurology, Columbia University Medical Center, New York, NY, United States of America.
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29
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Nikolac Perkovic M, Videtic Paska A, Konjevod M, Kouter K, Svob Strac D, Nedic Erjavec G, Pivac N. Epigenetics of Alzheimer's Disease. Biomolecules 2021; 11:biom11020195. [PMID: 33573255 PMCID: PMC7911414 DOI: 10.3390/biom11020195] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/19/2021] [Accepted: 01/26/2021] [Indexed: 02/07/2023] Open
Abstract
There are currently no validated biomarkers which can be used to accurately diagnose Alzheimer’s disease (AD) or to distinguish it from other dementia-causing neuropathologies. Moreover, to date, only symptomatic treatments exist for this progressive neurodegenerative disorder. In the search for new, more reliable biomarkers and potential therapeutic options, epigenetic modifications have emerged as important players in the pathogenesis of AD. The aim of the article was to provide a brief overview of the current knowledge regarding the role of epigenetics (including mitoepigenetics) in AD, and the possibility of applying these advances for future AD therapy. Extensive research has suggested an important role of DNA methylation and hydroxymethylation, histone posttranslational modifications, and non-coding RNA regulation (with the emphasis on microRNAs) in the course and development of AD. Recent studies also indicated mitochondrial DNA (mtDNA) as an interesting biomarker of AD, since dysfunctions in the mitochondria and lower mtDNA copy number have been associated with AD pathophysiology. The current evidence suggests that epigenetic changes can be successfully detected, not only in the central nervous system, but also in the cerebrospinal fluid and on the periphery, contributing further to their potential as both biomarkers and therapeutic targets in AD.
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Affiliation(s)
- Matea Nikolac Perkovic
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Ruder Boskovic Institute, HR-10000 Zagreb, Croatia; (M.N.P.); (M.K.); (D.S.S.); (G.N.E.)
| | - Alja Videtic Paska
- Medical Center for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (A.V.P.); (K.K.)
| | - Marcela Konjevod
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Ruder Boskovic Institute, HR-10000 Zagreb, Croatia; (M.N.P.); (M.K.); (D.S.S.); (G.N.E.)
| | - Katarina Kouter
- Medical Center for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia; (A.V.P.); (K.K.)
| | - Dubravka Svob Strac
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Ruder Boskovic Institute, HR-10000 Zagreb, Croatia; (M.N.P.); (M.K.); (D.S.S.); (G.N.E.)
| | - Gordana Nedic Erjavec
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Ruder Boskovic Institute, HR-10000 Zagreb, Croatia; (M.N.P.); (M.K.); (D.S.S.); (G.N.E.)
| | - Nela Pivac
- Laboratory for Molecular Neuropsychiatry, Division of Molecular Medicine, Ruder Boskovic Institute, HR-10000 Zagreb, Croatia; (M.N.P.); (M.K.); (D.S.S.); (G.N.E.)
- Correspondence: ; Tel.: +38-514-571-207
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Kołodziej-Wojnar P, Borkowska J, Wicik Z, Domaszewska-Szostek A, Połosak J, Cąkała-Jakimowicz M, Bujanowska O, Puzianowska-Kuznicka M. Alterations in the Genomic Distribution of 5hmC in In Vivo Aged Human Skin Fibroblasts. Int J Mol Sci 2020; 22:ijms22010078. [PMID: 33374812 PMCID: PMC7794952 DOI: 10.3390/ijms22010078] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022] Open
Abstract
5-Hydroxymethylcytosine (5hmC) is a functionally active epigenetic modification. We analyzed whether changes in DNA 5-hydroxymethylation are an element of age-related epigenetic drift. We tested primary fibroblast cultures originating from individuals aged 22-35 years and 74-94 years. Global quantities of methylation-related DNA modifications were estimated by the dot blot and colorimetric methods. Regions of the genome differentially hydroxymethylated with age (DHMRs) were identified by hMeDIP-seq and the MEDIPS and DiffBind algorithms. Global levels of DNA modifications were not associated with age. We identified numerous DHMRs that were enriched within introns and intergenic regions and most commonly associated with the H3K4me1 histone mark, promoter-flanking regions, and CCCTC-binding factor (CTCF) binding sites. However, only seven DHMRs were identified by both algorithms and all of their settings. Among them, hypo-hydroxymethylated DHMR in the intron of Rab Escort Protein 1 (CHM) coexisted with increased expression in old cells, while increased 5-hydroxymethylation in the bodies of Arginine and Serine Rich Protein 1 (RSRP1) and Mitochondrial Poly(A) Polymerase (MTPAP) did not change their expression. These age-related differences were not associated with changes in the expression of any of the ten-eleven translocation (TET) enzymes or their activity. In conclusion, the distribution of 5hmC in DNA of in vivo aged human fibroblasts underwent age-associated modifications. The identified DHMRs are, likely, marker changes.
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Affiliation(s)
- Paulina Kołodziej-Wojnar
- Department of Geriatrics and Gerontology, Medical Centre of Postgraduate Education, 01-813 Warsaw, Poland;
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, A. Pawinskiego 5, 02-106 Warsaw, Poland; (J.B.); (Z.W.); (A.D.-S.); (J.P.); (M.C.-J.); (O.B.)
| | - Joanna Borkowska
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, A. Pawinskiego 5, 02-106 Warsaw, Poland; (J.B.); (Z.W.); (A.D.-S.); (J.P.); (M.C.-J.); (O.B.)
| | - Zofia Wicik
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, A. Pawinskiego 5, 02-106 Warsaw, Poland; (J.B.); (Z.W.); (A.D.-S.); (J.P.); (M.C.-J.); (O.B.)
| | - Anna Domaszewska-Szostek
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, A. Pawinskiego 5, 02-106 Warsaw, Poland; (J.B.); (Z.W.); (A.D.-S.); (J.P.); (M.C.-J.); (O.B.)
| | - Jacek Połosak
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, A. Pawinskiego 5, 02-106 Warsaw, Poland; (J.B.); (Z.W.); (A.D.-S.); (J.P.); (M.C.-J.); (O.B.)
- Institute of Medical Science, Faculty of Medicine, Collegium Medicum, Cardinal Stefan Wyszynski University in Warsaw, 01-938 Warsaw, Poland
| | - Marta Cąkała-Jakimowicz
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, A. Pawinskiego 5, 02-106 Warsaw, Poland; (J.B.); (Z.W.); (A.D.-S.); (J.P.); (M.C.-J.); (O.B.)
| | - Olga Bujanowska
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, A. Pawinskiego 5, 02-106 Warsaw, Poland; (J.B.); (Z.W.); (A.D.-S.); (J.P.); (M.C.-J.); (O.B.)
| | - Monika Puzianowska-Kuznicka
- Department of Geriatrics and Gerontology, Medical Centre of Postgraduate Education, 01-813 Warsaw, Poland;
- Department of Human Epigenetics, Mossakowski Medical Research Centre, PAS, A. Pawinskiego 5, 02-106 Warsaw, Poland; (J.B.); (Z.W.); (A.D.-S.); (J.P.); (M.C.-J.); (O.B.)
- Correspondence: ; Tel.: +48-22-6086410
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31
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Zhang Y, Zhang Z, Li L, Xu K, Ma Z, Chow HM, Herrup K, Li J. Selective loss of 5hmC promotes neurodegeneration in the mouse model of Alzheimer's disease. FASEB J 2020; 34:16364-16382. [PMID: 33058355 DOI: 10.1096/fj.202001271r] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/20/2020] [Accepted: 10/02/2020] [Indexed: 11/11/2022]
Abstract
5-hydroxymethylcytosine (5hmC) is an intermediate stage of DNA de-methylation. Its location in the genome also serves as an important regulatory signal for many biological processes and its levels change significantly with the etiology of Alzheimer's disease (AD). In keeping with this relationship, the TET family of enzymes which convert 5-methylcytosine (5mC) to 5hmC are responsive to the presence of Aβ. Using hMeDIP-seq, we show that there is a genome-wide reduction of 5hmC that is found in neurons but not in astrocytes from 3xTg mice (an AD mouse model). Decreased TET enzymatic activities in the brains of persons who died with AD suggest that this reduction is the main cause for the loss of 5hmC. Overexpression of human TET catalytic domains (hTETCDs) from the TET family members, especially for hTET3CD, significantly attenuates the neurodegenerative process, including reduced Aβ accumulation as well as tau hyperphosphorylation, and improve synaptic dysfunction in 3xTg mouse brain. Our findings define a crucial role of deregulated 5hmC epigenetics in the events leading to AD neurodegeneration.
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Affiliation(s)
- Ying Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Zhongyu Zhang
- National Institute on Drug Dependence, Peking University, Beijing, China
| | - Lianwei Li
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, The Chinese University of Hongkong, Hong Kong, China
| | - Kaiyu Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Zhanshan Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hei-Man Chow
- School of Life Sciences, The Chinese University of Hongkong, Hong Kong, China
| | - Karl Herrup
- Department of Neurobiology, The University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jiali Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- National Institute on Drug Dependence, Peking University, Beijing, China
- IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
- Kunming Primate Research Center of the Chinese Academy of Sciences, Kunming, China
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32
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Zhang L, Silva TC, Young JI, Gomez L, Schmidt MA, Hamilton-Nelson KL, Kunkle BW, Chen X, Martin ER, Wang L. Epigenome-wide meta-analysis of DNA methylation differences in prefrontal cortex implicates the immune processes in Alzheimer's disease. Nat Commun 2020; 11:6114. [PMID: 33257653 PMCID: PMC7704686 DOI: 10.1038/s41467-020-19791-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/26/2020] [Indexed: 12/14/2022] Open
Abstract
DNA methylation differences in Alzheimer's disease (AD) have been reported. Here, we conducted a meta-analysis of more than 1000 prefrontal cortex brain samples to prioritize the most consistent methylation differences in multiple cohorts. Using a uniform analysis pipeline, we identified 3751 CpGs and 119 differentially methylated regions (DMRs) significantly associated with Braak stage. Our analysis identified differentially methylated genes such as MAMSTR, AGAP2, and AZU1. The most significant DMR identified is located on the MAMSTR gene, which encodes a cofactor that stimulates MEF2C. Notably, MEF2C cooperates with another transcription factor, PU.1, a central hub in the AD gene network. Our enrichment analysis highlighted the potential roles of the immune system and polycomb repressive complex 2 in pathological AD. These results may help facilitate future mechanistic and biomarker discovery studies in AD.
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Affiliation(s)
- Lanyu Zhang
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Tiago C Silva
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Juan I Young
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Michael A Schmidt
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Kara L Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Brian W Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Xi Chen
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Eden R Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
- Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
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33
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Xu K, Li B, McGinnis KA, Vickers-Smith R, Dao C, Sun N, Kember RL, Zhou H, Becker WC, Gelernter J, Kranzler HR, Zhao H, Justice AC. Genome-wide association study of smoking trajectory and meta-analysis of smoking status in 842,000 individuals. Nat Commun 2020; 11:5302. [PMID: 33082346 PMCID: PMC7598939 DOI: 10.1038/s41467-020-18489-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/20/2020] [Indexed: 12/12/2022] Open
Abstract
Here we report a large genome-wide association study (GWAS) for longitudinal smoking phenotypes in 286,118 individuals from the Million Veteran Program (MVP) where we identified 18 loci for smoking trajectory of current versus never in European Americans, one locus in African Americans, and one in Hispanic Americans. Functional annotations prioritized several dozen genes where significant loci co-localized with either expression quantitative trait loci or chromatin interactions. The smoking trajectories were genetically correlated with 209 complex traits, for 33 of which smoking was either a causal or a consequential factor. We also performed European-ancestry meta-analyses for smoking status in the MVP and GWAS & Sequencing Consortium of Alcohol and Nicotine use (GSCAN) (Ntotal = 842,717) and identified 99 loci for smoking initiation and 13 loci for smoking cessation. Overall, this large GWAS of longitudinal smoking phenotype in multiple populations, combined with a meta-GWAS for smoking status, adds new insights into the genetic vulnerability for smoking behavior. Genome-wide association studies (GWASs) for cigarette smoking have identified several hundred loci that account for a small proportion of the overall genetic risk. Here, the authors report a large GWAS for smoking trajectories and meta-analysis for smoking status, finding multiple plausible loci.
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Affiliation(s)
- Ke Xu
- Yale School of Medicine, New Haven, CT, 06511, USA.,VA Connecticut Healthcare System, West Haven, CT, 06516, USA
| | - Boyang Li
- VA Connecticut Healthcare System, West Haven, CT, 06516, USA.,Yale School of Public Health, New Haven, CT, 06511, USA
| | | | | | - Cecilia Dao
- VA Connecticut Healthcare System, West Haven, CT, 06516, USA.,Yale School of Public Health, New Haven, CT, 06511, USA
| | - Ning Sun
- Yale School of Public Health, New Haven, CT, 06511, USA
| | - Rachel L Kember
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.,Crescenz Veterans Affairs Medical Center, Philadelphia, PA, 19104, USA
| | - Hang Zhou
- Yale School of Medicine, New Haven, CT, 06511, USA.,VA Connecticut Healthcare System, West Haven, CT, 06516, USA
| | - William C Becker
- Yale School of Medicine, New Haven, CT, 06511, USA.,VA Connecticut Healthcare System, West Haven, CT, 06516, USA
| | - Joel Gelernter
- Yale School of Medicine, New Haven, CT, 06511, USA.,VA Connecticut Healthcare System, West Haven, CT, 06516, USA
| | - Henry R Kranzler
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.,Crescenz Veterans Affairs Medical Center, Philadelphia, PA, 19104, USA
| | - Hongyu Zhao
- Yale School of Medicine, New Haven, CT, 06511, USA.,Yale School of Public Health, New Haven, CT, 06511, USA
| | - Amy C Justice
- Yale School of Medicine, New Haven, CT, 06511, USA. .,VA Connecticut Healthcare System, West Haven, CT, 06516, USA.
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Xiao X, Liu X, Jiao B. Epigenetics: Recent Advances and Its Role in the Treatment of Alzheimer's Disease. Front Neurol 2020; 11:538301. [PMID: 33178099 PMCID: PMC7594522 DOI: 10.3389/fneur.2020.538301] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 09/03/2020] [Indexed: 12/14/2022] Open
Abstract
Objective: This review summarizes recent findings on the epigenetics of Alzheimer's disease (AD) and provides therapeutic strategies for AD. Methods: We searched the following keywords: “genetics,” “epigenetics,” “Alzheimer's disease,” “DNA methylation,” “DNA hydroxymethylation,” “histone modifications,” “non-coding RNAs,” and “therapeutic strategies” in PubMed. Results: In this review, we summarizes recent studies of epigenetics in AD, including DNA methylation/hydroxymethylation, histone modifications, and non-coding RNAs. There are no consistent results of global DNA methylation/hydroxymethylation in AD. Epigenetic genome-wide association studies show that many differentially methylated sites exist in AD. Several studies investigate the role of histone modifications in AD; for example, histone acetylation decreases, whereas H3 phosphorylation increases significantly in AD. In addition, non-coding RNAs, such as microRNA-16 and BACE1-antisense transcript (BACE1-AS), are associated with the pathology of AD. These epigenetic changes provide us with novel insights into the pathogenesis of AD and may be potential therapeutic strategies for AD. Conclusion: Epigenetics is associated with the pathogenesis of AD, including DNA methylation/hydroxymethylation, histone modifications, and non-coding RNAs, which provide potential therapeutic strategies for AD.
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Affiliation(s)
- Xuewen Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xixi Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Bin Jiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
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35
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DNA methylation in Alzheimer’s disease: In brain and peripheral blood. Mech Ageing Dev 2020; 191:111319. [DOI: 10.1016/j.mad.2020.111319] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 12/30/2022]
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36
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Smith AR, Wheildon G, Lunnon K. Invited Review – A 5‐year update on epigenome‐wide association studies of DNA modifications in Alzheimer’s disease: progress, practicalities and promise. Neuropathol Appl Neurobiol 2020; 46:641-653. [DOI: 10.1111/nan.12650] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 07/10/2020] [Accepted: 07/12/2020] [Indexed: 12/12/2022]
Affiliation(s)
- A. R. Smith
- University of Exeter Medical School College of Medicine and Health Exeter University Exeter UK
| | - G. Wheildon
- University of Exeter Medical School College of Medicine and Health Exeter University Exeter UK
| | - K. Lunnon
- University of Exeter Medical School College of Medicine and Health Exeter University Exeter UK
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37
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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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Epigenetic Clock: DNA Methylation in Aging. Stem Cells Int 2020; 2020:1047896. [PMID: 32724310 PMCID: PMC7366189 DOI: 10.1155/2020/1047896] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/11/2020] [Accepted: 06/20/2020] [Indexed: 02/07/2023] Open
Abstract
Aging, which is accompanied by decreased organ function and increased disease incidence, limits human lifespan and has attracted investigators for thousands of years. In recent decades, with the rapid development of biology, scientists have shown that epigenetic modifications, especially DNA methylation, are key regulators involved in this process. Regular fluctuations in global DNA methylation levels have been shown to accurately estimate biological age and disease prognosis. In this review, we discuss recent findings regarding the relationship between variations in DNA methylation level patterns and aging. In addition, we introduce the known mechanisms by which DNA methylation regulators affect aging and related diseases. As more studies uncover the mechanisms by which DNA methylation regulates aging, antiaging interventions and treatments for related diseases may be developed that enable human life extension.
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Chouliaras L, Kumar GS, Thomas AJ, Lunnon K, Chinnery PF, O'Brien JT. Epigenetic regulation in the pathophysiology of Lewy body dementia. Prog Neurobiol 2020; 192:101822. [PMID: 32407744 DOI: 10.1016/j.pneurobio.2020.101822] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 04/09/2020] [Accepted: 05/06/2020] [Indexed: 12/18/2022]
Abstract
Lewy body dementia encompasses both dementia with Lewy bodies and Parkinson's disease dementia. Although both are common causes of dementia, they remain relatively understudied. The review summarises the clinico-pathologic characteristics of Lewy Body dementia and discusses the genetic and environmental evidence contributing to the risk of developing the condition. Considering that the pathophysiology of Lewy body dementia is not yet fully understood, here we focus on the role of epigenetic mechanisms as potential key mediators of gene-environment interactions in the development of the disease. We examine available important data on genomics, epigenomics, gene expression and proteomic studies in Lewy body dementia on human post-mortem brain and peripheral tissues. Genetic variation and epigenetic modifications in key genes involved in the disorder, such as apolipoprotein E (APOE), α-synuclein (SNCA) and glucocerobrosidase (GBA), suggest a central involvement of epigenetics in DLB but conclusive evidence is scarce. This is due to limitations of existing literature, such as small sample sizes, lack of replication and lack of studies interrogating cell-type specific epigenetic modifications in the brain. Future research in the field can improve the understanding of this common but complex and rapidly progressing type of dementia and potentially open early diagnostic and effective therapeutic targets.
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Affiliation(s)
| | - Gautham S Kumar
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Alan J Thomas
- Institute of Neuroscience, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, UK
| | - Katie Lunnon
- College of Medicine and Health, University of Exeter Medical School, Exeter University, Exeter, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences and MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - John T O'Brien
- Department of Psychiatry, University of Cambridge, Cambridge, UK
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Liu R, Chen L, Wang Z, Zheng X, Wang Y, Li H, Noda M, Liu J, Long J. Downregulation of the DNA 5-hydroxymethylcytosine is involved in mitochondrial dysfunction and neuronal impairment in high fat diet-induced diabetic mice. Free Radic Biol Med 2020; 148:42-51. [PMID: 31899342 DOI: 10.1016/j.freeradbiomed.2019.12.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/26/2019] [Accepted: 12/26/2019] [Indexed: 12/22/2022]
Abstract
DNA 5-hydroxymethylcytosine (5hmC), converted from 5-methylcytosine (5mC), is highly enriched in the central nervous system and is dynamically regulated during neural development and metabolic disorders. However, whether and how neural 5hmC is involved in metabolic disorders shows little evidence. In this study, significant downregulation of the DNA 5hmC were observed in the cerebral cortex of HFD-induced diabetic mice, while phosphated AMP-activated protein kinase (p-AMPK) and ten-eleven translocation 2 (TET2) reduced, and mitochondrial dysfunction. We futher demonstrated that dysregulation of 5hmC preceded mitochondrial dysfunction in palmitic acid-treated HT22 cells and decreased level of 5hmC led to mitochondrial respiratory activity and apoptosis in HT22 cells. Taken together, our results reveal that neural 5hmC undergoes remodeling during HFD-induced metabolic disorder, and 5hmC downregulation significantly impacts on mitochondrial respiration and cell apoptosis. This study suggests a novel link between metabolic disorder and neural impairment through neural DNA 5hmC remodeling and resultant mitochondrial dysfunction.
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Affiliation(s)
- Run Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Lei Chen
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China; Institute of Nutrition & Health, Qingdao University, 308 Ningxia Road, Qingdao, 266071, China
| | - Zhen Wang
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xuewei Zheng
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yan Wang
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Hua Li
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Mami Noda
- Laboratory of Pathophysiology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Jiankang Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Jiangang Long
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.
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Ferrucci L, Gonzalez‐Freire M, Fabbri E, Simonsick E, Tanaka T, Moore Z, Salimi S, Sierra F, de Cabo R. Measuring biological aging in humans: A quest. Aging Cell 2020; 19:e13080. [PMID: 31833194 PMCID: PMC6996955 DOI: 10.1111/acel.13080] [Citation(s) in RCA: 307] [Impact Index Per Article: 76.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/22/2019] [Accepted: 10/27/2019] [Indexed: 12/16/2022] Open
Abstract
The global population of individuals over the age of 65 is growing at an unprecedented rate and is expected to reach 1.6 billion by 2050. Most older individuals are affected by multiple chronic diseases, leading to complex drug treatments and increased risk of physical and cognitive disability. Improving or preserving the health and quality of life of these individuals is challenging due to a lack of well-established clinical guidelines. Physicians are often forced to engage in cycles of "trial and error" that are centered on palliative treatment of symptoms rather than the root cause, often resulting in dubious outcomes. Recently, geroscience challenged this view, proposing that the underlying biological mechanisms of aging are central to the global increase in susceptibility to disease and disability that occurs with aging. In fact, strong correlations have recently been revealed between health dimensions and phenotypes that are typical of aging, especially with autophagy, mitochondrial function, cellular senescence, and DNA methylation. Current research focuses on measuring the pace of aging to identify individuals who are "aging faster" to test and develop interventions that could prevent or delay the progression of multimorbidity and disability with aging. Understanding how the underlying biological mechanisms of aging connect to and impact longitudinal changes in health trajectories offers a unique opportunity to identify resilience mechanisms, their dynamic changes, and their impact on stress responses. Harnessing how to evoke and control resilience mechanisms in individuals with successful aging could lead to writing a new chapter in human medicine.
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Affiliation(s)
- Luigi Ferrucci
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
| | - Marta Gonzalez‐Freire
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
| | - Elisa Fabbri
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
- Department of Medical and Surgical SciencesUniversity of BolognaBolognaItaly
| | - Eleanor Simonsick
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
| | - Toshiko Tanaka
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
| | - Zenobia Moore
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
| | - Shabnam Salimi
- Department of Epidemiology and Public HealthUniversity of Maryland School of MedicineBaltimoreMDUSA
| | - Felipe Sierra
- Division of Aging BiologyNational Institute on AgingNIHBethesdaMDUSA
| | - Rafael de Cabo
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
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Qin L, Xu Q, Li Z, Chen L, Li Y, Yang N, Liu Z, Guo J, Shen L, Allen EG, Chen C, Ma C, Wu H, Zhu X, Jin P, Tang B. Ethnicity-specific and overlapping alterations of brain hydroxymethylome in Alzheimer's disease. Hum Mol Genet 2020; 29:149-158. [PMID: 31814020 PMCID: PMC7001720 DOI: 10.1093/hmg/ddz273] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/30/2019] [Accepted: 11/04/2019] [Indexed: 01/06/2023] Open
Abstract
5-Methylcytosine (5mC), generated through the covalent addition of a methyl group to the fifth carbon of cytosine, is the most prevalent DNA modification in humans and functions as a critical player in the regulation of tissue and cell-specific gene expression. 5mC can be oxidized to 5-hydroxymethylcytosine (5hmC) by ten-eleven translocation (TET) enzymes, which is enriched in brain. Alzheimer's disease (AD) is the most common neurodegenerative disorder, and several studies using the samples collected from Caucasian cohorts have found that epigenetics, particularly cytosine methylation, could play a role in the etiological process of AD. However, little research has been conducted using the samples of other ethnic groups. Here we generated genome-wide profiles of both 5mC and 5hmC in human frontal cortex tissues from late-onset Chinese AD patients and cognitively normal controls. We identified both Chinese-specific and overlapping differentially hydroxymethylated regions (DhMRs) with Caucasian cohorts. Pathway analyses revealed specific pathways enriched among Chinese-specific DhMRs, as well as the shared DhMRs with Caucasian cohorts. Furthermore, two important transcription factor-binding motifs, hypoxia-inducible factor 2α (HIF2α) and hypoxia-inducible factor 1α (HIF1α), were enriched in the DhMRs. Our analyses provide the first genome-wide profiling of DNA hydroxymethylation of the frontal cortex of AD patients from China, emphasizing an important role of 5hmC in AD pathogenesis and highlighting both ethnicity-specific and overlapping changes of brain hydroxymethylome in AD.
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Affiliation(s)
- Lixia Qin
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders (XIANGYA), Changsha, Hunan 410078, China
| | - Ziyi Li
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA 30322, USA
| | - Li Chen
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yujing Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nannan Yang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhenhua Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders (XIANGYA), Changsha, Hunan 410078, China
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders (XIANGYA), Changsha, Hunan 410078, China
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
| | - Emily G Allen
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Chao Chen
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Chao Ma
- Department of Human Anatomy, Histology and Embryology, Institute of Basic Medical Sciences, Neuroscience Center, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100000, China
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA 30322, USA
| | - Xiongwei Zhu
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National Clinical Research Center for Geriatric Disorders (XIANGYA), Changsha, Hunan 410078, China
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
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Lardenoije R, Roubroeks JAY, Pishva E, Leber M, Wagner H, Iatrou A, Smith AR, Smith RG, Eijssen LMT, Kleineidam L, Kawalia A, Hoffmann P, Luck T, Riedel-Heller S, Jessen F, Maier W, Wagner M, Hurlemann R, Kenis G, Ali M, del Sol A, Mastroeni D, Delvaux E, Coleman PD, Mill J, Rutten BPF, Lunnon K, Ramirez A, van den Hove DLA. Alzheimer's disease-associated (hydroxy)methylomic changes in the brain and blood. Clin Epigenetics 2019; 11:164. [PMID: 31775875 PMCID: PMC6880587 DOI: 10.1186/s13148-019-0755-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/26/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Late-onset Alzheimer's disease (AD) is a complex multifactorial affliction, the pathogenesis of which is thought to involve gene-environment interactions that might be captured in the epigenome. The present study investigated epigenome-wide patterns of DNA methylation (5-methylcytosine, 5mC) and hydroxymethylation (5-hydroxymethylcytosine, 5hmC), as well as the abundance of unmodified cytosine (UC), in relation to AD. RESULTS We identified epigenetic differences in AD patients (n = 45) as compared to age-matched controls (n = 35) in the middle temporal gyrus, pertaining to genomic regions close to or overlapping with genes such as OXT (- 3.76% 5mC, pŠidák = 1.07E-06), CHRNB1 (+ 1.46% 5hmC, pŠidák = 4.01E-04), RHBDF2 (- 3.45% UC, pŠidák = 4.85E-06), and C3 (- 1.20% UC, pŠidák = 1.57E-03). In parallel, in an independent cohort, we compared the blood methylome of converters to AD dementia (n = 54) and non-converters (n = 42), at a preclinical stage. DNA methylation in the same region of the OXT promoter as found in the brain was found to be associated with subsequent conversion to AD dementia in the blood of elderly, non-demented individuals (+ 3.43% 5mC, pŠidák = 7.14E-04). CONCLUSIONS The implication of genome-wide significant differential methylation of OXT, encoding oxytocin, in two independent cohorts indicates it is a promising target for future studies on early biomarkers and novel therapeutic strategies in AD.
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Affiliation(s)
- Roy Lardenoije
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Janou A. Y. Roubroeks
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Ehsan Pishva
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Markus Leber
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, 50937 Cologne, Germany
| | - Holger Wagner
- Department of Neurodegeneration and Gerontopsychiatry, University of Bonn, 53127 Bonn, Germany
| | - Artemis Iatrou
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
| | - Adam R. Smith
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Rebecca G. Smith
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Lars M. T. Eijssen
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
- Department of Bioinformatics—BiGCaT, Maastricht University, Maastricht, The Netherlands
| | - Luca Kleineidam
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, 50937 Cologne, Germany
- Department of Neurodegeneration and Gerontopsychiatry, University of Bonn, 53127 Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Amit Kawalia
- Department of Neurodegeneration and Gerontopsychiatry, University of Bonn, 53127 Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany
- Division of Medical Genetics, University Hospital and Department of Biomedicine, University of Basel, CH-4058 Basel, Switzerland
| | - Tobias Luck
- Institute of Social Medicine, Occupational Health and Public Health, University of Leipzig, 04103 Leipzig, Germany
| | - Steffi Riedel-Heller
- Institute of Social Medicine, Occupational Health and Public Health, University of Leipzig, 04103 Leipzig, Germany
| | - Frank Jessen
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
- Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, 50937 Cologne, Germany
| | - Wolfgang Maier
- Department of Neurodegeneration and Gerontopsychiatry, University of Bonn, 53127 Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Michael Wagner
- Department of Neurodegeneration and Gerontopsychiatry, University of Bonn, 53127 Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - René Hurlemann
- Department of Psychiatry and Division of Medical Psychology, University of Bonn, 53105 Bonn, Germany
| | - Gunter Kenis
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
| | - Muhammad Ali
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Antonio del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russian Federation
- CIC bioGUNE, Bizkaia Technology Park, 801 Building, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Dolgoprudny Bilbao, Spain
| | - Diego Mastroeni
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
- L.J. Roberts Center for Alzheimer’s Research Banner Sun Health Research Institute, Sun City, AZ USA
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ USA
| | - Elaine Delvaux
- L.J. Roberts Center for Alzheimer’s Research Banner Sun Health Research Institute, Sun City, AZ USA
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ USA
| | - Paul D. Coleman
- L.J. Roberts Center for Alzheimer’s Research Banner Sun Health Research Institute, Sun City, AZ USA
- Biodesign Institute, Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ USA
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
- Institute of Psychiatry, King’s College London, London, UK
| | - Bart P. F. Rutten
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
| | - Katie Lunnon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Alfredo Ramirez
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, 50937 Cologne, Germany
- Department of Neurodegeneration and Gerontopsychiatry, University of Bonn, 53127 Bonn, Germany
| | - Daniël L. A. van den Hove
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands
- Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
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Malloy MA, Kochmanski JJ, Jones TR, Colacino JA, Goodrich JM, Dolinoy DC, Svoboda LK. Perinatal Bisphenol A Exposure and Reprogramming of Imprinted Gene Expression in the Adult Mouse Brain. Front Genet 2019; 10:951. [PMID: 31649729 PMCID: PMC6796247 DOI: 10.3389/fgene.2019.00951] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/05/2019] [Indexed: 12/11/2022] Open
Abstract
Genomic imprinting, a phenomenon by which genes are expressed in a monoallelic, parent-of-origin-dependent fashion, is critical for normal brain development. Expression of imprinted genes is regulated via epigenetic mechanisms, including DNA methylation (5-methylcytosine, 5mC), and disruptions in imprinting can lead to disease. Early-life exposure to the endocrine disrupting chemical bisphenol A (BPA) is associated with abnormalities in brain development and behavior, as well as with disruptions in epigenetic patterning, including 5mC and DNA hydroxymethylation (5-hydroxymethylcytosine, 5hmC). Using an established mouse model of perinatal environmental exposure, the objective of this study was to examine the effects of perinatal BPA exposure on epigenetic regulation of imprinted gene expression in adult mice. Two weeks prior to mating, dams were assigned to control chow or chow containing an environmentally relevant dose (50 µg/kg) of BPA. Exposure continued until offspring were weaned at post-natal day 21, and animals were followed until 10 months of age. Expression of three imprinted genes—Pde10a, Ppp1r9a, and Kcnq1, as well as three genes encoding proteins critical for regulation of 5mC and 5hmC—Dnmt1, Tet1, and Tet2, were evaluated in the right cortex and midbrain using qRT-PCR. Perinatal BPA exposure was associated with a significant increase in adult Kcnq1 (p = 0.04) and Dnmt1 (p = 0.02) expression in the right cortex, as well as increased expression of Tet2 in the midbrain (p = 0.03). Expression of Tet2 and Kcnq1 were positively correlated in the midbrain. Analysis of 5mC and 5hmC at the Kcnq1 locus was conducted in parallel samples using standard and oxidative bisulfite conversion followed by pyrosequencing. This analysis revealed enrichment of both 5mC and 5hmC at this locus in both brain regions. No significant changes in 5mC and 5hmC at Kcnq1 were observed with perinatal BPA exposure. Together, these data suggest that perinatal BPA exposure results in altered expression of Kcnq1, Dnmt1, and Tet2 in the adult mouse brain. Further studies with larger sample sizes are necessary to understand the mechanistic basis for these changes, as well as to determine the implications they have for brain development and function.
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Affiliation(s)
- Maureen A Malloy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Joseph J Kochmanski
- Department of Translational Science & Molecular Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Tamara R Jones
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States.,Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Laurie K Svoboda
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
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Johnson ND, Huang L, Li R, Li Y, Yang Y, Kim HR, Grant C, Wu H, Whitsel EA, Kiel DP, Baccarelli AA, Jin P, Murabito JM, Conneely KN. Age-related DNA hydroxymethylation is enriched for gene expression and immune system processes in human peripheral blood. Epigenetics 2019; 15:294-306. [PMID: 31506003 DOI: 10.1080/15592294.2019.1666651] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
DNA methylation (DNAm) has a well-established association with age in many tissues, including peripheral blood mononuclear cells (PBMCs). Compared to DNAm, the closely related epigenetic modification known as DNA hydroxymethylation (DNAhm) was much more recently discovered in mammals. Preliminary investigations have observed a positive correlation between gene body DNAhm and cis-gene expression. While some of these studies have observed an association between age and global DNAhm, none have investigated region-specific age-related DNAhm in human blood samples. In this study, we investigated DNAhm and gene expression in PBMCs of 10 young and 10 old, healthy female volunteers. Thousands of regions were differentially hydroxymethylated in the old vs. young individuals in gene bodies, exonic regions, enhancers, and promoters. Consistent with previous work, we observed directional consistency between age-related differences in DNAhm and gene expression. Further, age-related DNAhm and genes with high levels of DNAhm were enriched for immune system processes which may support a role of age-related DNAhm in immunosenescence.
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Affiliation(s)
- Nicholas D Johnson
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA, USA
| | - Luoxiu Huang
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Ronghua Li
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.,Department of Biostatistics, Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Yuchen Yang
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Hye Rim Kim
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Cancer Biology Graduate Program, Emory University, Atlanta, GA, USA
| | - Crystal Grant
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA, USA
| | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA.,Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Douglas P Kiel
- Hebrew SeniorLife, Department of Medicine Beth Israel Deaconess Medical Center and Harvard Medical School, Hinda and Arthur Marcus Institute for Aging Research, Boston, MA, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Peng Jin
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Joanne M Murabito
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, USA.,Section of General Internal Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Karen N Conneely
- Department of Human Genetics, Emory University, Atlanta, GA, USA.,Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA, USA
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46
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Zhang Y, Zhang Y, Chen D, Wang C, Chen L, Gao C, Fan W, Shi J, Zhang J, Li B. Genome-Wide Alteration of 5-Hydroxymethylcytosine in Hypoxic-Ischemic Neonatal Rat Model of Cerebral Palsy. Front Mol Neurosci 2019; 12:214. [PMID: 31551709 PMCID: PMC6737274 DOI: 10.3389/fnmol.2019.00214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 08/21/2019] [Indexed: 01/08/2023] Open
Abstract
Cerebral palsy (CP) is a neurodevelopmental disorder usually occurring early in life and persisting through the whole life. Several risk factors, including perinatal hypoxia-ischemia (HI), may contribute to occurrence of CP in preterm infants. DNA hydroxymethylation has been shown to play an important role in neurodevelopment and neurodegenerative disorders. However, the effect of DNA hydroxymethylation in CP remains unknown. The aim of this study is to explore whether and how DNA hydroxymethylation is involved in CP pathogenesis. We observed that overall 5-hydroxymethylcytosine (5hmC) abundance in the cortex of the temporal lobe of rat pups was decreased significantly after hypoxic-ischemic injury, and the reduced expression of Tet1 and Tet2 enzymes might be responsible for this change. Identified differential hydroxymethylation regions (DhMRs) were richly involved in multiple signaling pathways related to neuronal development and function. Furthermore, we found that reduced 5hmC modification on the DhMRs-related genes were accompanied by decrease of their mRNA expression levels. These results suggest that 5hmC modifications are involved in the CP pathogenesis and may potentially serve as a new therapeutic target.
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Affiliation(s)
- Yunpeng Zhang
- Research Center for Clinical Medicine, Jinshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Yaodong Zhang
- Department of Pediatrics, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Danmei Chen
- Research Center for Clinical Medicine, Jinshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Cuiting Wang
- Research Center for Clinical Medicine, Jinshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Long Chen
- Department of Neurology, Jinshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Chao Gao
- Department of Rehabilitation, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Wei Fan
- Research Center for Clinical Medicine, Jinshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Jimin Shi
- Research Center for Clinical Medicine, Jinshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Jihong Zhang
- Research Center for Clinical Medicine, Jinshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Bing Li
- Research Center for Clinical Medicine, Jinshan Hospital Affiliated to Fudan University, Shanghai, China
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47
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Konki M, Malonzo M, Karlsson IK, Lindgren N, Ghimire B, Smolander J, Scheinin NM, Ollikainen M, Laiho A, Elo LL, Lönnberg T, Röyttä M, Pedersen NL, Kaprio J, Lähdesmäki H, Rinne JO, Lund RJ. Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer's disease. Clin Epigenetics 2019; 11:130. [PMID: 31477183 PMCID: PMC6721173 DOI: 10.1186/s13148-019-0729-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/16/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Alzheimer's disease results from a neurodegenerative process that starts well before the diagnosis can be made. New prognostic or diagnostic markers enabling early intervention into the disease process would be highly valuable. Environmental and lifestyle factors largely modulate the disease risk and may influence the pathogenesis through epigenetic mechanisms, such as DNA methylation. As environmental and lifestyle factors may affect multiple tissues of the body, we hypothesized that the disease-associated DNA methylation signatures are detectable in the peripheral blood of discordant twin pairs. RESULTS Comparison of 23 disease discordant Finnish twin pairs with reduced representation bisulfite sequencing revealed peripheral blood DNA methylation differences in 11 genomic regions with at least 15.0% median methylation difference and FDR adjusted p value ≤ 0.05. Several of the affected genes are primarily associated with neuronal functions and pathologies and do not display disease-associated differences in gene expression in blood. The DNA methylation mark in ADARB2 gene was found to be differentially methylated also in the anterior hippocampus, including entorhinal cortex, of non-twin cases and controls. Targeted bisulfite pyrosequencing of the DNA methylation mark in ADARB2 gene in 62 Finnish and Swedish twin pairs revealed that, in addition to the disease status, DNA methylation of this region is influenced by gender, age, zygosity, APOE genotype, and smoking. Further analysis of 120 Swedish twin pairs indicated that this specific DNA methylation mark is not predictive for Alzheimer's disease and becomes differentially methylated after disease onset. CONCLUSIONS DNA methylation differences can be detected in the peripheral blood of twin pairs discordant for Alzheimer's disease. These DNA methylation signatures may have value as disease markers and provide insights into the molecular mechanisms of pathogenesis. We found no evidence that the DNA methylation marks would be associated with gene expression in blood. Further studies are needed to elucidate the potential importance of the associated genes in neuronal functions and to validate the prognostic or diagnostic value of the individual marks or marker panels.
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Affiliation(s)
- Mikko Konki
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland.,Turku Doctoral Programme of Molecular Medicine, University of Turku, FI-20014, Turku, Finland
| | - Maia Malonzo
- Department of Computer Science, Aalto University School of Science, FI-00076, Helsinki, Finland
| | - Ida K Karlsson
- Institute of Gerontology and Aging Research Network-Jönköping (ARN-J), School of Health and Welfare, Jönköping University, SE-55111, Jönköping, Sweden.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177, Stockholm, Sweden
| | - Noora Lindgren
- Drug Research Doctoral Program, University of Turku, FI-20014, Turku, Finland.,Turku PET Centre, University of Turku, FI-20520, Turku, Finland
| | - Bishwa Ghimire
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland.,Institute for Molecular Medicine Finland, University of Helsinki, FI-00014, Helsinki, Finland
| | - Johannes Smolander
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland
| | - Noora M Scheinin
- Turku PET Centre, University of Turku, FI-20520, Turku, Finland.,Turku Brain and Mind Center, FinnBrain Birth Cohort Study, Institute of Clinical Medicine, University of Turku, FI-20014, Turku, Finland.,Department of Psychiatry, University of Turku and Turku University Hospital, FI-20014, Turku, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland, University of Helsinki, FI-00014, Helsinki, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland
| | - Tapio Lönnberg
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland
| | - Matias Röyttä
- Department of Pathology/Neuropathology, Turku University Hospital, University of Turku, FI-20014, Turku, Finland
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-17177, Stockholm, Sweden.,Department of Psychology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, FI-00014, Helsinki, Finland.,Department of Public Health, University of Helsinki, FI-00271, Helsinki, Finland
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University School of Science, FI-00076, Helsinki, Finland
| | - Juha O Rinne
- Turku PET Centre, University of Turku, FI-20520, Turku, Finland.,Division of Clinical Neurosciences, Turku University Hospital, FI-20014, Turku, Finland
| | - Riikka J Lund
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FIN-20520, Turku, Finland.
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48
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Fetahu IS, Ma D, Rabidou K, Argueta C, Smith M, Liu H, Wu F, Shi YG. Epigenetic signatures of methylated DNA cytosine in Alzheimer's disease. SCIENCE ADVANCES 2019; 5:eaaw2880. [PMID: 31489368 PMCID: PMC6713504 DOI: 10.1126/sciadv.aaw2880] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 07/18/2019] [Indexed: 05/23/2023]
Abstract
Alzheimer's disease (AD), a progressive neurodegenerative disorder, is the most common untreatable form of dementia. Identifying molecular biomarkers that allow early detection remains a key challenge in the diagnosis, treatment, and prognostic evaluation of the disease. Here, we report a novel experimental and analytical model characterizing epigenetic alterations during AD onset and progression. We generated the first integrated base-resolution genome-wide maps of the distribution of 5-methyl-cytosine (5mC), 5-hydroxymethyl-cytosine (5hmC), and 5-formyl/carboxy-cytosine (5fC/caC) in normal and AD neurons. We identified 27 AD region-specific and 39 CpG site-specific epigenetic signatures that were independently validated across our familial and sporadic AD models, and in an independent clinical cohort. Thus, our work establishes a new model and strategy to study the epigenetic alterations underlying AD onset and progression and provides a set of highly reliable AD-specific epigenetic signatures that may have early diagnostic and prognostic implications.
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Affiliation(s)
- Irfete S. Fetahu
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Dingailu Ma
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Kimberlie Rabidou
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Christian Argueta
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Michael Smith
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Hang Liu
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Feizhen Wu
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Yujiang G. Shi
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
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49
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Lutz MW, Sprague D, Chiba-Falek O. Bioinformatics strategy to advance the interpretation of Alzheimer's disease GWAS discoveries: The roads from association to causation. Alzheimers Dement 2019; 15:1048-1058. [PMID: 31262699 PMCID: PMC6699885 DOI: 10.1016/j.jalz.2019.04.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 03/20/2019] [Accepted: 04/17/2019] [Indexed: 11/16/2022]
Abstract
INTRODUCTION Genome-wide association studies (GWAS) discovered multiple late-onset Alzheimer's disease (LOAD)-associated SNPs and inferred the genes based on proximity; however, the actual causal genes are yet to be identified. METHODS We defined LOAD-GWAS regions by the most significantly associated SNP ±0.5 Mb and developed a bioinformatics pipeline that uses and integrates chromatin state segmentation track to map active enhancers and virtual 4C software to visualize interactions between active enhancers and gene promoters. We augmented our pipeline with biomedical and functional information. RESULTS We applied the bioinformatics pipeline using three ∼1 Mb LOAD-GWAS loci: BIN1, PICALM, CELF1. These loci contain 10-24 genes, an average of 106 active enhancers and 80 CTCF sites. Our strategy identified all genes corresponding to the promoters that interact with the active enhancer that is closest to the LOAD-GWAS-SNP and generated a shorter list of prioritized candidate LOAD genes (5-14/loci), feasible for post-GWAS investigations of causality. DISCUSSION Interpretation of LOAD-GWAS discoveries requires the integration of brain-specific functional genomic data sets and information related to regulatory activity.
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Affiliation(s)
- Michael W Lutz
- Department of Neurology, Duke University Medical Center, Durham, NC, USA
| | - Daniel Sprague
- Department of Neurology, Duke University Medical Center, Durham, NC, USA; Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA
| | - Ornit Chiba-Falek
- Department of Neurology, Duke University Medical Center, Durham, NC, USA; Center for Genomic and Computational Biology, Duke University Medical Center, Durham, NC, USA.
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50
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Hydrazones as novel epigenetic modulators: Correlation between TET 1 protein inhibition activity and their iron(II) binding ability. Bioorg Chem 2019; 88:102809. [DOI: 10.1016/j.bioorg.2019.02.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/16/2019] [Accepted: 02/15/2019] [Indexed: 02/06/2023]
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