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Jain N, Li JL, Tong L, Jasmine F, Kibriya MG, Demanelis K, Oliva M, Chen LS, Pierce BL. DNA methylation correlates of chronological age in diverse human tissue types. Epigenetics Chromatin 2024; 17:25. [PMID: 39118140 PMCID: PMC11308253 DOI: 10.1186/s13072-024-00546-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/15/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND While the association of chronological age with DNA methylation (DNAm) in whole blood has been extensively studied, the tissue-specificity of age-related DNAm changes remains an active area of research. Studies investigating the association of age with DNAm in tissues such as brain, skin, immune cells, fat, and liver have identified tissue-specific and non-specific effects, thus, motivating additional studies of diverse human tissue and cell types. RESULTS Here, we performed an epigenome-wide association study, leveraging DNAm data (Illumina EPIC array) from 961 tissue samples representing 9 tissue types (breast, lung, colon, ovary, prostate, skeletal muscle, testis, whole blood, and kidney) from the Genotype-Tissue Expression (GTEx) project. We identified age-associated CpG sites (false discovery rate < 0.05) in 8 tissues (all except skeletal muscle, n = 47). This included 162,002 unique hypermethylated and 90,626 hypomethylated CpG sites across all tissue types, with 130,137 (80%) hypermethylated CpGs and 74,703 (82%) hypomethylated CpG sites observed in a single tissue type. While the majority of age-associated CpG sites appeared tissue-specific, the patterns of enrichment among genomic features, such as chromatin states and CpG islands, were similar across most tissues, suggesting common mechanisms underlying cellular aging. Consistent with previous findings, we observed that hypermethylated CpG sites are enriched in regions with repressed polycomb signatures and CpG islands, while hypomethylated CpG sites preferentially occurred in non-CpG islands and enhancers. To gain insights into the functional effects of age-related DNAm changes, we assessed the correlation between DNAm and local gene expression changes to identify age-related expression quantitative trait methylation (age-eQTMs). We identified several age-eQTMs present in multiple tissue-types, including in the CDKN2A, HENMT1, and VCWE regions. CONCLUSION Overall, our findings will aid future efforts to develop biomarkers of aging and understand mechanisms of aging in diverse human tissue types.
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Affiliation(s)
- Niyati Jain
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - James L Li
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
- Interdisciplinary Scientist Training Program, University of Chicago, Chicago, IL, 60637, USA
| | - Lin Tong
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Farzana Jasmine
- Institute for Population and Precision Health (IPPH), Biological Sciences Division, University of Chicago, Chicago, IL, 60637, USA
| | - Muhammad G Kibriya
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Kathryn Demanelis
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15232, USA
| | - Meritxell Oliva
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
- Genomics Research Center, AbbVie, North Chicago, IL, 60064, USA
| | - Lin S Chen
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Brandon L Pierce
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
- Comprehensive Cancer Center, University of Chicago, Chicago, IL, 60637, USA.
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Lossi L, Castagna C, Merighi A. An Overview of the Epigenetic Modifications in the Brain under Normal and Pathological Conditions. Int J Mol Sci 2024; 25:3881. [PMID: 38612690 PMCID: PMC11011998 DOI: 10.3390/ijms25073881] [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: 03/10/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Epigenetic changes are changes in gene expression that do not involve alterations to the DNA sequence. These changes lead to establishing a so-called epigenetic code that dictates which and when genes are activated, thus orchestrating gene regulation and playing a central role in development, health, and disease. The brain, being mostly formed by cells that do not undergo a renewal process throughout life, is highly prone to the risk of alterations leading to neuronal death and neurodegenerative disorders, mainly at a late age. Here, we review the main epigenetic modifications that have been described in the brain, with particular attention on those related to the onset of developmental anomalies or neurodegenerative conditions and/or occurring in old age. DNA methylation and several types of histone modifications (acetylation, methylation, phosphorylation, ubiquitination, sumoylation, lactylation, and crotonylation) are major players in these processes. They are directly or indirectly involved in the onset of neurodegeneration in Alzheimer's or Parkinson's disease. Therefore, this review briefly describes the roles of these epigenetic changes in the mechanisms of brain development, maturation, and aging and some of the most important factors dynamically regulating or contributing to these changes, such as oxidative stress, inflammation, and mitochondrial dysfunction.
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Affiliation(s)
| | | | - Adalberto Merighi
- Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco, Italy; (L.L.); (C.C.)
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Fila M, Pawlowska E, Szczepanska J, Blasiak J. Different Aspects of Aging in Migraine. Aging Dis 2023; 14:2028-2050. [PMID: 37199585 PMCID: PMC10676778 DOI: 10.14336/ad.2023.0313] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/13/2023] [Indexed: 05/19/2023] Open
Abstract
Migraine is a common neurological disease displaying an unusual dependence on age. For most patients, the peak intensity of migraine headaches occurs in 20s and lasts until 40s, but then headache attacks become less intense, occur less frequently and the disease is more responsive to therapy. This relationship is valid in both females and males, although the prevalence of migraine in the former is 2-4 times greater than the latter. Recent concepts present migraine not only as a pathological event, but rather as a part of evolutionary adaptive response to protect organism against consequences of stress-induced brain energy deficit. However, these concepts do not fully explain that unusual dependence of migraine prevalence on age. Many aspects of aging, both molecular/cellular and social/cognitive, are interwound in migraine pathogenesis, but they neither explain why only some persons are affected by migraine, nor suggest any causal relationship. In this narrative/hypothesis review we present information on associations of migraine with chronological aging, brain aging, cellular senescence, stem cell exhaustion as well as social, cognitive, epigenetic, and metabolic aging. We also underline the role of oxidative stress in these associations. We hypothesize that migraine affects only individuals who have inborn, genetic/epigenetic, or acquired (traumas, shocks or complexes) migraine predispositions. These predispositions weakly depend on age and affected individuals are more prone to migraine triggers than others. Although the triggers can be related to many aspects of aging, social aging may play a particularly important role as the prevalence of its associated stress has a similar age-dependence as the prevalence of migraine. Moreover, social aging was shown to be associated with oxidative stress, important in many aspects of aging. In perspective, molecular mechanisms underlying social aging should be further explored and related to migraine with a closer association with migraine predisposition and difference in prevalence by sex.
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Affiliation(s)
- Michal Fila
- Department of Developmental Neurology and Epileptology, Polish Mother’s Memorial Hospital Research Institute, 93-338 Lodz, Poland.
| | - Elzbieta Pawlowska
- Department of Pediatric Dentistry, Medical University of Lodz, 92-216 Lodz, Poland.
| | - Joanna Szczepanska
- Department of Pediatric Dentistry, Medical University of Lodz, 92-216 Lodz, Poland.
| | - Janusz Blasiak
- Department of Molecular Genetics, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland.
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Kim JP, Kim BH, Bice PJ, Seo SW, Bennett DA, Saykin AJ, Nho K. Integrative Co-methylation Network Analysis Identifies Novel DNA Methylation Signatures and Their Target Genes in Alzheimer's Disease. Biol Psychiatry 2023; 93:842-851. [PMID: 36150909 PMCID: PMC9789210 DOI: 10.1016/j.biopsych.2022.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 06/16/2022] [Accepted: 06/16/2022] [Indexed: 12/26/2022]
Abstract
BACKGROUND DNA methylation is a key epigenetic marker, and its alternations may be involved in Alzheimer's disease (AD). CpGs sharing similar biological functions or pathways tend to be co-methylated. METHODS We performed an integrative network-based DNA methylation analysis on 2 independent cohorts (N = 941) using brain DNA methylation profiles and RNA-sequencing as well as AD pathology data. RESULTS Weighted co-methylation network analysis identified 6 modules as significantly associated with neuritic plaque burden. In total, 15 hub CpGs including 3 novel CpGs were identified and replicated as being significantly associated with AD pathology. Furthermore, we identified and replicated 4 target genes (ATP6V1G2, VCP, RAD52, and LST1) as significantly regulated by DNA methylation at hub CpGs. In particular, VCP gene expression was also associated with AD pathology in both cohorts. CONCLUSIONS This integrative network-based multiomics study provides compelling evidence for a potential role of DNA methylation alternations and their target genes in AD.
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Affiliation(s)
- Jun Pyo Kim
- Center for Neuroimaging, Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana; Medical Research Institute, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Bo-Hyun Kim
- Department of Biomedical Engineering, Hanyang University, Seoul, Korea
| | - Paula J Bice
- Center for Neuroimaging, Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana; Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, Indiana
| | - Sang Won Seo
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois
| | - Andrew J Saykin
- Center for Neuroimaging, Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana; Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, Indiana; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Kwangsik Nho
- Center for Neuroimaging, Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, Indiana; Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, Indianapolis, Indiana; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana.
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MGMT Promoter Methylation as a Prognostic Factor in Primary Glioblastoma: A Single-Institution Observational Study. Biomedicines 2022; 10:biomedicines10082030. [PMID: 36009577 PMCID: PMC9405779 DOI: 10.3390/biomedicines10082030] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Glioblastoma is the most malignant central nervous system tumor, which represents 50% of all glial tumors. The understanding of glioma genesis, prognostic evaluation, and treatment planning has been significantly enhanced by the discovery of molecular genetic biomarkers. This study aimed to evaluate survival in patients with primary glioblastoma concerning O6-methylguanine–DNA methyltransferase (MGMT) promoter methylation and other clinical factors. The study included 41 newly diagnosed glioblastoma patients treated from 2011 to 2014 in the 10th Military Research Hospital and Polyclinic, Poland. All patients underwent surgical resection followed by radiation and chemotherapy with alkylating agents. The MGMT promoter methylation was evaluated in all patients, and 43% were found to be methylated. In 26 and 15 cases, gross total resection and subtotal resection were conducted, respectively. Patients with a methylated MGMT promoter had a median survival of 504 days, while those without methylation had a median survival of 329 days. The group that was examined had a median age of 53. In a patient group younger than 53 years, those with methylation had significantly longer overall survival (639 days), compared to 433.5 days for patients without methylation. The most prolonged survival (551 days) was in patients with MGMT promoter methylation after gross total resection. The value of MGMT promoter methylation as a predictive biomarker is widely acknowledged. However, its prognostic significance remains unclear. Our findings proved that MGMT promoter methylation is also an essential positive prognostic biomarker.
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Tay EXY, Chia K, Ong DST. Epigenetic plasticity and redox regulation of neural stem cell state and fate. Free Radic Biol Med 2021; 170:116-130. [PMID: 33684459 DOI: 10.1016/j.freeradbiomed.2021.02.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 01/20/2021] [Accepted: 02/24/2021] [Indexed: 12/16/2022]
Abstract
The neural stem cells (NSCs) are essential for normal brain development and homeostasis. The cell state (i.e. quiescent versus activated) and fate (i.e. the cell lineage of choice upon differentiation) of NSCs are tightly controlled by various redox and epigenetic regulatory mechanisms. There is an increasing appreciation that redox and epigenetic regulations are intimately linked, but how this redox-epigenetics crosstalk affects NSC activity remains poorly understood. Another unresolved topic is whether the NSCs actually contribute to brain ageing and neurodegenerative diseases. In this review, we aim to 1) distill concepts that underlie redox and epigenetic regulation of NSC state and fate; 2) provide examples of the redox-epigenetics crosstalk in NSC biology; and 3) highlight potential redox- and epigenetic-based therapeutic opportunities to rescue NSC dysfunctions in ageing and neurodegenerative diseases.
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Affiliation(s)
- Emmy Xue Yun Tay
- Department of Physiology, National University of Singapore, Singapore, 117593, Singapore
| | - Kimberly Chia
- Department of Physiology, National University of Singapore, Singapore, 117593, Singapore
| | - Derrick Sek Tong Ong
- Department of Physiology, National University of Singapore, Singapore, 117593, Singapore; Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore; National Neuroscience Institute, Singapore, 308433, Singapore.
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Gao L, Li J, Yan M, Aili M. Methylation factor MRPL15 identified as a potential biological target in Alzheimer's disease. Aging (Albany NY) 2021; 13:13560-13570. [PMID: 34016794 PMCID: PMC8202902 DOI: 10.18632/aging.202862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/03/2020] [Indexed: 12/12/2022]
Abstract
Alzheimer’s disease (AD) is the most common form of dementia. However, the molecular basis of the development and progression of AD is still unclear. To elucidate the molecular processes related to AD, we obtained the expression profiles and analyzed the differentially expressed genes (DEGs). The genes potentially involved in the AD process were identified by PPI network and STEM analysis. The molecular mechanisms related to the recognition of AD were determined by GSEA and enrichment analysis. The differences from immune cells in AD were calculated. The methylation factors were identified by methylation difference analysis. Among them, MRPL15 was identified as suitable for diagnosing AD. Its expression trend had been verified in GSE5281. Importantly, MRPL15 was also a methylation factor. In addition, macrophages and neutrophils were up-regulated in AD patients. This was consistent with previous immune inflammation responses identified as being involved in the development of AD. The results of the present study revealed the genetic changes and molecular mechanisms involved in the process of the development and deterioration of AD patients. The potential AD risk genes and potential biological targets were identified. It provided evidence that immune inflammation and immune cells play an important role in AD.
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Affiliation(s)
- Li Gao
- Prescription Laboratory of Xinjiang Traditional Uyghur Medicine, Xinjiang Institute of Traditional Uighur Medicine, Urmuqi 830011, China
| | - Jianmei Li
- Prescription Laboratory of Xinjiang Traditional Uyghur Medicine, Xinjiang Institute of Traditional Uighur Medicine, Urmuqi 830011, China
| | - Ming Yan
- Prescription Laboratory of Xinjiang Traditional Uyghur Medicine, Xinjiang Institute of Traditional Uighur Medicine, Urmuqi 830011, China
| | - Maimaiti Aili
- Prescription Laboratory of Xinjiang Traditional Uyghur Medicine, Xinjiang Institute of Traditional Uighur Medicine, Urmuqi 830011, China
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The Effect of a Rat Diet Without Added Cu on Redox Status in Tissues and Epigenetic Changes in the Brain. ANNALS OF ANIMAL SCIENCE 2020. [DOI: 10.2478/aoas-2019-0075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
The aim of the study was to determine whether feeding rats a diet without added Cu increases oxidation of macromolecules in tissues, as well as epigenetic changes in the brain. The rats were divided into two groups: the Cu-6.5 group which was fed a diet with a standard content of Cu in mineral mixture – 6.5 mg Cu from CuCO3 per kg of diet; and the Cu-0 group which was fed a diet with a mineral mix without Cu supplementation. At the end of the experiment the rats were weighed and blood samples were collected. Finally, the rats were euthanized and then the liver, small intestine, spleen, kidneys, heart, brain, lung, testes and leg muscles were removed and weighed. In the blood of Cu-0 rats the lower Cp activity and greater GPx and CAT activity than in Cu-6.5 rats were noticed. In the liver, lungs, heart and testes of Cu-0 rats, a decreased content of Cu were noticed. Application of Cu-0 diets resulted in increased LOOH level in the small intestine, liver, and heart, as well as increased MDA content in the liver, spleen, lungs, brain and testes. The Cu-0 treatment caused a decrease in SOD activity in the heart, lungs and testes of the rats and a decrease in CAT activity in the small intestine. In the brain and testes of rats from the Cu-0 treatment, lower content of GSH + GSSG was observed. The brain of rats from the Cu-0 treatment showed an increase in the level of PCs, 8-OHdG, Casp 8 and DNA methylation. The research has shown that a deficiency of Cu in the diet impairs the body’s antioxidant defences, which in turn leads to increased lipid oxidation in the liver, small intestinal wall, heart, spleen, lungs, brain and testes, as well as to oxidation of proteins and DNA in the brain. A deficiency of Cu in the diet also increases methylation of cytosine in the brain.
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Lim WJ, Kim KH, Kim JY, Kim HJ, Kim M, Park JL, Yoon S, Oh JH, Cho JW, Kim YS, Kim N. Investigation of Gene Expression and DNA Methylation From Seven Different Brain Regions of a Crab-Eating Monkey as Determined by RNA-Seq and Whole-Genome Bisulfite Sequencing. Front Genet 2019; 10:694. [PMID: 31428131 PMCID: PMC6690020 DOI: 10.3389/fgene.2019.00694] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/02/2019] [Indexed: 01/04/2023] Open
Abstract
The crab-eating monkey is widely used in biomedical research for pharmacological experiments. Epigenetic regulation in the brain regions of primates involves complex patterns of DNA methylation. Previous studies of methylated CpG-binding domains using microarray technology or peak identification of sequence reads mostly focused on developmental stages or disease, rather than normal brains. To identify correlations between gene expression and DNA methylation levels that may be related to transcriptional regulation, we generated RNA-seq and whole-genome bisulfite sequencing data from seven different brain regions from a single crab-eating monkey. We identified 92 genes whose expression levels were significantly correlated, positively or negatively, with DNA methylation levels. Among them, 11 genes exhibited brain region-specific characteristics, and their expression patterns were strongly correlated with DNA methylation level. Nine genes (SLC2A5, MCM5, DRAM1, TTC12, DHX40, COR01A, LRAT, FLVCR2, and PTER) had effects on brain and eye function and development, and two (LHX6 and MEST) were previously identified as genes in which DNA methylation levels change significantly in the promoter region and are therefore considered brain epigenetic markers. Furthermore, we characterized DNA methylation of repetitive elements at the whole genome through repeat annotation at single-base resolution. Our results reveal the diverse roles of DNA methylation at single-base resolution throughout the genome and reflect the epigenetic variations in adult brain tissues.
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Affiliation(s)
- Won-Jun Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
| | - Kyoung Hyoun Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
| | - Jae-Yoon Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
| | - Hee-Jin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Mirang Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Jong-Lyul Park
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Seokjoo Yoon
- Predictive Toxicity Department, Korea Institute of Toxicology (KIT), Daejeon, South Korea
| | - Jung-Hwa Oh
- Predictive Toxicity Department, Korea Institute of Toxicology (KIT), Daejeon, South Korea
| | - Jae-Woo Cho
- Predictive Toxicity Department, Korea Institute of Toxicology (KIT), Daejeon, South Korea
| | - Yong Sung Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, South Korea
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DNA methylation in the human frontal cortex reveals a putative mechanism for age-by-disease interactions. Transl Psychiatry 2019; 9:39. [PMID: 30696804 PMCID: PMC6351569 DOI: 10.1038/s41398-019-0372-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 12/02/2018] [Accepted: 12/09/2018] [Indexed: 12/19/2022] Open
Abstract
A consistent gene set undergoes age-associated expression changes in the human cerebral cortex, and our Age-by-Disease Model posits that these changes contribute to psychiatric diseases by "pushing" the expression of disease-associated genes in disease-promoting directions. DNA methylation (DNAm) is an attractive candidate mechanism for age-associated gene expression changes. We used the Illumina HumanMethylation450 array to characterize genome-wide DNAm in the postmortem orbital frontal cortex from 20 younger (<42 years) and 19 older (>60 years) subjects. DNAm data were integrated with existing normal brain aging expression data and sets of psychiatric disease risk genes to test the hypothesis that age-associated DNAm changes contribute to age-associated gene expression changes and, by extension, susceptibility to psychiatric diseases. We found that age-associated differentially methylated regions (aDMRs) are common, robust, bidirectional, concentrated in CpG island shelves and sea, depleted in CpG islands, and enriched among genes undergoing age-associated expression changes (OR = 2.30, p = 1.69 × 10-27). We found the aDMRs are enriched among genetic association-based risk genes for schizophrenia, Alzheimer's disease (AD), and major depressive disorder (MDD) (OR = 2.51, p = 0.00015; OR = 2.38, p = 0.036; and OR = 3.08, p = 0.018, respectively) as well as expression-based MDD-associated genes (OR = 1.48, p = 0.00012). Similar patterns of enrichment were found for aDMRs that correlate with local gene expression. These results were replicated in a large publically-available dataset, and confirmed by meta-analysis of the two datasets. Our findings suggest DNAm is a molecular mechanism for age-associated gene expression changes and support a role for DNAm in age-by-disease interactions through preferential targeting of disease-associated genes.
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Jovanović N, Mitrović T, Cvetković VJ, Tošić S, Vitorović J, Stamenković S, Nikolov V, Kostić A, Vidović N, Jevtović-Stoimenov T, Pavlović D. Prognostic significance of MGMT promoter methylation in diffuse glioma patients. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1604158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Nikola Jovanović
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Niš, Serbia
| | - Tatjana Mitrović
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Niš, Serbia
| | - Vladimir J. Cvetković
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Niš, Serbia
| | - Svetlana Tošić
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Niš, Serbia
| | - Jelena Vitorović
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Niš, Serbia
| | - Slaviša Stamenković
- Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Niš, Serbia
| | - Vesna Nikolov
- Clinic of Neurosurgery, Clinical Center, Faculty of Medicine, University of Niš, Niš, Serbia
| | - Aleksandar Kostić
- Clinic of Neurosurgery, Clinical Center, Faculty of Medicine, University of Niš, Niš, Serbia
| | - Nataša Vidović
- Pathology and Pathological Anatomy Center, Faculty of Medicine, University of Niš, Niš, Serbia
| | | | - Dušica Pavlović
- Institute of Biochemistry, Faculty of Medicine, University of Niš, Niš, Serbia
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Lemche E. Early Life Stress and Epigenetics in Late-onset Alzheimer's Dementia: A Systematic Review. Curr Genomics 2018; 19:522-602. [PMID: 30386171 PMCID: PMC6194433 DOI: 10.2174/1389202919666171229145156] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 07/27/2017] [Accepted: 12/12/2017] [Indexed: 11/22/2022] Open
Abstract
Involvement of life stress in Late-Onset Alzheimer's Disease (LOAD) has been evinced in longitudinal cohort epidemiological studies, and endocrinologic evidence suggests involvements of catecholamine and corticosteroid systems in LOAD. Early Life Stress (ELS) rodent models have successfully demonstrated sequelae of maternal separation resulting in LOAD-analogous pathology, thereby supporting a role of insulin receptor signalling pertaining to GSK-3beta facilitated tau hyper-phosphorylation and amyloidogenic processing. Discussed are relevant ELS studies, and findings from three mitogen-activated protein kinase pathways (JNK/SAPK pathway, ERK pathway, p38/MAPK pathway) relevant for mediating environmental stresses. Further considered were the roles of autophagy impairment, neuroinflammation, and brain insulin resistance. For the meta-analytic evaluation, 224 candidate gene loci were extracted from reviews of animal studies of LOAD pathophysiological mechanisms, of which 60 had no positive results in human LOAD association studies. These loci were combined with 89 gene loci confirmed as LOAD risk genes in previous GWAS and WES. Of the 313 risk gene loci evaluated, there were 35 human reports on epigenomic modifications in terms of methylation or histone acetylation. 64 microRNA gene regulation mechanisms were published for the compiled loci. Genomic association studies support close relations of both noradrenergic and glucocorticoid systems with LOAD. For HPA involvement, a CRHR1 haplotype with MAPT was described, but further association of only HSD11B1 with LOAD found; however, association of FKBP1 and NC3R1 polymorphisms was documented in support of stress influence to LOAD. In the brain insulin system, IGF2R, INSR, INSRR, and plasticity regulator ARC, were associated with LOAD. Pertaining to compromised myelin stability in LOAD, relevant associations were found for BIN1, RELN, SORL1, SORCS1, CNP, MAG, and MOG. Regarding epigenetic modifications, both methylation variability and de-acetylation were reported for LOAD. The majority of up-to-date epigenomic findings include reported modifications in the well-known LOAD core pathology loci MAPT, BACE1, APP (with FOS, EGR1), PSEN1, PSEN2, and highlight a central role of BDNF. Pertaining to ELS, relevant loci are FKBP5, EGR1, GSK3B; critical roles of inflammation are indicated by CRP, TNFA, NFKB1 modifications; for cholesterol biosynthesis, DHCR24; for myelin stability BIN1, SORL1, CNP; pertaining to (epi)genetic mechanisms, hTERT, MBD2, DNMT1, MTHFR2. Findings on gene regulation were accumulated for BACE1, MAPK signalling, TLR4, BDNF, insulin signalling, with most reports for miR-132 and miR-27. Unclear in epigenomic studies remains the role of noradrenergic signalling, previously demonstrated by neuropathological findings of childhood nucleus caeruleus degeneration for LOAD tauopathy.
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Affiliation(s)
- Erwin Lemche
- Section of Cognitive Neuropsychiatry, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
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13
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Deconstructing and targeting the genomic architecture of human neurodegeneration. Nat Neurosci 2018; 21:1310-1317. [PMID: 30258235 DOI: 10.1038/s41593-018-0240-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 08/23/2018] [Indexed: 01/17/2023]
Abstract
The field of neurodegenerative disease research has seen tremendous advances over the last two decades as new technologies and analytic methods have enabled well-powered human genomic studies. Driven first by genetic studies and more recently by transcriptomic and epigenomic studies of proper size, we have uncovered a large repertoire of loci, genes, and molecular features that are implicated in discrete, syndromically defined neurodegenerative conditions, such as Alzheimer's disease, amyotrophic lateral sclerosis, frontotemporal dementia, multiple sclerosis, and Parkinson's disease. As we begin to understand the impact of these genomic features in each disease, we also appreciate that many aging individuals accumulate each of these pathologies without fulfilling criteria for syndromic diagnoses, that other pathologies are common in individuals with a given diagnosis, and that there may be shared protective factors against central nervous system injury. Thus, we now need to bring these disparate observations together into a person-centered approach that considers all neurodegenerative and protective processes simultaneously to modulate the trajectory of cognitive and functional decline that comes with brain aging.
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De Jager PL, Ma Y, McCabe C, Xu J, Vardarajan BN, Felsky D, Klein HU, White CC, Peters MA, Lodgson B, Nejad P, Tang A, Mangravite LM, Yu L, Gaiteri C, Mostafavi S, Schneider JA, Bennett DA. A multi-omic atlas of the human frontal cortex for aging and Alzheimer's disease research. Sci Data 2018; 5:180142. [PMID: 30084846 PMCID: PMC6080491 DOI: 10.1038/sdata.2018.142] [Citation(s) in RCA: 286] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/26/2018] [Indexed: 12/14/2022] Open
Abstract
We initiated the systematic profiling of the dorsolateral prefrontal cortex obtained from a subset of autopsied individuals enrolled in the Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP), which are jointly designed prospective studies of aging and dementia with detailed, longitudinal cognitive phenotyping during life and a quantitative, structured neuropathologic examination after death. They include over 3,322 subjects. Here, we outline the first generation of data including genome-wide genotypes (n=2,090), whole genome sequencing (n=1,179), DNA methylation (n=740), chromatin immunoprecipitation with sequencing using an anti-Histone 3 Lysine 9 acetylation (H3K9Ac) antibody (n=712), RNA sequencing (n=638), and miRNA profile (n=702). Generation of other omic data including ATACseq, proteomic and metabolomics profiles is ongoing. Thanks to its prospective design and recruitment of older, non-demented individuals, these data can be repurposed to investigate a large number of syndromic and quantitative neuroscience phenotypes. The many subjects that are cognitively non-impaired at death also offer insights into the biology of the human brain in older non-impaired individuals.
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Affiliation(s)
- Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, 630 West 168 street, New York, NY 10032, USA
- Cell Circuits Program, Broad Institute, 415 Main street, Cambridge MA 02142, USA
| | - Yiyi Ma
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, 630 West 168 street, New York, NY 10032, USA
| | - Cristin McCabe
- Cell Circuits Program, Broad Institute, 415 Main street, Cambridge MA 02142, USA
| | - Jishu Xu
- Cell Circuits Program, Broad Institute, 415 Main street, Cambridge MA 02142, USA
| | - Badri N. Vardarajan
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, 630 West 168 street, New York, NY 10032, USA
| | - Daniel Felsky
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, 630 West 168 street, New York, NY 10032, USA
- Cell Circuits Program, Broad Institute, 415 Main street, Cambridge MA 02142, USA
| | - Hans-Ulrich Klein
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, 630 West 168 street, New York, NY 10032, USA
- Cell Circuits Program, Broad Institute, 415 Main street, Cambridge MA 02142, USA
| | - Charles C. White
- Cell Circuits Program, Broad Institute, 415 Main street, Cambridge MA 02142, USA
| | - Mette A. Peters
- Sage Bionetworks, 1100 Fairview Avenue N. Seattle WA 98109, USA
| | - Ben Lodgson
- Sage Bionetworks, 1100 Fairview Avenue N. Seattle WA 98109, USA
| | - Parham Nejad
- Cell Circuits Program, Broad Institute, 415 Main street, Cambridge MA 02142, USA
| | - Anna Tang
- Cell Circuits Program, Broad Institute, 415 Main street, Cambridge MA 02142, USA
| | | | - Lei Yu
- Rush Alzehimer Disease Center, RUSH University, 600 South Paulina Street, Chicago IL 60612, USA
| | - Chris Gaiteri
- Rush Alzehimer Disease Center, RUSH University, 600 South Paulina Street, Chicago IL 60612, USA
| | - Sara Mostafavi
- Departments of Statistics and Medical Genetics and Centre for Molecular Medicine and Therapeutics, University of British Columbia, 950 West 28 Avenue, Vancouver, British Columbia BC V5Z 4H4, Canada
| | - Julie A. Schneider
- Rush Alzehimer Disease Center, RUSH University, 600 South Paulina Street, Chicago IL 60612, USA
| | - David A. Bennett
- Rush Alzehimer Disease Center, RUSH University, 600 South Paulina Street, Chicago IL 60612, USA
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Girdhar K, Hoffman GE, Jiang Y, Brown L, Kundakovic M, Hauberg ME, Francoeur NJ, Wang YC, Shah H, Kavanagh DH, Zharovsky E, Jacobov R, Wiseman JR, Park R, Johnson JS, Kassim BS, Sloofman L, Mattei E, Weng Z, Sieberts SK, Peters MA, Harris BT, Lipska BK, Sklar P, Roussos P, Akbarian S. Cell-specific histone modification maps in the human frontal lobe link schizophrenia risk to the neuronal epigenome. Nat Neurosci 2018; 21:1126-1136. [PMID: 30038276 PMCID: PMC6063773 DOI: 10.1038/s41593-018-0187-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 05/25/2018] [Indexed: 12/13/2022]
Abstract
Risk variants for schizophrenia affect more than 100 genomic loci, yet cell- and tissue-specific roles underlying disease liability remain poorly characterized. We have generated for two cortical areas implicated in psychosis, the dorsolateral prefrontal cortex and anterior cingulate cortex, 157 reference maps from neuronal, neuron-depleted and bulk tissue chromatin for two histone marks associated with active promoters and enhancers, H3-trimethyl-Lys4 (H3K4me3) and H3-acetyl-Lys27 (H3K27ac). Differences between neuronal and neuron-depleted chromatin states were the major axis of variation in histone modification profiles, followed by substantial variability across subjects and cortical areas. Thousands of significant histone quantitative trait loci were identified in neuronal and neuron-depleted samples. Risk variants for schizophrenia, depressive symptoms and neuroticism were significantly over-represented in neuronal H3K4me3 and H3K27ac landscapes. Our Resource, sponsored by PsychENCODE and CommonMind, highlights the critical role of cell-type-specific signatures at regulatory and disease-associated noncoding sequences in the human frontal lobe.
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Affiliation(s)
- Kiran Girdhar
- Department of Genetics and Genomic Sciences, Icahn Institute of Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gabriel E Hoffman
- Department of Genetics and Genomic Sciences, Icahn Institute of Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Yan Jiang
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Leanne Brown
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marija Kundakovic
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Mads E Hauberg
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Nancy J Francoeur
- Department of Genetics and Genomic Sciences, Icahn Institute of Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ying-Chih Wang
- Department of Genetics and Genomic Sciences, Icahn Institute of Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn Institute of Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David H Kavanagh
- Department of Genetics and Genomic Sciences, Icahn Institute of Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elizabeth Zharovsky
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rivka Jacobov
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jennifer R Wiseman
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Royce Park
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica S Johnson
- Department of Genetics and Genomic Sciences, Icahn Institute of Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bibi S Kassim
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Sloofman
- Department of Genetics and Genomic Sciences, Icahn Institute of Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eugenio Mattei
- Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | | | | | - Brent T Harris
- Department of Neurology, Georgetown University, Washington, DC, USA
- Human Brain Collection Core, NIMH, Bethesda, MD, USA
| | | | - Pamela Sklar
- Department of Genetics and Genomic Sciences, Icahn Institute of Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn Institute of Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mental Illness Research, Education, and Clinical Center, James J. Peters VA Medical Center, Bronx, NY, USA.
| | - Schahram Akbarian
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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16
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Reproductive period and epigenetic modifications of the oxidative phosphorylation pathway in the human prefrontal cortex. PLoS One 2018; 13:e0199073. [PMID: 30052629 PMCID: PMC6063396 DOI: 10.1371/journal.pone.0199073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 05/31/2018] [Indexed: 01/13/2023] Open
Abstract
PURPOSE Human females have a unique duration of post-reproductive longevity, during which sex-specific mechanisms ma influence later-life mechanisms of neuronal resilience and vulnerability. The maintenance of energy metabolism, through the oxidative phosphorylation (OXPHOS) apparatus, is essential for brain health. Given the known association between reproductive period (years from menarche to menopause) and cognitive aging, we examined the hypothesis that cumulative estrogen exposure across the lifetime may be associated with differential methylation of genes in the OXPHOS pathway. METHODS Using DNA methylation patterns in the post-mortem dorsolateral prefrontal cortex (DLPFC) of 426 women prospectively followed until death in the Religious Orders Study and Rush Memory and Aging Project, we examined the relationship between reproductive period (subtracting age at menarche from age at menopause) and DNA methylation of a published set of autosomal OXPHOS genes previously implicated in stroke susceptibility. We then performed an unsupervised analysis of methylation levels across the Hallmark pathways from the Molecular Signatures Database. RESULTS We observed a strong association between reproductive period and DNA methylation status across OXPHOS CpGs. We replicated this association between reproductive period and DNA methylation in a much larger set of OXPHOS genes in our unsupervised analysis. Here, reproductive period also showed associations with methylation in genes related to E2F, MYC and MTORC1 signaling, fatty acid metabolism and DNA repair. CONCLUSION This study provides evidence from both a supervised and unsupervised analyses, that lifetime cumulative endogenous steroid exposures may play a role in maintenance of post-menopausal cellular balance, including in brain tissue.
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Tulloch J, Leong L, Chen S, Keene CD, Millard SP, Shutes-David A, Lopez OL, Kofler J, Kaye JA, Woltjer R, Nelson PT, Neltner JH, Jicha GA, Galasko D, Masliah E, Leverenz JB, Yu CE, Tsuang D. APOE DNA methylation is altered in Lewy body dementia. Alzheimers Dement 2018; 14:889-894. [PMID: 29544979 DOI: 10.1016/j.jalz.2018.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 02/07/2018] [Indexed: 10/17/2022]
Abstract
INTRODUCTION Inheritance of the ε4 allele of apolipoprotein E (APOE) increases a person's risk of developing both Alzheimer's disease (AD) and Lewy body dementia (LBD), yet the underlying mechanisms behind this risk are incompletely understood. The recent identification of reduced APOE DNA methylation in AD postmortem brains prompted this study to investigate APOE methylation in LBD. METHODS Genomic DNA from postmortem brain tissues (frontal lobe and cerebellum) of neuropathological pure (np) controls and npAD, LBD + AD, and npLBD subjects were bisulfite pyrosequenced. DNA methylation levels of two APOE subregions were then compared for these groups. RESULTS APOE DNA methylation was significantly reduced in npLBD compared with np controls, and methylation levels were lowest in the LBD + AD group. DISCUSSION Given that npLBD and npAD postmortem brains shared a similar reduction in APOE methylation, it is possible that an aberrant epigenetic change in APOE is linked to risk for both diseases.
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Affiliation(s)
- Jessica Tulloch
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA; Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, USA.
| | - Lesley Leong
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Sunny Chen
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - C Dirk Keene
- Neuropathology Division, Department of Pathology, University of Washington, Seattle, WA, USA
| | - Steven P Millard
- Mental Illness Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA
| | - Andrew Shutes-David
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA; Mental Illness Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA
| | - Oscar L Lopez
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Julia Kofler
- Division of Neuropathology, Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jeffrey A Kaye
- Department of Neurology, Oregon Health and Science University, Portland, OR, USA
| | - Randy Woltjer
- Department of Pathology, Oregon Health and Science University, Portland, OR, USA
| | - Peter T Nelson
- Department of Pathology, University of Kentucky, Lexington, KY, USA
| | - Janna H Neltner
- Department of Pathology, University of Kentucky, Lexington, KY, USA
| | - Gregory A Jicha
- Department of Neurology, University of Kentucky, Lexington, KY, USA
| | - Douglas Galasko
- Department of Neurosciences, University of California San Diego, San Diego CA, USA
| | - Eliezer Masliah
- National Institutes of Health, Division of Neuroscience, National Institute on Aging, Bethesda, MD, USA
| | | | - Chang-En Yu
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA; Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Debby Tsuang
- Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA; Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
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Bennett DA, Buchman AS, Boyle PA, Barnes LL, Wilson RS, Schneider JA. Religious Orders Study and Rush Memory and Aging Project. J Alzheimers Dis 2018; 64:S161-S189. [PMID: 29865057 PMCID: PMC6380522 DOI: 10.3233/jad-179939] [Citation(s) in RCA: 650] [Impact Index Per Article: 108.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND The Religious Orders Study and Rush Memory and Aging Project are both ongoing longitudinal clinical-pathologic cohort studies of aging and Alzheimer's disease (AD). OBJECTIVES To summarize progress over the past five years and its implications for understanding neurodegenerative diseases. METHODS Participants in both studies are older adults who enroll without dementia and agree to detailed longitudinal clinical evaluations and organ donation. The last review summarized findings through the end of 2011. Here we summarize progress and study findings over the past five years and discuss new directions for how these studies can inform on aging and AD in the future. RESULTS We summarize 1) findings on the relation of neurobiology to clinical AD; 2) neurobiologic pathways linking risk factors to clinical AD; 3) non-cognitive AD phenotypes including motor function and decision making; 4) the development of a novel drug discovery platform. CONCLUSION Complexity at multiple levels needs to be understood and overcome to develop effective treatments and preventions for cognitive decline and AD dementia.
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Affiliation(s)
- David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Aron S. Buchman
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Patricia A. Boyle
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA
- Department of Behavioral Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Lisa L. Barnes
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA
- Department of Behavioral Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Robert S. Wilson
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA
- Department of Behavioral Sciences, Rush University Medical Center, Chicago, IL., USA
| | - Julie A Schneider
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL., USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL., USA
- Department of Pathology (Neuropathology), Rush University Medical Center, Chicago, IL., USA
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19
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Yu L, Dawe RJ, Boyle PA, Gaiteri C, Yang J, Buchman AS, Schneider JA, Arfanakis K, De Jager PL, Bennett DA. Association Between Brain Gene Expression, DNA Methylation, and Alteration of Ex Vivo Magnetic Resonance Imaging Transverse Relaxation in Late-Life Cognitive Decline. JAMA Neurol 2017; 74:1473-1480. [PMID: 29084334 PMCID: PMC5729739 DOI: 10.1001/jamaneurol.2017.2807] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance Alteration of ex vivo magnetic resonance imaging transverse relaxation is associated with late-life cognitive decline even after controlling for common neuropathologic conditions. However, the underlying neurobiology of this association is unknown. Objective To investigate the association between brain gene expression, DNA methylation, and alteration of magnetic resonance imaging transverse relaxation in late-life cognitive decline. Design, Setting, and Participants Data came from 2 community-based longitudinal cohort studies of aging and dementia, the Religious Orders Study, which began in 1993, and the Rush Memory and Aging Project, which began in 1997. All participants agreed to undergo annual clinical evaluations and to donate their brains after death. By October 24, 2016, a total of 1358 individuals had died and had brain autopsies that were approved by board-certified neuropathologists. Of those, 552 had undergone ex vivo imaging. The gene expression analysis was limited to 174 individuals with both imaging and brain RNA sequencing data. The DNA methylation analysis was limited to 225 individuals with both imaging and brain methylation data. Main Outcomes and Measures Maps of ex vivo magnetic resonance imaging transverse relaxation were generated using fast spin echo imaging. The target was a composite measure of the transverse relaxation rate (R2) that was associated with cognitive decline after controlling for common neuropathologic conditions. Next-generation RNA sequencing and DNA methylation data were generated using frozen tissue from the dorsolateral prefrontal cortex. Genome-wide association analysis was used to investigate gene expression and, separately, DNA methylation for signals associated with the R2 measure. Results Of the 552 individuals with ex vivo imaging data, 394 were women and 158 were men, and the mean (SD) age at death was 90.4 (6.0) years. Four co-expressed genes (PADI2 [Ensembl ENSG00000117115], ZNF385A [Ensembl ENSG00000161642], PSD2 [Ensembl ENSG00000146005], and A2ML1 [Ensembl ENSG00000166535]) were identified, of which higher expressions were associated with slower R2. The association of R2 with cognitive decline was attenuated when the gene expression signals were added to the model, such that the mean (SE) coefficient of association was reduced from 0.028 (0.008) (P < .001) to 0.019 (0.009) (P = .03). The DNA methylation scan did not detect a genome-wide significant signal, but it revealed an anticorrelation between R2 and DNA methylation in many of the cytosine-guanine dinucleotides. Conclusions and Relevance Brain gene expression and DNA methylation dysregulations are implicated in the alteration of brain tissue properties associated with late-life cognitive decline above and beyond the influence of common neuropathologic conditions.
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Affiliation(s)
- Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois
| | - Robert J Dawe
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois
- Department of Diagnostic Radiology and Nuclear Medicine, Rush University Medical Center, Chicago, Illinois
| | - Patricia A Boyle
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois
- Department of Behavioral Sciences, Rush University Medical Center, Chicago, Illinois
| | - Chris Gaiteri
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois
| | - Jingyun Yang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois
| | - Aron S Buchman
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois
- Department of Pathology, Rush University Medical Center, Chicago, Illinois
| | - Konstantinos Arfanakis
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Columbia University Medical Center, New York, New York
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois
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Time-dependent genetic effects on gene expression implicate aging processes. Genome Res 2017; 27:545-552. [PMID: 28302734 PMCID: PMC5378173 DOI: 10.1101/gr.207688.116] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 01/23/2017] [Indexed: 01/04/2023]
Abstract
Gene expression is dependent on genetic and environmental factors. In the last decade, a large body of research has significantly improved our understanding of the genetic architecture of gene expression. However, it remains unclear whether genetic effects on gene expression remain stable over time. Here, we show, using longitudinal whole-blood gene expression data from a twin cohort, that the genetic architecture of a subset of genes is unstable over time. In addition, we identified 2213 genes differentially expressed across time points that we linked with aging within and across studies. Interestingly, we discovered that most differentially expressed genes were affected by a subset of 77 putative causal genes. Finally, we observed that putative causal genes and down-regulated genes were affected by a loss of genetic control between time points. Taken together, our data suggest that instability in the genetic architecture of a subset of genes could lead to widespread effects on the transcriptome with an aging signature.
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Iatrou A, Kenis G, Rutten BPF, Lunnon K, van den Hove DLA. Epigenetic dysregulation of brainstem nuclei in the pathogenesis of Alzheimer's disease: looking in the correct place at the right time? Cell Mol Life Sci 2017; 74:509-523. [PMID: 27628303 PMCID: PMC5241349 DOI: 10.1007/s00018-016-2361-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 08/15/2016] [Accepted: 09/07/2016] [Indexed: 12/20/2022]
Abstract
Even though the etiology of Alzheimer's disease (AD) remains unknown, it is suggested that an interplay among genetic, epigenetic and environmental factors is involved. An increasing body of evidence pinpoints that dysregulation in the epigenetic machinery plays a role in AD. Recent developments in genomic technologies have allowed for high throughput interrogation of the epigenome, and epigenome-wide association studies have already identified unique epigenetic signatures for AD in the cortex. Considerable evidence suggests that early dysregulation in the brainstem, more specifically in the raphe nuclei and the locus coeruleus, accounts for the most incipient, non-cognitive symptomatology, indicating a potential causal relationship with the pathogenesis of AD. Here we review the advancements in epigenomic technologies and their application to the AD research field, particularly with relevance to the brainstem. In this respect, we propose the assessment of epigenetic signatures in the brainstem as the cornerstone of interrogating causality in AD. Understanding how epigenetic dysregulation in the brainstem contributes to AD susceptibility could be of pivotal importance for understanding the etiology of the disease and for the development of novel diagnostic and therapeutic strategies.
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Affiliation(s)
- A Iatrou
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Universiteitssingel 50, 6200 MD, Maastricht, The Netherlands
| | - G Kenis
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Universiteitssingel 50, 6200 MD, Maastricht, The Netherlands
| | - B P F Rutten
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Universiteitssingel 50, 6200 MD, Maastricht, The Netherlands
| | - K Lunnon
- University of Exeter Medical School, RILD, University of Exeter, Barrack Road, Devon, UK
| | - D L A van den Hove
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Universiteitssingel 50, 6200 MD, Maastricht, The Netherlands.
- Laboratory of Translational Neuroscience, Department of Psychiatry, Psychosomatics and Psychotherapy, University of Wuerzburg, Fuechsleinstrasse 15, 97080, Würzburg, Germany.
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22
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Epigenetics in Alzheimer's Disease: Perspective of DNA Methylation. Mol Neurobiol 2017; 55:1026-1044. [PMID: 28092081 DOI: 10.1007/s12035-016-0357-6] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 12/28/2016] [Indexed: 12/12/2022]
Abstract
Research over the years has shown that causes of Alzheimer's disease are not well understood, but over the past years, the involvement of epigenetic mechanisms in the developing memory formation either under pathological or physiological conditions has become clear. The term epigenetics represents the heredity of changes in phenotype that are independent of altered DNA sequences. Different studies validated that cytosine methylation of genomic DNA decreases with age in different tissues of mammals, and therefore, the role of epigenetic factors in developing neurological disorders in aging has been under focus. In this review, we summarized and reviewed the involvement of different epigenetic mechanisms especially the DNA methylation in Alzheimer's disease (AD), late-onset Alzheimer's disease (LOAD), familial Alzheimer's disease (FAD), and autosomal dominant Alzheimer's disease (ADAD). Down to the minutest of details, we tried to discuss the methylation patterns like mitochondrial DNA methylation and ribosomal DNA (rDNA) methylation. Additionally, we mentioned some therapeutic approaches related to epigenetics, which could provide a potential cure for AD. Moreover, we reviewed some recent studies that validate DNA methylation as a potential biomarker and its role in AD. We hope that this review will provide new insights into the understanding of AD pathogenesis from the epigenetic perspective especially from the perspective of DNA methylation.
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A genome-wide profiling of brain DNA hydroxymethylation in Alzheimer's disease. Alzheimers Dement 2017; 13:674-688. [PMID: 28089213 DOI: 10.1016/j.jalz.2016.10.004] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 10/18/2016] [Indexed: 01/13/2023]
Abstract
INTRODUCTION DNA methylation is a key epigenetic mechanism in brain aging and Alzheimer's disease (AD). The newly discovered 5-hydroxymethylcytosine mediates DNA demethylation, is highly abundant in the brain, and is dynamically regulated by life experiences. However, little is known about its genome-wide patterns and potential role in AD. METHODS Using a genome-wide capture followed by high-throughput sequencing, we studied the genome-wide distribution of 5-hydroxymethylcytosine at specific genomic loci in human AD brain and identified differentially hydroxymethylated regions (DhMRs) associated with AD pathology. RESULTS We identified 517 DhMRs significantly associated with neuritic plaques and 60 DhMRs associated with neurofibrillary tangles. DNA hydroxymethylation in gene bodies was predominantly positively correlated with cis-acting gene expression. Moreover, genes showing differential hydroxymethylation were significantly enriched in neurobiological processes and clustered in functional gene ontology categories. DISCUSSION Our results reveal a critical role of DNA hydroxymethylation in AD pathology and provide mechanistic insight into the molecular mechanisms underlying AD.
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Klein HU, Bennett DA, De Jager PL. The epigenome in Alzheimer's disease: current state and approaches for a new path to gene discovery and understanding disease mechanism. Acta Neuropathol 2016; 132:503-14. [PMID: 27573688 DOI: 10.1007/s00401-016-1612-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/14/2016] [Accepted: 08/24/2016] [Indexed: 02/07/2023]
Abstract
The advent of new technologies and analytic approaches is beginning to provide an unprecedented look at features of the human genome that affect RNA expression. These "epigenomic" features are found in a number of different forms: they include DNA methylation, covalent modifications of histone proteins and non-coding RNAs. Some of these features have now been implicated in Alzheimer's disease (AD). Here, we focus on recent studies that have identified robust observations relating to DNA methylation and chromatin in human brain tissue; these findings will ground the next generation of studies and provide a model for the design of such studies. Stemming from observations that compounds with histone deacetylase activity may be beneficial in AD, epigenome-wide studies in cortical samples from large numbers of human subjects have now shown that AD-associated epigenomic changes are reproducible, are not driven by genetic risk factors, and are widespread at specific locations in the genome. A fundamental question of whether such changes are causal remains to be demonstrated, but it is already clear that well-powered investigations of the human epigenome in the target organ of a neurodegenerative disease are feasible, are implicating new areas of the genome in the disease, and will be an important tool for future studies. We are now at an inflection point: as genome-wide association studies of genetic variants come to an end, a new generation of studies exploring the epigenome will provide an important new layer of information with which to enrich our understanding of AD pathogenesis and to possibly guide development of new therapeutic targets.
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Affiliation(s)
- Hans-Ulrich Klein
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB 168, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Philip L De Jager
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, 77 Avenue Louis Pasteur, NRB 168, Boston, MA, 02115, USA.
- Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
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25
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Rescue of Early bace-1 and Global DNA Demethylation by S-Adenosylmethionine Reduces Amyloid Pathology and Improves Cognition in an Alzheimer's Model. Sci Rep 2016; 6:34051. [PMID: 27681803 PMCID: PMC5041108 DOI: 10.1038/srep34051] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 09/05/2016] [Indexed: 02/04/2023] Open
Abstract
General DNA hypomethylation is associated with Alzheimer's disease (AD), but it is unclear when DNA hypomethylation starts or plays a role in AD pathology or whether DNA re-methylation would rescue early amyloid-related cognitive impairments. In an APP transgenic mouse model of AD-like amyloid pathology we found that early intraneuronal amyloid beta build-up is sufficient to unleash a global and beta-site amyloid precursor protein cleaving enzyme 1 (bace-1) DNA demethylation in AD-vulnerable brain regions. S-adenosylmethionine administration at these early stages abolished this hypomethylation, diminished the amyloid pathology and restored cognitive capabilities. To assess a possible human significance of findings, we examined the methylation at 12 CpGs sites in the bace-1 promoter, using genome-wide DNA methylation data from 740 postmortem human brains. Thus, we found significant associations of bace-1 promoter methylation with β-amyloid load among persons with AD dementia, and PHFtau tangle density. Our results support a plausible causal role for the earliest amyloid beta accumulation to provoke DNA hypomethylation, influencing AD pathological outcomes.
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Bell CG, Xia Y, Yuan W, Gao F, Ward K, Roos L, Mangino M, Hysi PG, Bell J, Wang J, Spector TD. Novel regional age-associated DNA methylation changes within human common disease-associated loci. Genome Biol 2016; 17:193. [PMID: 27663977 PMCID: PMC5034469 DOI: 10.1186/s13059-016-1051-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/31/2016] [Indexed: 12/19/2022] Open
Abstract
Background Advancing age progressively impacts on risk and severity of chronic disease. It also modifies the epigenome, with changes in DNA methylation, due to both random drift and variation within specific functional loci. Results In a discovery set of 2238 peripheral-blood genome-wide DNA methylomes aged 19–82 years, we identify 71 age-associated differentially methylated regions within the linkage disequilibrium blocks of the single nucleotide polymorphisms from the NIH genome-wide association study catalogue. This included 52 novel regions, 29 within loci not covered by 450 k or 27 k Illumina array, and with enrichment for DNase-I Hypersensitivity sites across the full range of tissues. These age-associated differentially methylated regions also show marked enrichment for enhancers and poised promoters across multiple cell types. In a replication set of 2084 DNA methylomes, 95.7 % of the age-associated differentially methylated regions showed the same direction of ageing effect, with 80.3 % and 53.5 % replicated to p < 0.05 and p < 1.85 × 10–8, respectively. Conclusion By analysing the functionally enriched disease and trait-associated regions of the human genome, we identify novel epigenetic ageing changes, which could be useful biomarkers or provide mechanistic insights into age-related common diseases. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1051-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher G Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK. .,MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK. .,Human Development and Health Academic Unit, Institute of Developmental Sciences, University of Southampton, Southampton, UK. .,Epigenomic Medicine, Biological Sciences, Faculty of Environmental and Natural Sciences, University of Southampton, Southampton, UK.
| | | | - Wei Yuan
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK.,Institute of Cancer Research, Sutton, UK
| | - Fei Gao
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Kirsten Ward
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Leonie Roos
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Massimo Mangino
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Pirro G Hysi
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Jordana Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Timothy D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
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Klein HU, De Jager PL. Uncovering the Role of the Methylome in Dementia and Neurodegeneration. Trends Mol Med 2016; 22:687-700. [PMID: 27423266 DOI: 10.1016/j.molmed.2016.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 06/13/2016] [Accepted: 06/15/2016] [Indexed: 12/14/2022]
Abstract
Our understanding of the epigenome has advanced dramatically over the past decade, particularly in terms of DNA methylation, a modification found throughout the genome. Studies of the brain and neurons have outlined an increasingly complex architecture involving not just CG dinucleotide methylation but also methylation of other dinucleotides, and modifications of methylated bases such as 5-hydroxymethylcytosine. Different modifications may play an important role in brain development, function and decline; recent descriptions of the effects of aging and neurodegenerative processes such as Alzheimer disease on methylation profiles have ushered in an era of DNA methylome-wide association studies. Rapidly improving technologies and study designs are returning robust results, and investigations of the human brain's epigenome are increasingly feasible, complementing insights gained from genetic studies.
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Affiliation(s)
- Hans-Ulrich Klein
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Philip L De Jager
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
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28
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Herbert J, Lucassen PJ. Depression as a risk factor for Alzheimer's disease: Genes, steroids, cytokines and neurogenesis - What do we need to know? Front Neuroendocrinol 2016; 41:153-71. [PMID: 26746105 DOI: 10.1016/j.yfrne.2015.12.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/23/2015] [Accepted: 12/27/2015] [Indexed: 01/18/2023]
Abstract
Depression (MDD) is prodromal to, and a component of, Alzheimer's disease (AD): it may also be a trigger for incipient AD. MDD is not a unitary disorder, so there may be particular subtypes of early life MDD that pose independent high risks for later AD, though the identification of these subtypes is problematical. There may either be a common pathological event underlying both MDD and AD, or MDD may sensitize the brain to a second event ('hit') that precipitates AD. MDD may also accelerate brain ageing, including altered DNA methylation, increased cortisol but decreasing DHEA and thus the risk for AD. So far, genes predicting AD (e.g. APOEε4) are not risk factors for MDD, and those implicated in MDD (e.g. SLC6A4) are not risks for AD, so a common genetic predisposition looks unlikely. There is as yet no strong indication that an epigenetic event occurs during some forms of MDD that predisposes to later AD, though the evidence is limited. Glucocorticoids (GCs) are disturbed in some cases of MDD and in AD. GCs have marked degenerative actions on the hippocampus, a site of early β-amyloid deposition, and rare genetic variants of GC-regulating enzymes (e.g. 11β-HSD) predispose to AD. GCs also inhibit hippocampal neurogenesis and plasticity, and thus episodic memory, a core symptom of AD. Disordered GCs in MDD may inhibit neurogenesis, but the contribution of diminished neurogenesis to the onset or progression of AD is still debated. GCs and cytokines also reduce BDNF, implicated in both MDD and AD and hippocampal neurogenesis, reinforcing the notion that those cases of MDD with disordered GCs may be a risk for AD. Cytokines, including IL1β, IL6 and TNFα, are increased in the blood in some cases of MDD. They also reduce hippocampal neurogenesis, and increased cytokines are a known risk for later AD. Inflammatory changes occur in both MDD and AD (e.g. raised CRP, TNFα). Both cytokines and GCs can have pro-inflammatory actions in the brain. Inflammation (e.g. microglial activation) may be a common link, but this has not been systematically investigated. We lack substantial, rigorous and comprehensive follow-up studies to better identify possible subtypes of MDD that may represent a major predictor for later AD. This would enable specific interventions during critical episodes of these subtypes of MDD that should reduce this substantial risk.
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Affiliation(s)
- Joe Herbert
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, UK.
| | - Paul J Lucassen
- Swammerdam Institute for Life Sciences, Center for Neuroscience, University of Amsterdam, The Netherlands
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Pennington KL, DeAngelis MM. Epigenetic Mechanisms of the Aging Human Retina. J Exp Neurosci 2016; 9:51-79. [PMID: 26966390 PMCID: PMC4777243 DOI: 10.4137/jen.s25513] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 01/07/2016] [Accepted: 01/13/2016] [Indexed: 12/20/2022] Open
Abstract
Degenerative retinal diseases, such as glaucoma, age-related macular degeneration, and diabetic retinopathy, have complex etiologies with environmental, genetic, and epigenetic contributions to disease pathology. Much effort has gone into elucidating both the genetic and the environmental risk factors for these retinal diseases. However, little is known about how these genetic and environmental risk factors bring about molecular changes that lead to pathology. Epigenetic mechanisms have received extensive attention of late for their promise of bridging the gap between environmental exposures and disease development via their influence on gene expression. Recent studies have identified epigenetic changes that associate with the incidence and/or progression of each of these retinal diseases. Therefore, these epigenetic modifications may be involved in the underlying pathological mechanisms leading to blindness. Further genome-wide epigenetic studies that incorporate well-characterized tissue samples, consider challenges similar to those relevant to gene expression studies, and combine the genome-wide epigenetic data with genome-wide genetic and expression data to identify additional potentially causative agents of disease are needed. Such studies will allow researchers to create much-needed therapeutics to prevent and/or intervene in disease progression. Improved therapeutics will greatly enhance the quality of life and reduce the burden of disease management for millions of patients living with these potentially blinding conditions.
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Affiliation(s)
- Katie L Pennington
- Postdoctoral Fellow, Department of Ophthalmology & Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, UT, USA
| | - Margaret M DeAngelis
- Associate Professor, Department of Ophthalmology & Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, UT, USA
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Cacabelos R, Torrellas C. Epigenetics of Aging and Alzheimer's Disease: Implications for Pharmacogenomics and Drug Response. Int J Mol Sci 2015; 16:30483-543. [PMID: 26703582 PMCID: PMC4691177 DOI: 10.3390/ijms161226236] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/16/2015] [Accepted: 12/08/2015] [Indexed: 02/07/2023] Open
Abstract
Epigenetic variability (DNA methylation/demethylation, histone modifications, microRNA regulation) is common in physiological and pathological conditions. Epigenetic alterations are present in different tissues along the aging process and in neurodegenerative disorders, such as Alzheimer’s disease (AD). Epigenetics affect life span and longevity. AD-related genes exhibit epigenetic changes, indicating that epigenetics might exert a pathogenic role in dementia. Epigenetic modifications are reversible and can potentially be targeted by pharmacological intervention. Epigenetic drugs may be useful for the treatment of major problems of health (e.g., cancer, cardiovascular disorders, brain disorders). The efficacy and safety of these and other medications depend upon the efficiency of the pharmacogenetic process in which different clusters of genes (pathogenic, mechanistic, metabolic, transporter, pleiotropic) are involved. Most of these genes are also under the influence of the epigenetic machinery. The information available on the pharmacoepigenomics of most drugs is very limited; however, growing evidence indicates that epigenetic changes are determinant in the pathogenesis of many medical conditions and in drug response and drug resistance. Consequently, pharmacoepigenetic studies should be incorporated in drug development and personalized treatments.
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Affiliation(s)
- Ramón Cacabelos
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165-Bergondo, Corunna, Spain.
- Chair of Genomic Medicine, Camilo José Cela University, 28692-Madrid, Spain.
| | - Clara Torrellas
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165-Bergondo, Corunna, Spain.
- Chair of Genomic Medicine, Camilo José Cela University, 28692-Madrid, Spain.
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