1
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Latchney SE, Cadney MD, Hopkins A, Garland T. Maternal upbringing and selective breeding for voluntary exercise behavior modify patterns of DNA methylation and expression of genes in the mouse brain. GENES, BRAIN, AND BEHAVIOR 2023; 22:e12858. [PMID: 37519068 PMCID: PMC10733581 DOI: 10.1111/gbb.12858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/26/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023]
Abstract
Selective breeding has been utilized to study the genetic basis of exercise behavior, but research suggests that epigenetic mechanisms, such as DNA methylation, also contribute to this behavior. In a previous study, we demonstrated that the brains of mice from a genetically selected high runner (HR) line have sex-specific changes in DNA methylation patterns in genes known to be genomically imprinted compared to those from a non-selected control (C) line. Through cross-fostering, we also found that maternal upbringing can modify the DNA methylation patterns of additional genes. Here, we identify an additional set of genes in which DNA methylation patterns and gene expression may be altered by selection for increased wheel-running activity and maternal upbringing. We performed bisulfite sequencing and gene expression assays of 14 genes in the brain and found alterations in DNA methylation and gene expression for Bdnf, Pde4d and Grin2b. Decreases in Bdnf methylation correlated with significant increases in Bdnf gene expression in the hippocampus of HR compared to C mice. Cross-fostering also influenced the DNA methylation patterns for Pde4d in the cortex and Grin2b in the hippocampus, with associated changes in gene expression. We also found that the DNA methylation patterns for Atrx and Oxtr in the cortex and Atrx and Bdnf in the hippocampus were further modified by sex. Together with our previous study, these results suggest that DNA methylation and the resulting change in gene expression may interact with early-life influences to shape adult exercise behavior.
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Affiliation(s)
- Sarah E. Latchney
- Department of BiologySt. Mary's College of MarylandSt. Mary's CityMarylandUSA
| | - Marcell D. Cadney
- Department of Evolution, Ecology, and Organismal BiologyUniversity of CaliforniaRiversideCaliforniaUSA
- Neuroscience Research Institute, University of CaliforniaSanta BarbaraCaliforniaUSA
| | | | - Theodore Garland
- Department of Evolution, Ecology, and Organismal BiologyUniversity of CaliforniaRiversideCaliforniaUSA
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2
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Song H, Chen J, Huang J, Sun P, Liu Y, Xu L, Wei C, Mu X, Lu X, Wang W, Zhang N, Shang M, Mo M, Zhang W, Zhao H, Han F. Epigenetic modification in Parkinson's disease. Front Cell Dev Biol 2023; 11:1123621. [PMID: 37351278 PMCID: PMC10283008 DOI: 10.3389/fcell.2023.1123621] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/18/2023] [Indexed: 06/24/2023] Open
Abstract
Parkinson's disease (PD) is a common neurodegenerative disorder caused by genetic, epigenetic, and environmental factors. Recent advance in genomics and epigenetics have revealed epigenetic mechanisms in PD. These epigenetic modifications include DNA methylation, post-translational histone modifications, chromatin remodeling, and RNA-based mechanisms, which regulate cellular functions in almost all cells. Epigenetic alterations are involved in multiple aspects of neuronal development and neurodegeneration in PD. In this review, we discuss current understanding of the epigenetic mechanisms that regulate gene expression and neural degeneration and then highlight emerging epigenetic targets and diagnostic and therapeutic biomarkers for treating or preventing PD.
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Affiliation(s)
- Hao Song
- The Innovation Institute for Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Juanli Chen
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Jin Huang
- Laboratory of Basic Medical Research, PLA Strategic Support Force Characteristic Medical Centre, Beijing, China
| | - Peng Sun
- The Innovation Institute for Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Yanming Liu
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Li Xu
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Chuanfei Wei
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Xin Mu
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Xianjie Lu
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Wei Wang
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Nan Zhang
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Miwei Shang
- The Innovation Institute for Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Mei Mo
- The Innovation Institute for Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Wei Zhang
- Affiliated Yidu Central Hospital, Weifang Medical University, Weifang, China
| | - Hui Zhao
- Zhengzhou Revogene Scientific Co., LTD., Zhengzhou, Henan, China
| | - Fabin Han
- The Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University/The Liaocheng People’s Hospital, Liaocheng, Shandong, China
- Zhengzhou Revogene Scientific Co., LTD., Zhengzhou, Henan, China
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3
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Raval M, Mishra S, Tiwari AK. Epigenetic regulons in Alzheimer's disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:185-247. [DOI: 10.1016/bs.pmbts.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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4
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Shao X, Vishweswaraiah S, Čuperlović-Culf M, Yilmaz A, Greenwood CMT, Surendra A, McGuinness B, Passmore P, Kehoe PG, Maddens ME, Bennett SAL, Green BD, Radhakrishna U, Graham SF. Dementia with Lewy bodies post-mortem brains reveal differentially methylated CpG sites with biomarker potential. Commun Biol 2022; 5:1279. [PMID: 36418427 PMCID: PMC9684551 DOI: 10.1038/s42003-022-03965-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 09/08/2022] [Indexed: 11/25/2022] Open
Abstract
Dementia with Lewy bodies (DLB) is a common form of dementia with known genetic and environmental interactions. However, the underlying epigenetic mechanisms which reflect these gene-environment interactions are poorly studied. Herein, we measure genome-wide DNA methylation profiles of post-mortem brain tissue (Broadmann area 7) from 15 pathologically confirmed DLB brains and compare them with 16 cognitively normal controls using Illumina MethylationEPIC arrays. We identify 17 significantly differentially methylated CpGs (DMCs) and 17 differentially methylated regions (DMRs) between the groups. The DMCs are mainly located at the CpG islands, promoter and first exon regions. Genes associated with the DMCs are linked to "Parkinson's disease" and "metabolic pathway", as well as the diseases of "severe intellectual disability" and "mood disorders". Overall, our study highlights previously unreported DMCs offering insights into DLB pathogenesis with the possibility that some of these could be used as biomarkers of DLB in the future.
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Affiliation(s)
- Xiaojian Shao
- National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Canada.
| | | | - Miroslava Čuperlović-Culf
- National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Canada
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, sand Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Ali Yilmaz
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA
- Beaumont Research Institute, Royal Oak, MI, 48073, USA
| | - Celia M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Canada
| | - Anuradha Surendra
- National Research Council of Canada, Digital Technologies Research Centre, Ottawa, Canada
| | - Bernadette McGuinness
- Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Peter Passmore
- Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Patrick G Kehoe
- Dementia Research Group, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Michael E Maddens
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA
- Beaumont Research Institute, Royal Oak, MI, 48073, USA
| | - Steffany A L Bennett
- Ottawa Institute of Systems Biology, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology, sand Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Brian D Green
- Institute for Global Food Security, School of Biological Sciences, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Northern Ireland, UK
| | - Uppala Radhakrishna
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA
- Beaumont Research Institute, Royal Oak, MI, 48073, USA
| | - Stewart F Graham
- Oakland University-William Beaumont School of Medicine, Rochester, MI, 48309, USA.
- Beaumont Research Institute, Royal Oak, MI, 48073, USA.
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5
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Latchney SE, Cadney MD, Hopkins A, Garland T. DNA Methylation Analysis of Imprinted Genes in the Cortex and Hippocampus of Cross-Fostered Mice Selectively Bred for Increased Voluntary Wheel-Running. Behav Genet 2022; 52:281-297. [PMID: 35988119 PMCID: PMC9463359 DOI: 10.1007/s10519-022-10112-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/26/2022] [Indexed: 11/03/2022]
Abstract
We have previously shown that high runner (HR) mice (from a line genetically selected for increased wheel-running behavior) have distinct, genetically based, neurobiological phenotypes as compared with non-selected control (C) mice. However, developmental programming effects during early life, including maternal care and parent-of-origin-dependent expression of imprinted genes, can also contribute to variation in physical activity. Here, we used cross-fostering to address two questions. First, do HR mice have altered DNA methylation profiles of imprinted genes in the brain compared to C mice? Second, does maternal upbringing further modify the DNA methylation status of these imprinted genes? To address these questions, we cross-fostered all offspring at birth to create four experimental groups: C pups to other C dams, HR pups to other HR dams, C pups to HR dams, and HR pups to C dams. Bisulfite sequencing of 16 imprinted genes in the cortex and hippocampus revealed that the HR line had altered DNA methylation patterns of the paternally imprinted genes, Rasgrf1 and Zdbf2, as compared with the C line. Both fostering between the HR and C lines and sex modified the DNA methylation profiles for the paternally expressed genes Mest, Peg3, Igf2, Snrpn, and Impact. Ig-DMR, a gene with multiple paternal and maternal imprinted clusters, was also affected by maternal upbringing and sex. Our results suggest that differential methylation patterns of imprinted genes in the brain could contribute to evolutionary increases in wheel-running behavior and are also dependent on maternal upbringing and sex.
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Affiliation(s)
- Sarah E Latchney
- Department of Biology, St. Mary's College of Maryland, 18952 E. Fisher Rd, Saint Mary's City, MD, 20686, USA.
| | - Marcell D Cadney
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | | | - Theodore Garland
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA
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6
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Li D, Huang LT, Zhang CP, Li Q, Wang JH. Insights Into the Role of Platelet-Derived Growth Factors: Implications for Parkinson’s Disease Pathogenesis and Treatment. Front Aging Neurosci 2022; 14:890509. [PMID: 35847662 PMCID: PMC9283766 DOI: 10.3389/fnagi.2022.890509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Parkinson’s disease (PD), the second most common neurodegenerative disease after Alzheimer’s disease, commonly occurs in the elderly population, causing a significant medical and economic burden to the aging society worldwide. At present, there are few effective methods that achieve satisfactory clinical results in the treatment of PD. Platelet-derived growth factors (PDGFs) and platelet-derived growth factor receptors (PDGFRs) are important neurotrophic factors that are expressed in various cell types. Their unique structures allow for specific binding that can effectively regulate vital functions in the nervous system. In this review, we summarized the possible mechanisms by which PDGFs/PDGFRs regulate the occurrence and development of PD by affecting oxidative stress, mitochondrial function, protein folding and aggregation, Ca2+ homeostasis, and cell neuroinflammation. These modes of action mainly depend on the type and distribution of PDGFs in different nerve cells. We also summarized the possible clinical applications and prospects for PDGF in the treatment of PD, especially in genetic treatment. Recent advances have shown that PDGFs have contradictory roles within the central nervous system (CNS). Although they exert neuroprotective effects through multiple pathways, they are also associated with the disruption of the blood–brain barrier (BBB). Our recommendations based on our findings include further investigation of the contradictory neurotrophic and neurotoxic effects of the PDGFs acting on the CNS.
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Affiliation(s)
- Dan Li
- Department of Family Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Le-Tian Huang
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Cheng-pu Zhang
- Department of Family Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qiang Li
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Qiang Li,
| | - Jia-He Wang
- Department of Family Medicine, Shengjing Hospital of China Medical University, Shenyang, China
- Jia-He Wang,
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7
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He X, Pei S, Meng X, Hua Q, Zhang T, Wang Y, Zhang Z, Zhu X, Liu R, Guo Y, Chen L, Li D. Punicalagin Attenuates Neuronal Apoptosis by Upregulating 5-Hydroxymethylcytosine in the Diabetic Mouse Brain. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4995-5004. [PMID: 35412829 DOI: 10.1021/acs.jafc.2c00863] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Punicalagin exerts neuroprotective activity by improving AMP-activated kinase (AMPK) and mitochondrial Krebs cycle. AMPK and Krebs cycle metabolites regulate 5-hydroxymethylcytosine (5hmC) via acting on ten-eleven translocation (TET) enzymes. Therefore, we hypothesized that punicalagin inhibits diabetes-related neuronal apoptosis by upregulating 5hmC in the diabetic mouse brain. C57BL/6J mice aged 8 weeks were randomly separated into five groups (n = 10), normal control (NC), diabetes mellitus (DM), resveratrol (RES), low-dose punicalagin (LPU), and high-dose punicalagin (HPU). Compared with other groups, the neuronal apoptosis rate was significantly higher and the 5hmC level of the cerebral cortex was significantly lower in the DM group. The levels of TET2 and P-AMPKα/AMPKα were significantly lower in the DM group than in both LPU and HPU groups. The ratio of (succinic acid + fumaric acid)/α-ketoglutarate was significantly higher in the DM group than in other groups. The present results suggest that punicalagin upregulates 5hmC via activating AMPK and maintaining Krebs cycle homeostasis, thus inhibiting neuronal apoptosis in the diabetic mouse brain.
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Affiliation(s)
- Xin He
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Shengjie Pei
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Xiangyuan Meng
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Qinglian Hua
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Tianyu Zhang
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Yan Wang
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Zhizhao Zhang
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Xinyu Zhu
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Run Liu
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Yurong Guo
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710062, China
| | - Lei Chen
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
| | - Duo Li
- School of Public Health, Qingdao University, Qingdao 266000, China
- Institute of Nutrition & Health, Qingdao University, Qingdao 266000, China
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8
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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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9
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Matsumoto S, Tateishi-Karimata H, Ohyama T, Sugimoto N. Effect of DNA modifications on the transition between canonical and non-canonical DNA structures in CpG islands during senescence. RSC Adv 2021; 11:37205-37217. [PMID: 35496393 PMCID: PMC9043837 DOI: 10.1039/d1ra07201c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/08/2021] [Indexed: 12/22/2022] Open
Abstract
Patterns and levels of DNA modifications play important roles in senescence. Two major epigenetic modifications of DNA, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC), target CpG sites. Importantly, CpG concentrated regions, known as CpG islands, contain GC-rich sequences, which have the potential to fold into non-canonical DNA structures such as i-motifs and G-quadruplexes. In this study, we investigated the effect of 5mC and 5hmC modifications on the transition between a duplex, and i-motif and G-quadruplexes. To examine the transition, we firstly investigated the stability and structure of the i-motif and G-quadruplexes, considering the molecular environment in senescent cells. Analyses of their stability showed that the modifications did not drastically affect the stability. However, noteworthily, the modification can weaken the (de)stabilisation effect on G-quadruplexes caused by cosolute(s) and cations. Circular dichroism analyses indicated that the surrounding environments, including the molecular crowding and the type of cations such as K+ and Na+, regulate the topology of G-quadruplexes, while neither 5mC nor 5hmC had a drastic effect. On the other hand, the modifications changed the transition between duplexes and quadruplexes. Unmodified DNA preferred to fold into quadruplexes, whereas DNA with 5mC and 5hmC preferred to fold into duplexes in the absence of PEG200; on the other hand, DNA with or without modifications tended to fold into i-motifs under crowded conditions. Furthermore, an investigation of quadruplexes forming sequences in CpG islands, which are hyper- or hypomethylated during senescence, followed by gene ontology enrichment analysis for each gene group classified by the presence of quadruplexes, showed a difference in function between genes with and without quadruplexes in the CpG region. These results indicate that it is important to consider the effects of patterns and levels of DNA modifications on the transition between canonical and non-canonical DNA structures to understand gene regulation by epigenetic modification during senescence. The modification of DNA can regulate the transition between a duplex and quadruplexes during senescence responding to surrounding environments.![]()
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Affiliation(s)
- Saki Matsumoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University 7-1-20 Minatojima-minamimachi Kobe 650-0047 Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University 7-1-20 Minatojima-minamimachi Kobe 650-0047 Japan
| | - Tatsuya Ohyama
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University 7-1-20 Minatojima-minamimachi Kobe 650-0047 Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University 7-1-20 Minatojima-minamimachi Kobe 650-0047 Japan .,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University 7-1-20 Minatojima-minamimachi Kobe 650-0047 Japan
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10
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Puigoriol-Illamola D, Companys-Alemany J, McGuire K, Homer NZM, Leiva R, Vázquez S, Mole DJ, Griñán-Ferré C, Pallàs M. Inhibition of 11β-HSD1 Ameliorates Cognition and Molecular Detrimental Changes after Chronic Mild Stress in SAMP8 Mice. Pharmaceuticals (Basel) 2021; 14:ph14101040. [PMID: 34681264 PMCID: PMC8540242 DOI: 10.3390/ph14101040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 09/28/2021] [Accepted: 10/08/2021] [Indexed: 11/16/2022] Open
Abstract
Impaired glucocorticoid (GC) signaling is a significant factor in aging, stress, and neurodegenerative diseases such as Alzheimer's disease. Therefore, the study of GC-mediated stress responses to chronic moderately stressful situations, which occur in daily life, is of huge interest for the design of pharmacological strategies toward the prevention of neurodegeneration. To address this issue, SAMP8 mice were exposed to the chronic mild stress (CMS) paradigm for 4 weeks and treated with RL-118, an 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) inhibitor. The inhibition of this enzyme is linked with a reduction in GC levels and cognitive improvement, while CMS exposure has been associated with reduced cognitive performance. The aim of this project was to assess whether RL-118 treatment could reverse the deleterious effects of CMS on cognition and behavioral abilities and to evaluate the molecular mechanisms that compromise healthy aging in SAMP8 mice. First, we confirmed the target engagement between RL-118 and 11β-HSD1. Additionally, we showed that DNA methylation, hydroxymethylation, and histone phosphorylation were decreased by CMS induction, and increased by RL-118 treatment. In addition, CMS exposure caused the accumulation of reactive oxygen species (ROS)-induced damage and increased pro-oxidant enzymes-as well as pro-inflammatory mediators-through the NF-κB pathway and astrogliosis markers, such as GFAP. Of note, these modifications were reversed by 11β-HSD1 inhibition. Remarkably, although CMS altered mTORC1 signaling, autophagy was increased in the SAMP8 RL-118-treated mice. We also showed an increase in amyloidogenic processes and a decrease in synaptic plasticity and neuronal remodeling markers in mice under CMS, which were consequently modified by RL-118 treatment. In conclusion, 11β-HSD1 inhibition through RL-118 ameliorated the detrimental effects induced by CMS, including epigenetic and cognitive disturbances, indicating that GC-excess attenuation shows potential as a therapeutic strategy for age-related cognitive decline and AD.
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Affiliation(s)
- Dolors Puigoriol-Illamola
- Pharmacology Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Av. Joan XXIII, 27-31, 08028 Barcelona, Spain; (D.P.-I.); (J.C.-A.); (C.G.-F.)
- Institute of Neuroscience, University of Barcelona (NeuroUB), Passeig Vall d’Hebron 171, 08028 Barcelona, Spain
| | - Júlia Companys-Alemany
- Pharmacology Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Av. Joan XXIII, 27-31, 08028 Barcelona, Spain; (D.P.-I.); (J.C.-A.); (C.G.-F.)
- Institute of Neuroscience, University of Barcelona (NeuroUB), Passeig Vall d’Hebron 171, 08028 Barcelona, Spain
| | - Kris McGuire
- MRC Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK; (K.M.); (D.J.M.)
| | - Natalie Z. M. Homer
- Mass Spectrometry Core, Edinburgh Clinical Research Facility, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK;
| | - Rosana Leiva
- Medicinal Chemistry Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Av. Joan XXIII, 27-31, 08028 Barcelona, Spain; (R.L.); (S.V.)
| | - Santiago Vázquez
- Medicinal Chemistry Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Av. Joan XXIII, 27-31, 08028 Barcelona, Spain; (R.L.); (S.V.)
| | - Damian J. Mole
- MRC Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK; (K.M.); (D.J.M.)
| | - Christian Griñán-Ferré
- Pharmacology Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Av. Joan XXIII, 27-31, 08028 Barcelona, Spain; (D.P.-I.); (J.C.-A.); (C.G.-F.)
- Institute of Neuroscience, University of Barcelona (NeuroUB), Passeig Vall d’Hebron 171, 08028 Barcelona, Spain
| | - Mercè Pallàs
- Pharmacology Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Av. Joan XXIII, 27-31, 08028 Barcelona, Spain; (D.P.-I.); (J.C.-A.); (C.G.-F.)
- Institute of Neuroscience, University of Barcelona (NeuroUB), Passeig Vall d’Hebron 171, 08028 Barcelona, Spain
- Correspondence: ; Tel.: +34-4024531
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11
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Differential Epigenetic Signature of Corticospinal Motor Neurons in ALS. Brain Sci 2021; 11:brainsci11060754. [PMID: 34200232 PMCID: PMC8230084 DOI: 10.3390/brainsci11060754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 11/26/2022] Open
Abstract
Corticospinal motor neurons (CSMN) are an indispensable neuron population for the motor neuron circuitry. They are excitatory projection neurons, which collect information from different regions of the brain and transmit it to spinal cord targets, initiating and controlling motor function. CSMN degeneration is pronounced cellular event in motor neurons diseases, such as amyotrophic lateral sclerosis (ALS). Genetic mutations contribute to only about ten percent of ALS. Thus understanding the involvement of other factors, such as epigenetic controls, is immensely valuable. Here, we investigated epigenomic signature of CSMN that become diseased due to misfolded SOD1 toxicity and TDP-43 pathology, by performing quantitative analysis of 5-methylcytosine (5mC) and 5-hydroxymethycytosine (5hmC) expression profiles during end-stage of the disease in hSOD1G93A, and prpTDP-43A315T mice. Our analysis revealed that expression of 5mC was specifically reduced in CSMN of both hSOD1G93A and prpTDP-43A315T mice. However, 5hmC expression was increased in the CSMN that becomes diseased due to misfolded SOD1 and decreased in CSMN that degenerates due to TDP-43 pathology. These results suggest the presence of a distinct difference between different underlying causes. These differential epigenetic events might modulate the expression profiles of select genes, and ultimately contribute to the different paths that lead to CSMN vulnerability in ALS.
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12
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Morris-Blanco KC, Chokkalla AK, Bertogliat MJ, Vemuganti R. TET3 regulates DNA hydroxymethylation of neuroprotective genes following focal ischemia. J Cereb Blood Flow Metab 2021; 41:590-603. [PMID: 32380888 PMCID: PMC7922754 DOI: 10.1177/0271678x20912965] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The 5-hydroxymethylcytosine (5hmC) epigenetic modification is highly enriched in the CNS and a critical modulator of neuronal function and development. We found that cortical 5hmC was enhanced from 5 min to three days of reperfusion following focal ischemia in adult mice. Blockade of the 5hmC-producing enzyme ten-eleven translocase 3 (TET3) increased edema, infarct volume, and motor function impairments. To determine the mechanism by which TET3 provides ischemic neuroprotection, we assessed the genomic regions where TET3 modulates 5hmC. Genome-wide sequencing analysis of differentially hydroxymethylated regions (DhMRs) revealed that focal ischemia robustly increased 5hmC at the promoters of thousands of genes in a TET3-dependent manner. TET3 inhibition reduced 5hmC at the promoters of neuroprotective genes involved in cell survival, angiogenesis, neurogenesis, antioxidant defense, DNA repair, and metabolism demonstrating a role for TET3 in endogenous protection against stroke. The mRNA expression of several genes with known involvement in ischemic neuroprotection were also reduced with TET3 knockdown in both male and female mice, establishing a correlation between decreased promoter 5hmC levels and decreased gene expression. Collectively, our results indicate that TET3 globally increases 5hmC at regulatory regions and overwhelmingly modulates 5hmC in several neuroprotective pathways that may improve outcome after ischemic injury.
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Affiliation(s)
- Kahlilia C Morris-Blanco
- Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI, USA.,Department of Research, William S. Middleton Veterans Administration Hospital, Madison, WI, USA
| | - Anil K Chokkalla
- Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI, USA.,Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Mario J Bertogliat
- Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI, USA
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin-Madison, Madison, WI, USA.,Department of Research, William S. Middleton Veterans Administration Hospital, Madison, WI, USA.,Cellular and Molecular Pathology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA
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13
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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: 85] [Impact Index Per Article: 28.3] [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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14
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High-Resolution Analysis of 5-Hydroxymethylcytosine by TET-Assisted Bisulfite Sequencing. Methods Mol Biol 2021; 2198:321-331. [PMID: 32822042 DOI: 10.1007/978-1-0716-0876-0_25] [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] [Indexed: 12/12/2022]
Abstract
DNA cytosine modification is an important epigenetic mechanism that serves critical functions in a variety of biological processes in development and disease. 5-Methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are the two most common epigenetic marks found in the mammalian genome. 5hmC is generated from 5mC by the ten-eleven translocation (TET) family of dioxygenase enzymes. This modification can reach substantial levels in certain cell types such as embryonic stem cells and neurons. Standard bisulfite sequencing techniques cannot distinguish between 5mC and 5hmC. Therefore, the method of TET-assisted bisulfite sequencing has been developed for detecting 5hmC specifically. The method is based on protection of 5hmC by glycosylation followed by complete oxidation of both 5mC and 5fC to 5caC, which converts to uracil after bisulfite treatment leaving only 5hmC remaining as a cytosine signal after PCR and sequencing. The method requires a highly active TET protein for the conversion steps. Here, we present an efficient TET protein purification method and a streamlined TAB-sequencing protocol for 5hmC analysis at single base resolution.
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15
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Alvarez-Fischer D, Vernik T, Vulinovic F, Herrmann A, Westenberger A, Klein C. Transgenerational transduction of MPTP-induced alterations in a Parkinson's disease mouse model. Parkinsonism Relat Disord 2020; 79:88-90. [PMID: 32906083 DOI: 10.1016/j.parkreldis.2020.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 07/17/2020] [Accepted: 08/11/2020] [Indexed: 11/16/2022]
Abstract
Susceptibility to Parkinson's disease (PD) increases more than threefold in first-degree relatives of PD patients. Using a mouse model, we investigated in a proof-of-principle approach whether toxin exposure of F0 affects the F1 generation. We provide first evidence that disturbance of the nigrostriatal pathway can be transferred to the next generation.
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Affiliation(s)
- D Alvarez-Fischer
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany; Department of Psychiatry, University Hospital Schleswig-Holstein, Campus Lübeck, Germany.
| | - T Vernik
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany; Department of Neurosurgery, University Hospital Erlangen, Erlangen, Germany.
| | - F Vulinovic
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.
| | - A Herrmann
- Department of Psychology, University of Lübeck, Germany.
| | - A Westenberger
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.
| | - C Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.
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16
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Bordoni L, Gabbianelli R. Mitochondrial DNA and Neurodegeneration: Any Role for Dietary Antioxidants? Antioxidants (Basel) 2020; 9:E764. [PMID: 32824558 PMCID: PMC7466149 DOI: 10.3390/antiox9080764] [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: 07/14/2020] [Revised: 08/07/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023] Open
Abstract
The maintenance of the mitochondrial function is essential in preventing and counteracting neurodegeneration. In particular, mitochondria of neuronal cells play a pivotal role in sustaining the high energetic metabolism of these cells and are especially prone to oxidative damage. Since overproduction of reactive oxygen species (ROS) is involved in the pathogenesis of neurodegeneration, dietary antioxidants have been suggested to counteract the detrimental effects of ROS and to preserve the mitochondrial function, thus slowing the progression and limiting the extent of neuronal cell loss in neurodegenerative disorders. In addition to their role in the redox-system homeostasis, mitochondria are unique organelles in that they contain their own genome (mtDNA), which acts at the interface between environmental exposures and the molecular triggers of neurodegeneration. Indeed, it has been demonstrated that mtDNA (including both genetics and, from recent evidence, epigenetics) might play relevant roles in modulating the risk for neurodegenerative disorders. This mini-review describes the link between the mitochondrial genome and cellular oxidative status, with a particular focus on neurodegeneration; moreover, it provides an overview on potential beneficial effects of antioxidants in preserving mitochondrial functions through the protection of mtDNA.
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Affiliation(s)
- Laura Bordoni
- Unit of Molecular Biology, School of Pharmacy, University of Camerino, 62032 Camerino, Italy;
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17
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Zhang Z, Yan J, Li Z. Peroxotungstate oxidation-mediated two-phase amplification system (POM-TPAS) for bisulfite-free quantification of locus-specific 5-hydroxymethylcytosine. Chem Commun (Camb) 2020; 56:3111-3114. [PMID: 32090228 DOI: 10.1039/d0cc00167h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The peroxotungstate oxidation-mediated two-phase amplification system (POM-TPAS) is applied for the first time to the sensitive detection of locus-specific 5-hydroxymethylcytosine (5hmC) in DNA with low non-specific amplification. This strategy greatly shortens reaction time, improves sensitivity, and reduces non-specific amplification.
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Affiliation(s)
- Zhenhao Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, Shaanxi Province, P. R. China.
| | - Jingli Yan
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, Shaanxi Province, P. R. China.
| | - Zhengping Li
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, Shaanxi Province, P. R. China.
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18
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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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19
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Chronic Mild Stress Modified Epigenetic Mechanisms Leading to Accelerated Senescence and Impaired Cognitive Performance in Mice. Int J Mol Sci 2020; 21:ijms21031154. [PMID: 32050516 PMCID: PMC7037343 DOI: 10.3390/ijms21031154] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/04/2020] [Accepted: 02/06/2020] [Indexed: 12/17/2022] Open
Abstract
Cognitive and behavioural disturbances are a growing public healthcare issue for the modern society, as stressful lifestyle is becoming more and more common. Besides, several pieces of evidence state that environment is crucial in the development of several diseases as well as compromising healthy aging. Therefore, it is important to study the effects of stress on cognition and its relationship with aging. To address these queries, Chronic Mild Stress (CMS) paradigm was used in the senescence-accelerated mouse prone 8 (SAMP8) and resistant 1 (SAMR1). On one hand, we determined the changes produced in the three main epigenetic marks after 4 weeks of CMS treatment, such as a reduction in histone posttranslational modifications and DNA methylation, and up-regulation or down-regulation of several miRNA involved in different cellular processes in mice. In addition, CMS treatment induced reactive oxygen species (ROS) damage accumulation and loss of antioxidant defence mechanisms, as well as inflammatory signalling activation through NF-κB pathway and astrogliosis markers, like Gfap. Remarkably, CMS altered mTORC1 signalling in both strains, decreasing autophagy only in SAMR1 mice. We found a decrease in glycogen synthase kinase 3 β (GSK-3β) inactivation, hyperphosphorylation of Tau and an increase in sAPPβ protein levels in mice under CMS. Moreover, reduction in the non-amyloidogenic secretase ADAM10 protein levels was found in SAMR1 CMS group. Consequently, detrimental effects on behaviour and cognitive performance were detected in CMS treated mice, affecting mainly SAMR1 mice, promoting a turning to SAMP8 phenotype. In conclusion, CMS is a feasible intervention to understand the influence of stress on epigenetic mechanisms underlying cognition and accelerating senescence.
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20
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Kaut O, Kuchelmeister K, Moehl C, Wüllner U. 5-methylcytosine and 5-hydroxymethylcytosine in brains of patients with multiple system atrophy and patients with Parkinson’s disease. J Chem Neuroanat 2019; 96:41-48. [DOI: 10.1016/j.jchemneu.2018.12.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 12/14/2018] [Indexed: 12/26/2022]
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21
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Epigenetic Memory of Early-Life Parental Perturbation: Dopamine Decrease and DNA Methylation Changes in Offspring. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:1472623. [PMID: 30915194 PMCID: PMC6399534 DOI: 10.1155/2019/1472623] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 11/15/2018] [Accepted: 12/31/2018] [Indexed: 12/12/2022]
Abstract
Early-life exposure (from postnatal day 6 to postnatal day 21) to permethrin has been associated with long-term development of dopaminergic neurodegeneration in rats. Here, we first investigated if the dopamine decrease observed following early postnatal exposure to permethrin, an oxidative stressor, can impair the dopamine level in the brain of their untreated offspring. Secondly, we evaluated whether this adverse event affects the epigenome of both directly exposed rats (F0) and their untreated offspring (F1). The results show that early-life exposure to the stressor is associated with changes in global DNA methylation and hydroxymethylation in adult age. Furthermore, parental exposure leads to a significant reduction in dopamine level in the offspring (F1) born from parents or just mothers early-life treated (72.72% and 47.35%, respectively). About 2/3 of pups from exposed mothers showed a significant reduction in dopamine level compared to controls. Global DNA methylation and hydroxymethylation impairment was associated with the F1 pups that showed reduced dopamine. This study provides pivotal evidences on intergenerational effects of postnatal exposure to permethrin emphasizing that this xenobiotic can influence the epigenetic memory of early-life parental perturbations disturbing offspring health.
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22
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Cosín-Tomás M, Álvarez-López MJ, Companys-Alemany J, Kaliman P, González-Castillo C, Ortuño-Sahagún D, Pallàs M, Griñán-Ferré C. Temporal Integrative Analysis of mRNA and microRNAs Expression Profiles and Epigenetic Alterations in Female SAMP8, a Model of Age-Related Cognitive Decline. Front Genet 2018; 9:596. [PMID: 30619445 PMCID: PMC6297390 DOI: 10.3389/fgene.2018.00596] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 11/15/2018] [Indexed: 01/05/2023] Open
Abstract
A growing body of research shows that epigenetic mechanisms are critically involved in normal and pathological aging. The Senescence-Accelerated Mouse Prone 8 (SAMP8) can be considered a useful tool to better understand the dynamics of the global epigenetic landscape during the aging process since its phenotype is not fully explained by genetic factors. Here we investigated dysfunctional age-related transcriptional profiles and epigenetic programming enzymes in the hippocampus of 2- and 9-month-old SAMP8 female mice using the Senescent-Accelerated Resistant 1 (SAMR1) mouse strain as control. SAMP8 mice presented 1,062 genes dysregulated at 2 months of age, and 1,033 genes at 9 months, with 92 genes concurrently dysregulated at both ages compared to age-matched SAMR1. SAMP8 mice showed a significant decrease in global DNA methylation (5-mC) at 2 months while hydroxymethylation (5-hmC) levels were increased in SAMP8 mice at 2 and 9 months of age compared to SAMR1. These changes were accompanied by changes in the expression of several enzymes that regulate 5-mC and methylcytosine oxidation. Acetylated H3 and H4 histone levels were significantly diminished in SAMP8 mice at 2-month-old compared to SAMR1 and altered Histone DeACetylase (HDACs) profiles were detected in both young and old SAMP8 mice. We analyzed 84 different mouse miRNAs known to be altered in neurological diseases or involved in neuronal development. Compared with SAMR1, SAMP8 mice showed 28 and 17 miRNAs differentially expressed at 2 and 9 months of age, respectively; 6 of these miRNAs overlapped at both ages. We used several bioinformatic approaches to integrate our data in mRNA:miRNA regulatory networks and functional predictions for young and aged animals. In sum, our study reveals interplay between epigenetic mechanisms and gene networks that seems to be relevant for the progression toward a pathological aging and provides several potential markers and therapeutic candidates for Alzheimer's Disease (AD) and age-related cognitive impairment.
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Affiliation(s)
- Marta Cosín-Tomás
- Department of Pharmacology and Therapeutic Chemistry, Institute of Neuroscience, University of Barcelona, Barcelona, Spain.,Departments of Human Genetics and Pediatrics, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - María Jesús Álvarez-López
- Department of Pharmacology and Therapeutic Chemistry, Institute of Neuroscience, University of Barcelona, Barcelona, Spain
| | - Júlia Companys-Alemany
- Department of Pharmacology and Therapeutic Chemistry, Institute of Neuroscience, University of Barcelona, Barcelona, Spain
| | - Perla Kaliman
- Department of Pharmacology and Therapeutic Chemistry, Institute of Neuroscience, University of Barcelona, Barcelona, Spain.,Faculty of Health Sciences, Universitat Oberta de Catalunya, Barcelona, Spain
| | | | - Daniel Ortuño-Sahagún
- Centro Universitario de Ciencias de la Salud, Instituto de Investigación en Ciencias Biomédicas, Universidad de Guadalajara, Guadalajara, Mexico
| | - Mercè Pallàs
- Department of Pharmacology and Therapeutic Chemistry, Institute of Neuroscience, University of Barcelona, Barcelona, Spain
| | - Christian Griñán-Ferré
- Department of Pharmacology and Therapeutic Chemistry, Institute of Neuroscience, University of Barcelona, Barcelona, Spain
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23
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Baulch JE. Radiation-induced genomic instability, epigenetic mechanisms and the mitochondria: a dysfunctional ménage a trois? Int J Radiat Biol 2018; 95:516-525. [DOI: 10.1080/09553002.2018.1549757] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Janet E. Baulch
- Department of Radiation Oncology, University of California Irvine, Irvine, CA, USA
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24
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Ciccarone F, Valentini E, Malavolta M, Zampieri M, Bacalini MG, Calabrese R, Guastafierro T, Reale A, Franceschi C, Capri M, Breusing N, Grune T, Moreno‐Villanueva M, Bürkle A, Caiafa P. DNA Hydroxymethylation Levels Are Altered in Blood Cells From Down Syndrome Persons Enrolled in the MARK-AGE Project. J Gerontol A Biol Sci Med Sci 2018; 73:737-744. [PMID: 29069286 PMCID: PMC5946825 DOI: 10.1093/gerona/glx198] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 10/19/2017] [Indexed: 12/17/2022] Open
Abstract
Down syndrome (DS) is caused by the presence of part or an entire extra copy of chromosome 21, a phenomenon that can cause a wide spectrum of clinically defined phenotypes of the disease. Most of the clinical signs of DS are typical of the aging process including dysregulation of immune system. Beyond the causative genetic defect, DS persons display epigenetic alterations, particularly aberrant DNA methylation patterns that can contribute to the heterogeneity of the disease. In the present work, we investigated the levels of 5-hydroxymethylcytosine and of the Ten-eleven translocation dioxygenase enzymes, which are involved in DNA demethylation processes and are often deregulated in pathological conditions as well as in aging. Analyses were carried out on peripheral blood mononuclear cells of DS volunteers enrolled in the context of the MARK-AGE study, a large-scale cross-sectional population study with subjects representing the general population in eight European countries. We observed a decrease in 5-hydroxymethylcytosine, TET1, and other components of the DNA methylation/demethylation machinery in DS subjects, indicating that aberrant DNA methylation patterns in DS, which may have consequences on the transcriptional status of immune cells, may be due to a global disturbance of methylation control in DS.
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Affiliation(s)
- Fabio Ciccarone
- Department of Biology, University of Rome “Tor Vergata,” Rome
| | - Elisabetta Valentini
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome
- Pasteur Institute-Fondazione Cenci Bolognetti, Rome
| | - Marco Malavolta
- National Institute of Health and Science on Aging (INRCA), Nutrition and Ageing Centre, Scientific and Technological Research Area, Ancona
| | - Michele Zampieri
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome
- Pasteur Institute-Fondazione Cenci Bolognetti, Rome
| | | | - Roberta Calabrese
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome
- Pasteur Institute-Fondazione Cenci Bolognetti, Rome
| | - Tiziana Guastafierro
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome
- Pasteur Institute-Fondazione Cenci Bolognetti, Rome
| | - Anna Reale
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome
| | - Claudio Franceschi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna
- Department of Experimental, Diagnostic and Specialty Medicine, Bologna, Italy
- CIG-Interdepartmental Center “L. Galvani,” Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Miriam Capri
- Department of Experimental, Diagnostic and Specialty Medicine, Bologna, Italy
- CIG-Interdepartmental Center “L. Galvani,” Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Nicolle Breusing
- Institute of Nutritional Medicine (180c), University of Hohenheim, Stuttgart
| | - Tilman Grune
- German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal
| | - María Moreno‐Villanueva
- Department of Biology, Molecular Toxicology Group, University of Konstanz, Konstanz, Germany
| | - Alexander Bürkle
- Department of Biology, Molecular Toxicology Group, University of Konstanz, Konstanz, Germany
| | - Paola Caiafa
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome
- Pasteur Institute-Fondazione Cenci Bolognetti, Rome
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Hamzeiy H, Savaş D, Tunca C, Şen NE, Gündoğdu Eken A, Şahbaz I, Calini D, Tiloca C, Ticozzi N, Ratti A, Silani V, Başak AN. Elevated Global DNA Methylation Is Not Exclusive to Amyotrophic Lateral Sclerosis and Is Also Observed in Spinocerebellar Ataxia Types 1 and 2. NEURODEGENER DIS 2018; 18:38-48. [PMID: 29428949 DOI: 10.1159/000486201] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 12/08/2017] [Indexed: 12/12/2022] Open
Abstract
Adult-onset neurological disorders are caused and influenced by a multitude of different factors, including epigenetic modifications. Here, using an ELISA kit selected upon careful testing, we investigated global 5-methylcytosine (5-mC) levels in sporadic and familial amyotrophic lateral sclerosis (sALS and fALS), spinocerebellar ataxia types 1 and 2 (SCA1 and SCA2), Huntington's disease, Friedreich's ataxia, and myotonic dystrophy type 1. We report a significant elevation in global 5-mC levels of about 2-7% on average for sALS (p < 0.01 [F(1, 243) = 9.159, p = 0.0027]) and various forms of fALS along with SCA1 (p < 0.01 [F(1, 83) = 11.285], p = 0.0012) and SCA2 (p < 0.001 [F(1, 122) = 29.996, p = 0.0001]) when compared to age- and sex-matched healthy controls. C9orf72 expansion carrier ALS patients exhibit the highest global 5-mC levels along with C9orf72 promoter hypermethylation. We failed to measure global 5-hydroxymethylcytosine (5-hmC) levels in blood, probably due to the very low levels of 5-hmC and the limitations of the commercially available ELISA kits. Our results point towards a role for epigenetics modification in ALS, SCA1, and SCA2, and help conclude a dispute on the global 5-mC levels in sALS blood.
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Affiliation(s)
- Hamid Hamzeiy
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Doruk Savaş
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Ceren Tunca
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Nesli Ece Şen
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Aslı Gündoğdu Eken
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Irmak Şahbaz
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
| | - Daniela Calini
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Cinzia Tiloca
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Nicola Ticozzi
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Milan, Italy
| | - Antonia Ratti
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Milan, Italy
| | - Vincenzo Silani
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto Auxologico Italiano, Milan, Italy.,Department of Pathophysiology and Transplantation, "Dino Ferrari" Center, Università degli Studi di Milano, Milan, Italy
| | - A Nazlı Başak
- Suna and İnan Kıraç Foundation, Neurodegeneration Research Laboratory (NDAL), Molecular Biology and Genetics Department, Boğaziçi University, Istanbul, Turkey
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Abstract
The dominant polyglutamine (polyQ) disorders are a group of progressive and incurable neurodegenerative disorders, which are caused by unstable expanded CAG trinucleotide repeats in the coding regions of their respective causative genes. The most prevalent polyQ disorders worldwide are Huntington’s disease and spinocerebellar ataxia type 3. Epigenetic mechanisms, such as DNA methylation, histone modifications and chromatin remodeling and noncoding RNA regulation, regulate gene expression or genome function. Epigenetic dysregulation has been suggested to play a pivotal role in the pathogenesis of polyQ disorders. Here, we summarize the current knowledge of epigenetic changes present in several representative polyQ disorders and discuss the potentiality of miRNAs as therapeutic targets for the clinic therapy of these disorders.
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Affiliation(s)
- Hongmei Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Tie-Shan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
| | - Caixia Guo
- CAS Key Laboratory of Genomics & Precision Medicine, Beijing Institute of Genomics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100101, China
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28
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Andersen GB, Tost J. A Summary of the Biological Processes, Disease-Associated Changes, and Clinical Applications of DNA Methylation. Methods Mol Biol 2018; 1708:3-30. [PMID: 29224136 DOI: 10.1007/978-1-4939-7481-8_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA methylation at cytosines followed by guanines, CpGs, forms one of the multiple layers of epigenetic mechanisms controlling and modulating gene expression through chromatin structure. It closely interacts with histone modifications and chromatin remodeling complexes to form the local genomic and higher-order chromatin landscape. DNA methylation is essential for proper mammalian development, crucial for imprinting and plays a role in maintaining genomic stability. DNA methylation patterns are susceptible to change in response to environmental stimuli such as diet or toxins, whereby the epigenome seems to be most vulnerable during early life. Changes of DNA methylation levels and patterns have been widely studied in several diseases, especially cancer, where interest has focused on biomarkers for early detection of cancer development, accurate diagnosis, and response to treatment, but have also been shown to occur in many other complex diseases. Recent advances in epigenome engineering technologies allow now for the large-scale assessment of the functional relevance of DNA methylation. As a stable nucleic acid-based modification that is technically easy to handle and which can be analyzed with great reproducibility and accuracy by different laboratories, DNA methylation is a promising biomarker for many applications.
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Affiliation(s)
- Gitte Brinch Andersen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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29
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Lejart A, Salbert G, Huet S. Cytosine hydroxymethylation by TET enzymes: From the control of gene expression to the regulation of DNA repair mechanisms, and back. AIMS BIOPHYSICS 2018. [DOI: 10.3934/biophy.2018.3.182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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30
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Kader F, Ghai M, Maharaj L. The effects of DNA methylation on human psychology. Behav Brain Res 2017; 346:47-65. [PMID: 29237550 DOI: 10.1016/j.bbr.2017.12.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/01/2017] [Accepted: 12/05/2017] [Indexed: 01/05/2023]
Abstract
DNA methylation is a fundamental epigenetic modification in the human genome; pivotal in development, genomic imprinting, X inactivation, chromosome stability, gene expression and methylation aberrations are involved in an array of human diseases. Methylation at promoters is associated with transcriptional repression, whereas gene body methylation is generally associated with gene expression. Extrinsic factors such as age, diets and lifestyle affect DNA methylation which consequently alters gene expression. Stress, anxiety, depression, life satisfaction, emotion among numerous other psychological factors also modify DNA methylation patterns. This correlation is frequently investigated in four candidate genes; NR3C1, SLC6A4, BDNF and OXTR, since regulation of these genes directly impact responses to social situations, stress, threats, behaviour and neural functions. Such studies underpin the hypothesis that DNA methylation is involved in deviant human behaviour, psychological and psychiatric conditions. These candidate genes may be targeted in future to assess the correlation between methylation, social experiences and long-term behavioural phenotypes in humans; and may potentially serve as biomarkers for therapeutic intervention.
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Affiliation(s)
- Farzeen Kader
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000 South Africa.
| | - Meenu Ghai
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000 South Africa.
| | - Leah Maharaj
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000 South Africa.
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31
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Kovalchuk A, Rodriguez-Juarez R, Ilnytskyy Y, Byeon B, Shpyleva S, Melnyk S, Pogribny I, Kolb B, Kovalchuk O. Sex-specific effects of cytotoxic chemotherapy agents cyclophosphamide and mitomycin C on gene expression, oxidative DNA damage, and epigenetic alterations in the prefrontal cortex and hippocampus - an aging connection. Aging (Albany NY) 2017; 8:697-711. [PMID: 27032448 PMCID: PMC4925823 DOI: 10.18632/aging.100920] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 01/30/2016] [Indexed: 01/21/2023]
Abstract
Recent research shows that chemotherapy agents can be more toxic to healthy brain cells than to the target cancer cells. They cause a range of side effects, including memory loss and cognitive dysfunction that can persist long after the completion of treatment. This condition is known as chemo brain. The molecular and cellular mechanisms of chemo brain remain obscure. Here, we analyzed the effects of two cytotoxic chemotherapy drugs—cyclophosphamide (CPP) and mitomycin C (MMC) - on transcriptomic and epigenetic changes in the murine prefrontal cortex (PFC) and hippocampal regions. We for the first time showed that CPP and MMC treatments led to profound sex- and brain region-specific alterations in gene expression profiles. Gene expression changes were most prominent in the PFC tissues of female mice 3 weeks after MMC treatment, and the gene expression response was much greater for MCC than CPP exposure. MMC exposure resulted in oxidative DNA damage, evidenced by accumulation of 8-oxo-2′-deoxyguanosine (8-oxodG) and a decrease in the level of 8-oxodG repair protein OGG1 in the PFC of female animals 3 weeks after treatment. MMC treatment decreased global DNA methylation and increased DNA hydroxymethylation in the PFC tissues of female mice. The majority of the changes induced by chemotherapy in the PFC tissues of female mice resembled those that occur during the brain's aging processes. Therefore, our study suggests a link between chemotherapy-induced chemo brain and brain aging, and provides an important roadmap for future analysis.
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Affiliation(s)
- Anna Kovalchuk
- Department of Neuroscience, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada
| | - Rocio Rodriguez-Juarez
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada
| | - Yaroslav Ilnytskyy
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada
| | - Boseon Byeon
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada
| | - Svitlana Shpyleva
- Division of Biochemical Toxicology, Food and Drug Administration National Center for Toxicological Research, Jefferson, AR 72079, USA.,Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
| | - Stepan Melnyk
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
| | - Igor Pogribny
- Division of Biochemical Toxicology, Food and Drug Administration National Center for Toxicological Research, Jefferson, AR 72079, USA
| | - Bryan Kolb
- Department of Neuroscience, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada.,Alberta Epigenetics Network, Calgary, AB, T2L 2A6, Canada.,Canadian Institute for Advanced Research, Toronto, ON, M5G 1Z8, Canada
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, T1K3M4, Canada.,Alberta Epigenetics Network, Calgary, AB, T2L 2A6, Canada
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Montrose L, Faulk C, Francis J, Dolinoy D. Perinatal lead (Pb) exposure results in sex and tissue-dependent adult DNA methylation alterations in murine IAP transposons. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:540-550. [PMID: 28833526 PMCID: PMC5784428 DOI: 10.1002/em.22119] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/25/2017] [Accepted: 05/25/2017] [Indexed: 05/17/2023]
Abstract
Epidemiological and animal data suggest that adult chronic disease is influenced by early-life exposure-induced changes to the epigenome. Previously, we observed that perinatal lead (Pb) exposure results in persistent murine metabolic- and activity-related effects. Using phylogenetic and DNA methylation analysis, we have also identified novel intracisternal A particle (IAP) retrotransposons exhibiting regions of variable methylation as candidate loci for environmental effects on the epigenome. Here, we now evaluate brain and kidney DNA methylation profiles of four representative IAPs in adult mice exposed to human physiologically relevant levels of Pb two weeks prior to mating through lactation. When IAPs across the genome were evaluated globally, average (sd) methylation levels were 92.84% (3.74) differing by tissue (P < 0.001), but not sex or dose. By contrast, the four individual IAPs displayed tissue-specific Pb and sex effects. Medium Pb-exposed mice had 3.86% less brain methylation at IAP 110 (P < 0.01), while high Pb-exposed mice had 2.83% less brain methylation at IAP 236 (P = 0.01) and 1.77% less at IAP 506 (P = 0.05). Individual IAP DNA methylation differed by sex for IAP 110 in the brain and kidney, IAP 236 in the kidney, and IAP 1259 in the kidney. Using Tomtom, we identified three binding motifs that matched to each of our novel IAPs impacted by Pb, one of which (HMGA2) has been linked to metabolic-related conditions in both mice and humans. Thus, these recently identified IAPs display tissue-specific environmental lability as well as sex-specific differences supporting an epigenetic link between early exposure to Pb and later-in-life health outcomes. Environ. Mol. Mutagen. 58:540-550, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- L. Montrose
- Environmental Health Sciences, University of Michigan
| | - C. Faulk
- Animal Science, University of Minnesota
| | - J. Francis
- Environmental Health Sciences, University of Michigan
| | - D.C. Dolinoy
- Environmental Health Sciences, University of Michigan
- Nutritional Sciences, University of Michigan
- Corresponding author: Dana C. Dolinoy, 1415 Washington Heights, Ann Arbor, Michigan 48109-2029, Tel: 734 647-3155,
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López V, Fernández A, Fraga M. The role of 5-hydroxymethylcytosine in development, aging and age-related diseases. Ageing Res Rev 2017; 37:28-38. [PMID: 28499883 DOI: 10.1016/j.arr.2017.05.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/02/2017] [Accepted: 05/02/2017] [Indexed: 12/24/2022]
Abstract
DNA methylation at the fifth position of cytosines (5mC) represents a major epigenetic modification in mammals. The recent discovery of 5-hydroxymethylcytosine (5hmC), resulting from 5mC oxidation, is redefining our view of the epigenome, as multiple studies indicate that 5hmC is not simply an intermediate of DNA demethylation, but a genuine epigenetic mark that may play an important functional role in gene regulation. Currently, the availability of platforms that discriminates between the presence of 5mC and 5hmC at single-base resolution is starting to shed light on the functions of 5hmC. In this review, we provide an overview of the genomic distribution of 5hmC, and examine recent findings on the role of this mark and the potential consequences of its misregulation during three fundamental biological processes: cell differentiation, cancer and aging.
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CpG and Non-CpG Methylation in Epigenetic Gene Regulation and Brain Function. Genes (Basel) 2017; 8:genes8060148. [PMID: 28545252 PMCID: PMC5485512 DOI: 10.3390/genes8060148] [Citation(s) in RCA: 232] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/18/2017] [Accepted: 05/19/2017] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is a major epigenetic mark with important roles in genetic regulation. Methylated cytosines are found primarily at CpG dinucleotides, but are also found at non-CpG sites (CpA, CpT, and CpC). The general functions of CpG and non-CpG methylation include gene silencing or activation depending on the methylated regions. CpG and non-CpG methylation are found throughout the whole genome, including repetitive sequences, enhancers, promoters, and gene bodies. Interestingly, however, non-CpG methylation is restricted to specific cell types, such as pluripotent stem cells, oocytes, neurons, and glial cells. Thus, accumulation of methylation at non-CpG sites and CpG sites in neurons seems to be involved in development and disease etiology. Here, we provide an overview of CpG and non-CpG methylation and their roles in neurological diseases.
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Wang D, Huang JH, Zeng QH, Gu C, Ding S, Lu JY, Chen J, Yang SB. Increased 5-hydroxymethylcytosine and Ten-eleven Translocation Protein Expression in Ultraviolet B-irradiated HaCaT Cells. Chin Med J (Engl) 2017; 130:594-599. [PMID: 28229992 PMCID: PMC5339934 DOI: 10.4103/0366-6999.200539] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background: DNA hydroxymethylation refers to a chemical modification process in which 5-methylcytosine (5mC) is catalyzed to 5- hydroxymethylcytosine (5hmC) by ten-eleven translocation (TET) family proteins. Recent studies have revealed that aberrant TETs expression or 5hmC level may play important roles in the occurrence and development of various pathological and physiological processes including cancer and aging. This study aimed to explore the relation between aberrant DNA hydroxymethylation with skin photoaging and to investigate the levels of TETs, 5mC, and 5hmC expression 24 h after 40 mJ/cm2 and 80 mJ/cm2 doses of ultraviolet B (UVB) irradiation to HaCaT cells. Methods: To explore whether aberrant DNA hydroxymethylation is also related to skin photoaging, 40 mJ/cm2 and 80 mJ/cm2 doses of UVB were chosen to treat keratinocytes (HaCaT cells). After 24 h of UVB irradiation, 5mC and 5hmC levels were determined by immunohistochemistry (IHC) and immunofluorescence (IF), and at the same time, the expression levels of matrix metalloproteinase 1 (MMP-1) and TETs were assessed by reverse transcription-polymerase chain reaction or Western blot analysis. Results: After 40 mJ/cm2 and 80 mJ/cm2 doses of UVB exposure, both IHC and IF results showed that 5hmC levels increased significantly, while the 5mC levels did not exhibit significant changes in HaCaT cells, compared with HaCat cells without UVB exposure. Moreover, compared with HaCat cells without UVB exposure, the levels of TET1, TET2, and TET3 mRNA and protein expression were significantly upregulated (mRNA: P = 0.0022 and 0.0043 for TET1; all P < 0.0001 for TET2; all P = 0.0006 for TET3; protein: P = 0.0012 and 0.0006 for TET1; all P = 0.0022 for TET2; and all P = 0.0002 for TET3), and the levels of MMP-1 mRNA expression increased dose dependently in 40 mJ/cm2 and 80 mJ/cm2 UVB-irradiated groups. Conclusion: UVB radiation could cause increased 5hmC and TET expression, which might become a novel biomarker in UVB-related skin aging.
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Affiliation(s)
- Dan Wang
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Jin-Hua Huang
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Qing-Hai Zeng
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Can Gu
- Department of Community Nursing, Xiangya School of Nursing, Central South University, Changsha, Hunan 410013, China
| | - Shu Ding
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Jian-Yun Lu
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Jing Chen
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Sheng-Bo Yang
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
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Hasei J, Teramura T, Takehara T, Onodera Y, Horii T, Olmer M, Hatada I, Fukuda K, Ozaki T, Lotz MK, Asahara H. TWIST1 induces MMP3 expression through up-regulating DNA hydroxymethylation and promotes catabolic responses in human chondrocytes. Sci Rep 2017; 7:42990. [PMID: 28220902 PMCID: PMC5318945 DOI: 10.1038/srep42990] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 01/18/2017] [Indexed: 02/05/2023] Open
Abstract
The objective was to investigate the levels of TWIST1 in normal and OA cartilage and examine its role in regulating gene expression in chondrocytes. Human cartilage tissues and chondrocytes were obtained at autopsy from normal knee joints and from OA-affected joints at the time of total knee arthroplasty. TWIST1 expression was increased in human OA knee cartilage compared to normal knee cartilage. TWIST1 induced matrix metalloproteinase 3 (MMP3) expression without direct binding to MMP3 promoter and increased the 5-hydroxymethylcytosine (5hmC) level at the MMP3 promoter. The effect of TWIST1 on expression of TET family (TET1, 2 and 3) was measured in stable TWIST1 transfected TC28 cells, and TET1 expression was up-regulated. TWIST1 dependent upregulation of Mmp3 expression was suppressed in Tet triple KO fibroblast derived from mouse ES cells. Increased TWIST1 expression is a feature of OA-affected cartilage. We identified a novel mechanism of catabolic reaction where TWIST1 up-regulates MMP3 expression by enriching 5hmC levels at the MMP3 promoter via TET1 induction. These findings implicate TWIST1 as an important factor regulating OA related gene expression. Clarifying epigenetic mechanisms of 5hmC induced by TWIST1 is a critical molecule to understanding OA pathogenesis.
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Affiliation(s)
- Joe Hasei
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Takeshi Teramura
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Division of Cell Biology for Regenerative Medicine, Institute of Advanced Clinical Medicine, Kindai University, Faculty of Medicine, Osaka, Japan
| | - Toshiyuki Takehara
- Division of Cell Biology for Regenerative Medicine, Institute of Advanced Clinical Medicine, Kindai University, Faculty of Medicine, Osaka, Japan
| | - Yuta Onodera
- Division of Cell Biology for Regenerative Medicine, Institute of Advanced Clinical Medicine, Kindai University, Faculty of Medicine, Osaka, Japan
| | - Takuro Horii
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma, Japan
| | - Merissa Olmer
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Izuho Hatada
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma, Japan
| | - Kanji Fukuda
- Division of Cell Biology for Regenerative Medicine, Institute of Advanced Clinical Medicine, Kindai University, Faculty of Medicine, Osaka, Japan
- Department of Rehabilitation Medicine, Kindai University, Faculty of Medicine, Osaka, Japan
| | - Toshifumi Ozaki
- Science of Functional Recovery and Reconstruction, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Martin K. Lotz
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Hiroshi Asahara
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Department of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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37
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Ellison EM, Abner EL, Lovell MA. Multiregional analysis of global 5-methylcytosine and 5-hydroxymethylcytosine throughout the progression of Alzheimer's disease. J Neurochem 2017; 140:383-394. [PMID: 27889911 PMCID: PMC5250541 DOI: 10.1111/jnc.13912] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/19/2016] [Accepted: 11/22/2016] [Indexed: 12/16/2022]
Abstract
Epigenetic modifications to cytosine are known to alter transcriptional states and deregulate gene expression in cancer, embryonic development, and most recently in neurodegeneration. To test the hypothesis that global levels of cytosine modification are altered throughout the progression of Alzheimer's disease, 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) were quantified using gas chromatography/mass spectrometry (GC/MS) and stable labeled internal standards of cytosine, 5-mC, and 5-hmC. Cytosine modifications were quantified in DNA extracted from tissue specimens of four brain regions (cerebellum, inferior parietal lobe, superior and middle temporal gyrus, and hippocampus/parahippocampal gyrus) of cognitively normal control (NC) subjects and subjects with mild cognitive impairment (MCI), preclinical Alzheimer's disease (PCAD), late onset Alzheimer's disease, frontotemporal lobar degeneration (FTLD) and dementia with Lewy bodies (DLB). Repeated measures analyses of the data show significant alterations in 5-mC and 5-hmC in early stages of Alzheimer's disease (PCAD and MCI), as well as FTLD and DLB subjects, across multiple regions of the brain. These data suggest alterations in epigenetic regulation of genes may play an early role in the progression of AD as well as other types of neurodegeneration.
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Affiliation(s)
| | - Erin L. Abner
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Department of Epidemiology, University of Kentucky, Lexington, KY
| | - Mark A. Lovell
- Department of Chemistry, University of Kentucky, Lexington, KY
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
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38
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Wei H, Feng Y, Liang F, Cheng W, Wu X, Zhou R, Wang Y. Role of oxidative stress and DNA hydroxymethylation in the neurotoxicity of fine particulate matter. Toxicology 2017; 380:94-103. [PMID: 28153600 DOI: 10.1016/j.tox.2017.01.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 01/22/2017] [Accepted: 01/26/2017] [Indexed: 11/26/2022]
Abstract
Epidemiological studies have implicated fine particulate matter (PM2.5) as a risk factor for neurodegenerative diseases and neurodevelopmental disorders. However, the underlying molecular mechanisms and the influences of different components remain largely elusive. Here, we extended our previous work to investigate the role of oxidative stress and DNA hydroxymethylation in neuronal pathology of PM2.5. We found PM2.5 and its extracts (water-soluble extracts, organic extracts and carbon core component) differentially caused cell cycle arrest, cell apoptosis and the cell proliferation inhibition in neuronal cells. These effects were mechanistically related to each other and oxidative stress, suggesting PM2.5 and toxic compounds adsorbed on the particles may cause different types of brain damages. In addition, PM2.5 and its organic extracts increased global DNA hydroxymethylation and gene-specific DNA hydroxymethylation of neuronal genes, and subsequently interfered with their mRNA expression. The impairments in neuronal progression characterized with decreased length of neurite and reduced mRNA expression of neuronal markers and synaptic markers. The blocking effects of antioxidants demonstrated the involvement of oxidative stress-mediated hydroxymethylation abnormalities in PM2.5-induced defects in neurite outgrowth and synapse formation. Our results first revealed the role of oxidative stress-mediated abnormal DNA hydroxymethylation in neuronal impairments of PM2.5, and thoroughly evaluated the neurocytotoxicity of different components.
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Affiliation(s)
- Hongying Wei
- The Ninth People Hospital of Shanghai Jiao Tong University School of Medicine, No. 639 Zhizaoju Road, Shanghai 200011, China
| | - Yan Feng
- School of Public Health, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqing South Road, Shanghai 200025, China
| | - Fan Liang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqing South Road, Shanghai 200025, China
| | - Wei Cheng
- School of Public Health, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqing South Road, Shanghai 200025, China
| | - Xiaomeng Wu
- School of Public Health, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqing South Road, Shanghai 200025, China
| | - Ren Zhou
- School of Public Health, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqing South Road, Shanghai 200025, China
| | - Yan Wang
- The Ninth People Hospital of Shanghai Jiao Tong University School of Medicine, No. 639 Zhizaoju Road, Shanghai 200011, China; School of Public Health, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqing South Road, Shanghai 200025, China; MOE-Shanghai Key Laboratory of Children's Environmental Health, No. 1665 Kongjiang Road, Shanghai, 200092, China.
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Grzybek M, Golonko A, Walczak M, Lisowski P. Epigenetics of cell fate reprogramming and its implications for neurological disorders modelling. Neurobiol Dis 2016; 99:84-120. [PMID: 27890672 DOI: 10.1016/j.nbd.2016.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 11/03/2016] [Accepted: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
The reprogramming of human induced pluripotent stem cells (hiPSCs) proceeds in a stepwise manner with reprogramming factors binding and epigenetic composition changes during transition to maintain the epigenetic landscape, important for pluripotency. There arises a question as to whether the aberrant epigenetic state after reprogramming leads to epigenetic defects in induced stem cells causing unpredictable long term effects in differentiated cells. In this review, we present a comprehensive view of epigenetic alterations accompanying reprogramming, cell maintenance and differentiation as factors that influence applications of hiPSCs in stem cell based technologies. We conclude that sample heterogeneity masks DNA methylation signatures in subpopulations of cells and thus believe that beside a genetic evaluation, extensive epigenomic screening should become a standard procedure to ensure hiPSCs state before they are used for genome editing and differentiation into neurons of interest. In particular, we suggest that exploitation of the single-cell composition of the epigenome will provide important insights into heterogeneity within hiPSCs subpopulations to fast forward development of reliable hiPSC-based analytical platforms in neurological disorders modelling and before completed hiPSC technology will be implemented in clinical approaches.
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Affiliation(s)
- Maciej Grzybek
- Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-950 Lublin, Poland; Department of Molecular Biology, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, Postępu 36A, 05-552 Magdalenka, Poland.
| | - Aleksandra Golonko
- Department of Biotechnology, Faculty of Civil and Environmental Engineering, Bialystok University of Technology, Wiejska 45E, 15-351 Bialystok, Poland.
| | - Marta Walczak
- Department of Animal Behavior, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, Postępu 36A, 05-552 Magdalenka, Poland.
| | - Pawel Lisowski
- Department of Molecular Biology, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, Postępu 36A, 05-552 Magdalenka, Poland; iPS Cell-Based Disease Modelling Group, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Rössle-Str. 10, 13092 Berlin, Germany.
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40
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ALS and FTD: an epigenetic perspective. Acta Neuropathol 2016; 132:487-502. [PMID: 27282474 DOI: 10.1007/s00401-016-1587-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/17/2016] [Accepted: 06/02/2016] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are two fatal neurodegenerative diseases seen in comorbidity in up to 50 % of cases. Despite tremendous efforts over the last two decades, no biomarkers or effective therapeutics have been identified to prevent, decelerate, or stop neuronal death in patients. While the identification of multiple mutations in more than two dozen genes elucidated the involvement of several mechanisms in the pathogenesis of both diseases, identifying the hexanucleotide repeat expansion in C9orf72, the most common genetic abnormality in ALS and FTD, opened the door to the discovery of several novel pathogenic biological routes, including chromatin remodeling and transcriptome alteration. Epigenetic processes regulate DNA replication and repair, RNA transcription, and chromatin conformation, which in turn further dictate transcriptional regulation and protein translation. Transcriptional and post-transcriptional epigenetic regulation is mediated by enzymes and chromatin-modifying complexes that control DNA methylation, histone modifications, and RNA editing. While the alteration of DNA methylation and histone modification has recently been reported in ALS and FTD, the assessment of epigenetic involvement in both diseases is still at an early stage, and the involvement of multiple epigenetic players still needs to be evaluated. As the epigenome serves as a way to alter genetic information not only during aging, but also following environmental signals, epigenetic mechanisms might play a central role in initiating ALS and FTD, especially for sporadic cases. Here, we provide a review of what is currently known about altered epigenetic processes in both ALS and FTD and discuss potential therapeutic strategies targeting epigenetic mechanisms. As approximately 85 % of ALS and FTD cases are still genetically unexplained, epigenetic therapeutics explored for other diseases might represent a profitable direction for the field.
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41
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Hack LM, Dick AL, Provençal N. Epigenetic mechanisms involved in the effects of stress exposure: focus on 5-hydroxymethylcytosine. ENVIRONMENTAL EPIGENETICS 2016; 2:dvw016. [PMID: 29492296 PMCID: PMC5804530 DOI: 10.1093/eep/dvw016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 06/03/2016] [Accepted: 06/11/2016] [Indexed: 05/31/2023]
Abstract
5-hydroxymethylcytosine (5hmC) is a recently re-discovered transient intermediate in the active demethylation pathway that also appears to play an independent role in modulating gene function. Epigenetic marks, particularly 5-methylcytosine, have been widely studied in relation to stress-related disorders given the long-lasting effect that stress has on these marks. 5hmC is a good candidate for involvement in the etiology of these disorders given its elevated concentration in mammalian neurons, its dynamic regulation during development of the central nervous system, and its high variability among individuals. Although we are unaware of any studies published to date examining 5 hmC profiles in human subjects who have developed a psychiatric disorder after a life stressor, there is emerging evidence from the animal literature that 5hmC profiles are altered in the context of fear-conditioning paradigms and stress exposure, suggesting a possible role for 5hmC in the biological underpinnings of stress-related disorders. In this review, the authors examine the available approaches for profiling 5hmC and describe their advantages and disadvantages as well as discuss the studies published thus far investigating 5hmC in the context of fear-related learning and stress exposure in animals. The authors also highlight the global versus locus-specific regulation of 5hmC in these studies. Finally, the limitations of the current studies and their implications are discussed.
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Affiliation(s)
- Laura M. Hack
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University Medical School, Atlanta, GA, USA
| | - Alec L.W. Dick
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Nadine Provençal
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
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Buscarlet M, Tessier A, Provost S, Mollica L, Busque L. Human blood cell levels of 5-hydroxymethylcytosine (5hmC) decline with age, partly related to acquired mutations in TET2. Exp Hematol 2016; 44:1072-1084. [PMID: 27475703 DOI: 10.1016/j.exphem.2016.07.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/08/2016] [Accepted: 07/14/2016] [Indexed: 12/15/2022]
Abstract
Epigenetic alteration may play a role in age-associated dysfunction of stem cells and predispose to the development of hematological cancers. We analyzed global levels of hematopoietic 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) in a cross-sectional study comprising 198 unrelated individuals from four age categories (neonates, 25-30, 70-75, and >90 years old) by liquid chromatography-electrospray ionization-tandem mass spectrometry with multiple reaction monitoring. X-chromosome inactivation (XCI) ratios and telomere length (TL) were measured in all individuals by polymerase chain reaction. Sequencing of epigenetic regulator genes (including TET2, DNMT3A, ASXL1, IDH1, IDH2, and WT1) was performed in the two older subcohorts. We found that global 5hmC levels declined with age in human blood cells (27.5% reduction from birth to old age, p < 0.0005). The levels of 5mC underwent a more modest reduction (2.4% drop) between newborns and the elderly (p < 0.0005). Low 5hmC was associated with increased skewing of XCI (age-adjusted p = 0.0304) and reduced TL (age-adjusted p = 0.0354), both surrogate markers of clonal dominance. Of the 100 individuals over the age of 70, 16 had somatic mutations in TET2, 14 in DNMT3A, and none in IDH1, IDH2, or WT1. Individuals with TET2 mutations had significantly lower 5hmC (relative to unmutated individuals), whereas DNMT3A-mutated subjects did not. However, mutations in TET2 cannot account solely for the decline in 5hmC levels observed with aging because unmutated older individuals also had lower 5hmC levels compared with younger individuals. This suggests that the age-associated decline in 5hmC is multifactorial. Larger prospective studies are needed to determine whether 5hmC reduction is a biomarker of hematological cancer development.
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Affiliation(s)
| | - Alain Tessier
- Centre for Biological Applications of Mass Spectrometry, Department of Chemistry and Biochemistry, Concordia University, Montreal, Canada
| | - Sylvie Provost
- Beaulieu-Saucier Pharmacogenomics Centre, Montreal Heart Institute Research Centre, Montreal, Canada
| | - Luigina Mollica
- Research Centre, Montreal, Canada; Department of Hematology, Installation Hôpital Maisonneuve-Rosemont, Montreal, Canada; Université de Montréal, Montreal, Canada
| | - Lambert Busque
- Research Centre, Montreal, Canada; Department of Hematology, Installation Hôpital Maisonneuve-Rosemont, Montreal, Canada; Université de Montréal, Montreal, Canada.
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Abstract
PURPOSE OF REVIEW The activation of inflammatory response is dependent upon genetic factors and epigenetic control mechanisms. This overview will highlight recent advances in the understanding of epigenetic dynamics during cellular inflammation. RECENT FINDINGS There is a growing body of evidence indicating that alterations of the chromatin state associate with an increased risk of chronic disease development and inflammation. Epigenetic alterations respond rapidly to environmental changes and have a profound effect on gene regulatory cross-wirings and transcriptional regulation. SUMMARY Systematic dissection of the mechanisms underlying epigenetic effects during inflammatory response is a critical step toward elucidation of the cell's molecular processes and holds potential for the development of novel therapies for the treatment of chronic diseases.
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Affiliation(s)
- Dashzeveg Bayarsaihan
- Institute for System Genomics and Center for Regenerative Medicine and Skeletal Development, University of Connecticut Health Center, Farmington, Connecticut, USA
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44
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Thomas EA. DNA methylation in Huntington's disease: Implications for transgenerational effects. Neurosci Lett 2016; 625:34-9. [PMID: 26522374 PMCID: PMC4864163 DOI: 10.1016/j.neulet.2015.10.060] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 10/08/2015] [Accepted: 10/23/2015] [Indexed: 12/29/2022]
Abstract
Huntington's disease (HD) is a devastating, neurodegenerative disorder caused by a CAG repeat mutation in the HTT gene. A growing body of evidence suggests that epigenetic modifications play a key role in HD pathogenesis. Expression of the disease protein, huntingtin, leads to extensive transcriptional dysregulation due to disruption of histone-modifying complexes and altered interactions with chromatin-related factors. Such epigenetic mechanisms also readily respond to environmental factors, which are now thought to influence the risk, onset and progression of neurodegenerative disorders, including HD. DNA methylation is an epigenetic modification that has been studied intensively, however, its role in HD is just emerging. In this review, DNA methylation differences associated with HD will be summarized, as well as the role of environmental factors to alter DNA methylation in a manner that could alter disease phenotypes. Further, transgenerational epigenetic inheritance will be discussed in the context of relevant environmental factors and their potential links to HD. The study of epigenetic states in HD presents an opportunity to gain new insights into risk factors and pathogenic mechanisms associated with HD, as well as to inform about treatment options.
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Affiliation(s)
- Elizabeth A Thomas
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, CA, United States.
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45
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Wüllner U, Kaut O, deBoni L, Piston D, Schmitt I. DNA methylation in Parkinson's disease. J Neurochem 2016; 139 Suppl 1:108-120. [DOI: 10.1111/jnc.13646] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/21/2016] [Accepted: 04/15/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Ullrich Wüllner
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
| | - Oliver Kaut
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
| | - Laura deBoni
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
| | - Dominik Piston
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
| | - Ina Schmitt
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
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46
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Abstract
5-Methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are fingerprints of epigenetic modifications. These bases have been found in the mitochondrial DNA (mtDNA) and together with the discovery of mitochondrial localization of DNA methyltransferases, this implies that mtDNA is under epigenetic regulation. However, the indirect methods hitherto used to assess mitochondrial 5mC and 5hmC require attention as they readily generate artificial signals that may lead to erroneous conclusions. Here, we demonstrate how three independent, frequently used methods to identify epigenetic modification of DNA readily generate false mtDNA epigenetic signals. The three methods were selective 5mC/5hmC-mediated inhibition of restriction enzymes, bisulfite conversion and 5hmC glucosylation-dependent immunocapture. Adequate controls for all methods are suggested.
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Affiliation(s)
- Tina Pawar
- a Department of Medical Biochemistry , Institute of Clinical Medicine, University of Oslo , Oslo , Norway
| | - Lars Eide
- a Department of Medical Biochemistry , Institute of Clinical Medicine, University of Oslo , Oslo , Norway
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47
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Miao Z, Xin N, Wei B, Hua X, Zhang G, Leng C, Zhao C, Wu D, Li J, Ge W, Sun M, Xu X. 5-hydroxymethylcytosine is detected in RNA from mouse brain tissues. Brain Res 2016; 1642:546-552. [PMID: 27117867 DOI: 10.1016/j.brainres.2016.04.055] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 04/10/2016] [Accepted: 04/22/2016] [Indexed: 01/05/2023]
Abstract
5-hydroxymethylcytosine (5hmC) is considered as a novel DNA modification and plays an important role in cancer, stem cells, and developmental diseases. In this study, we demonstrated the existence of RNA 5hmC modification in mouse brain RNA by using a dot blot analysis method. Our data indicated that 5hmC modification in RNA samples was less than that in DNA samples. Further, we optimized the conditions for 5hmC detection in RNA samples such as DNase treatment, denature reagents, denature time, sample air-dry time, and the cross-linking time between RNA and membrane. Our results demonstrated that DNase treatment and denature reagents were two important factors that affected the 5hmC detection in RNA samples. By using the optimal conditions for RNA 5hmC detection, we found that the brainstem, the hippocampus, and the cerebellum had high levels of 5hmC modification and 5mC modification in RNA. Finally, we found that RNA 5hmC modification decreased in MPTP-induced Parkinson's disease model in mice. These suggest that 5hmC modification in RNA might play an important regulative role on protein or microRNA expression in these brain tissues. Because DNA 5hmC modification plays an important role in neural differentiation and development as well as neurological diseases, the significance of 5hmC modification in RNA in different neurological diseases needs further investigation. In summary, our study demonstrated for the first time the abundance of 5hmC modification in brain RNA by using a dot blot analysis method and proved that dot blot analysis is a useful method for 5hmC detection in RNA samples.
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Affiliation(s)
- Zhigang Miao
- Department of Neurology, the Second Affiliated Hospital of Soochow University, Suzhou City, Jiangsu, China; Institute of Neuroscience, Soochow University, Suzhou City, Jiangsu, China
| | - Ning Xin
- Department of Neurology, the Second Affiliated Hospital of Soochow University, Suzhou City, Jiangsu, China
| | - Bin Wei
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu, China
| | - Xiaodong Hua
- Department of Emergency, Emory University Hospital, Atlanta, GA, USA; Department of Biochemistry, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA
| | - Gaocai Zhang
- Department of Neurology, the Second Affiliated Hospital of Soochow University, Suzhou City, Jiangsu, China; Institute of Neuroscience, Soochow University, Suzhou City, Jiangsu, China
| | - Cuihua Leng
- Department of Neurology, the Second Affiliated Hospital of Soochow University, Suzhou City, Jiangsu, China; Institute of Neuroscience, Soochow University, Suzhou City, Jiangsu, China
| | - Chenyu Zhao
- Department of Neurology, the Second Affiliated Hospital of Soochow University, Suzhou City, Jiangsu, China; Institute of Neuroscience, Soochow University, Suzhou City, Jiangsu, China
| | - Di Wu
- Department of Neurology, the Second Affiliated Hospital of Soochow University, Suzhou City, Jiangsu, China; Institute of Neuroscience, Soochow University, Suzhou City, Jiangsu, China
| | - Jizhen Li
- Department of Neurology, Suzhou Kowloon Hospital, Suzhou City, China
| | - Wei Ge
- Department of Neurology, the Second Affiliated Hospital of Soochow University, Suzhou City, Jiangsu, China; Department of Neurology, the Affiliated Hospital of Xuzhou Medical College, Xuzhou City, Jiangsu, China
| | - Miao Sun
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou City, Jiangsu, China.
| | - Xingshun Xu
- Department of Neurology, the Second Affiliated Hospital of Soochow University, Suzhou City, Jiangsu, China; Institute of Neuroscience, Soochow University, Suzhou City, Jiangsu, China.
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48
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Cadet JL, McCoy MT, Jayanthi S. Epigenetics and addiction. Clin Pharmacol Ther 2016; 99:502-11. [PMID: 26841306 DOI: 10.1002/cpt.345] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/18/2016] [Accepted: 01/26/2016] [Indexed: 12/13/2022]
Abstract
Addictions are public health menaces. However, despite advances in addiction research, the cellular or molecular mechanisms that cause transition from recreational use to addiction remain to be elucidated. We have recently suggested that addiction may be secondary to long-term epigenetic modifications that determine the clinical course of substance use disorders. A better understanding of epigenetic mechanisms in animal models that mimic human conditions should help to usher in a new area of drug development against addiction.
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Affiliation(s)
- J L Cadet
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
| | - M T McCoy
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
| | - S Jayanthi
- Molecular Neuropsychiatry Research Branch, NIH/NIDA Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
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49
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Alaghband Y, Bredy TW, Wood MA. The role of active DNA demethylation and Tet enzyme function in memory formation and cocaine action. Neurosci Lett 2016; 625:40-6. [PMID: 26806038 DOI: 10.1016/j.neulet.2016.01.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 11/29/2015] [Accepted: 01/14/2016] [Indexed: 01/12/2023]
Abstract
Active DNA modification is a major epigenetic mechanism that regulates gene expression in an experience-dependent manner, which is thought to establish stable changes in neuronal function and behavior. Recent discoveries regarding the Ten eleven translocation (Tet1-3) family of DNA hydroxylases have provided a new avenue for the study of active DNA demethylation, and may thus help to advance our understanding of how dynamic DNA modifications lead to long-lasting changes in brain regions underlying learning and memory, as well as drug-seeking and propensity for relapse following abstinence. Drug addiction is a complex, relapsing disorder in which compulsive drug-seeking behavior can persist despite aversive consequences. Therefore, understanding the molecular mechanisms that underlie the onset and persistence of drug addiction, as well as the pronounced propensity for relapse observed in addicts, is necessary for the development of selective treatments and therapies. In this mini-review, we provide an overview of the involvement of active DNA demethylation with an emphasis on the Tet family of enzymes and 5-hydroxymethylcytosine (5-hmC) in learning and memory, as well as in drug-seeking behavior. Memory and addiction share overlapping molecular, cellular, and circuit functions allowing research in one area to inform the other. Current discrepancies and directions for future studies focusing on the dynamic interplay between DNA methylation and demethylation, and how they orchestrate gene expression required for neuronal plasticity underlying memory formation, are discussed.
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Affiliation(s)
- Yasaman Alaghband
- Department of Neurobiology & Behavior, UC Irvine, USA; Center for the Neurobiology of Learning and Memory, UC Irvine, USA; UC Irvine Center for Addiction Neuroscience, UC Irvine, USA
| | - Timothy W Bredy
- Department of Neurobiology & Behavior, UC Irvine, USA; Center for the Neurobiology of Learning and Memory, UC Irvine, USA; Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Marcelo A Wood
- Department of Neurobiology & Behavior, UC Irvine, USA; Center for the Neurobiology of Learning and Memory, UC Irvine, USA; UC Irvine Center for Addiction Neuroscience, UC Irvine, USA.
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50
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Esanov R, Belle KC, van Blitterswijk M, Belzil VV, Rademakers R, Dickson DW, Petrucelli L, Boylan KB, Dykxhoorn DM, Wuu J, Benatar M, Wahlestedt C, Zeier Z. C9orf72 promoter hypermethylation is reduced while hydroxymethylation is acquired during reprogramming of ALS patient cells. Exp Neurol 2015; 277:171-177. [PMID: 26746986 DOI: 10.1016/j.expneurol.2015.12.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 12/17/2015] [Accepted: 12/29/2015] [Indexed: 12/13/2022]
Abstract
Among several genetic mutations known to cause amyotrophic lateral sclerosis (ALS), a hexanucleotide repeat expansion in the C9orf72 gene is the most common. In approximately 30% of C9orf72-ALS cases, 5-methylcytosine (5mC) levels within the C9orf72 promoter are increased, resulting in a modestly attenuated phenotype. The developmental timing of C9orf72 promoter hypermethylation and the reason why it occurs in only a subset of patients remain unknown. In order to model the acquisition of C9orf72 hypermethylation and examine the potential role of 5-hydroxymethylcytosine (5hmC), we generated induced pluripotent stem cells (iPSCs) from an ALS patient with C9orf72 promoter hypermethylation. Our data show that 5mC levels are reduced by reprogramming and then re-acquired upon neuronal specification, while 5hmC levels increase following reprogramming and are highest in iPSCs and motor neurons. We confirmed the presence of 5hmC within the C9orf72 promoter in post-mortem brain tissues of hypermethylated patients. These findings show that iPSCs are a valuable model system for examining epigenetic perturbations caused by the C9orf72 mutation and reveal a potential role for cytosine demethylation.
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Affiliation(s)
- Rustam Esanov
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Kinsley C Belle
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, USA; The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, USA
| | | | | | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | - Kevin B Boylan
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | - Derek M Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, USA; The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, USA
| | - Joanne Wuu
- Department of Neurology, University of Miami Miller School of Medicine, USA
| | - Michael Benatar
- Department of Neurology, University of Miami Miller School of Medicine, USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Zane Zeier
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Psychiatry & Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA.
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