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Raia T, Armeli F, Cavallaro RA, Ferraguti G, Businaro R, Lucarelli M, Fuso A. Perinatal S-Adenosylmethionine Supplementation Represses PSEN1 Expression by the Cellular Epigenetic Memory of CpG and Non-CpG Methylation in Adult TgCRD8 Mice. Int J Mol Sci 2023; 24:11675. [PMID: 37511434 PMCID: PMC10380323 DOI: 10.3390/ijms241411675] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
DNA methylation, the main epigenetic modification regulating gene expression, plays a role in the pathophysiology of neurodegeneration. Previous evidence indicates that 5'-flanking hypomethylation of PSEN1, a gene involved in the amyloidogenic pathway in Alzheimer's disease (AD), boosts the AD-like phenotype in transgenic TgCRND8 mice. Supplementation with S-adenosylmethionine (SAM), the methyl donor in the DNA methylation reactions, reverts the pathological phenotype. Several studies indicate that epigenetic signatures, driving the shift between normal and diseased aging, can be acquired during the first stages of life, even in utero, and manifest phenotypically later on in life. Therefore, we decided to test whether SAM supplementation during the perinatal period (i.e., supplementing the mothers from mating to weaning) could exert a protective role towards AD-like symptom manifestation. We therefore compared the effect of post-weaning vs. perinatal SAM treatment in TgCRND8 mice by assessing PSEN1 methylation and expression and the development of amyloid plaques. We found that short-term perinatal supplementation was as effective as the longer post-weaning supplementation in repressing PSEN1 expression and amyloid deposition in adult mice. These results highlight the importance of epigenetic memory and methyl donor availability during early life to promote healthy aging and stress the functional role of non-CpG methylation.
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Affiliation(s)
- Tiziana Raia
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Federica Armeli
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 04100 Latina, Italy
| | | | - Giampiero Ferraguti
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy
| | - Rita Businaro
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 04100 Latina, Italy
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy
- Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, 00161 Rome, Italy
| | - Andrea Fuso
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy
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2
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Blaconà G, Raso R, Castellani S, Pierandrei S, Del Porto P, Ferraguti G, Ascenzioni F, Conese M, Lucarelli M. Downregulation of epithelial sodium channel (ENaC) activity in cystic fibrosis cells by epigenetic targeting. Cell Mol Life Sci 2022; 79:257. [PMID: 35462606 PMCID: PMC9035428 DOI: 10.1007/s00018-022-04190-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/28/2022] [Accepted: 02/02/2022] [Indexed: 12/31/2022]
Abstract
The pathogenic mechanism of cystic fibrosis (CF) includes the functional interaction of the cystic fibrosis transmembrane conductance regulator (CFTR) protein with the epithelial sodium channel (ENaC). The reduction of ENaC activity may constitute a therapeutic option for CF. This hypothesis was evaluated using drugs that target the protease-dependent activation of the ENaC channel and the transcriptional activity of its coding genes. To this aim we used: camostat, a protease inhibitor; S-adenosyl methionine (SAM), showed to induce DNA hypermethylation; curcumin, known to produce chromatin condensation. SAM and camostat are drugs already clinically used in other pathologies, while curcumin is a common dietary compound. The experimental systems used were CF and non-CF immortalized human bronchial epithelial cell lines as well as human bronchial primary epithelial cells. ENaC activity and SCNN1A, SCNN1B and SCNN1G gene expression were analyzed, in addition to SCNN1B promoter methylation. In both immortalized and primary cells, the inhibition of extracellular peptidases and the epigenetic manipulations reduced ENaC activity. Notably, the reduction in primary cells was much more effective. The SCNN1B appeared to be the best target to reduce ENaC activity, in respect to SCNN1A and SCNN1G. Indeed, SAM treatment resulted to be effective in inducing hypermethylation of SCNN1B gene promoter and in lowering its expression. Importantly, CFTR expression was unaffected, or even upregulated, after treatments. These results open the possibility of CF patients’ treatment by epigenetic targeting.
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Affiliation(s)
- Giovanna Blaconà
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Roberto Raso
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Stefano Castellani
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Silvia Pierandrei
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Paola Del Porto
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Giampiero Ferraguti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Fiorentina Ascenzioni
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Massimo Conese
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy.
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy. .,Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy.
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3
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Wang XX, Jia HJ, Lv YR, Sun HH, Wei XL, Tan JY, Jing ZZ. A Luciferase-EGFP Reporter System for the Evaluation of DNA Methylation in Mammalian Cells. Mol Biol 2021; 55:742-751. [PMID: 34226765 PMCID: PMC8244672 DOI: 10.1134/s0026893321040099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 10/22/2020] [Accepted: 11/03/2020] [Indexed: 11/23/2022]
Abstract
DNA methylation is an essential epigenetic modification involved in numerous biological processes. Here, we present a cell-based system pLTR-Luc2P-EGFP for evaluation of DNA methylation in mammalian cells. In this system, the expression of reporter gene luciferase2P (Luc2P)-EGFP is under the control of HIV-1 promoter 5' long terminal repeat (LTR), which contains multiple CpG sites. Once these sites are methylated, the expression of Luc2P-EGFP is turned off, which may be visualized under fluorescence microscopy, with quantification performed in luciferase activity assay. As a proof of principle, pLTR-Luc2P-EGFP was methylated in vitro, and transfected into 293T cells, where the reduction of Luc2P-EGFP expression was confirmed. Premixed reporter DNA samples with the methylation levels varying from 0 to 100% were used for quantitative measurements of DNA methylation. The resulting standard curves indicated the accuracy of luciferase activity exceeding that of the Western blotting against EGFP. The Bland–Altman analysis showed that data from luciferase activity assay were in good agreement with the actual DNA methylation levels. In summary, we have established a reporter system coupled with reliable detection technique capable of efficient quantifying the changes in methylation in mammalian cells. This system may be utilized as a high throughput screening tool for identifying molecules that modulate DNA methylation.
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Affiliation(s)
- X X Wang
- School of Public Health, Lanzhou University, 730000 Lanzhou, China
| | - H J Jia
- State Key Laboratory of Veterinary of Etiological Biology, Key Laboratory of Veterinary Public Health of Agricultural Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730000 Lanzhou, China
| | - Y R Lv
- School of Public Health, Lanzhou University, 730000 Lanzhou, China.,State Key Laboratory of Veterinary of Etiological Biology, Key Laboratory of Veterinary Public Health of Agricultural Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730000 Lanzhou, China
| | - H H Sun
- School of Public Health, Lanzhou University, 730000 Lanzhou, China.,State Key Laboratory of Veterinary of Etiological Biology, Key Laboratory of Veterinary Public Health of Agricultural Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730000 Lanzhou, China
| | - X L Wei
- Institute of Immunology, School of Basic Medical Sciences, Lanzhou University, 730000 Lanzhou, China
| | - J Y Tan
- Institute of Immunology, School of Basic Medical Sciences, Lanzhou University, 730000 Lanzhou, China
| | - Z Z Jing
- State Key Laboratory of Veterinary of Etiological Biology, Key Laboratory of Veterinary Public Health of Agricultural Ministry, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 730000 Lanzhou, China
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4
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Pierandrei S, Truglio G, Ceci F, Del Porto P, Bruno SM, Castellani S, Conese M, Ascenzioni F, Lucarelli M. DNA Methylation Patterns Correlate with the Expression of SCNN1A, SCNN1B, and SCNN1G (Epithelial Sodium Channel, ENaC) Genes. Int J Mol Sci 2021; 22:ijms22073754. [PMID: 33916525 PMCID: PMC8038451 DOI: 10.3390/ijms22073754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/12/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022] Open
Abstract
The interplay between the cystic fibrosis transmembrane conductance regulator (CFTR) and the epithelial sodium channel (ENaC) in respiratory epithelia has a crucial role in the pathogenesis of cystic fibrosis (CF). The comprehension of the mechanisms of transcriptional regulation of ENaC genes is pivotal to better detail the pathogenic mechanism and the genotype-phenotype relationship in CF, as well as to realize therapeutic approaches based on the transcriptional downregulation of ENaC genes. Since we aimed to study the epigenetic transcriptional control of ENaC genes, an assessment of their expression and DNA methylation patterns in different human cell lines, nasal brushing samples, and leucocytes was performed. The mRNA expression of CFTR and ENaC subunits α, β and γ (respectively SCNN1A, SCNN1B, and SCNN1G genes) was studied by real time PCR. DNA methylation of 5'-flanking region of SCNN1A, SCNN1B, and SCNN1G genes was studied by HpaII/PCR. The levels of expression and DNA methylation of ENaC genes in the different cell lines, brushing samples, and leukocytes were very variable. The DNA regions studied of each ENaC gene showed different methylation patterns. A general inverse correlation between expression and DNA methylation was evidenced. Leukocytes showed very low expression of all the 3 ENaC genes corresponding to a DNA methylated pattern. The SCNN1A gene resulted to be the most expressed in some cell lines that, accordingly, showed a completely demethylated pattern. Coherently, a heavy and moderate methylated pattern of, respectively, SCNN1B and SCNN1G genes corresponded to low levels of expression. As exceptions, we found that dexamethasone treatment appeared to stimulate the expression of all the 3 ENaC genes, without an evident modulation of the DNA methylation pattern, and that in nasal brushing a considerable expression of all the 3 ENaC genes were found despite an apparent methylated pattern. At least part of the expression modulation of ENaC genes seems to depend on the DNA methylation patterns of specific DNA regions. This points to epigenetics as a controlling mechanism of ENaC function and as a possible therapeutic approach for CF.
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Affiliation(s)
- Silvia Pierandrei
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Roma, Italy; (S.P.); (G.T.); (F.C.); (S.M.B.)
| | - Gessica Truglio
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Roma, Italy; (S.P.); (G.T.); (F.C.); (S.M.B.)
| | - Fabrizio Ceci
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Roma, Italy; (S.P.); (G.T.); (F.C.); (S.M.B.)
| | - Paola Del Porto
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Via dei Sardi 70, 00185 Roma, Italy;
| | - Sabina Maria Bruno
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Roma, Italy; (S.P.); (G.T.); (F.C.); (S.M.B.)
| | - Stefano Castellani
- Department of Biomedical Sciences and Human Oncology, University of Bari, Piazza Giulio Cesare 11, 70124 Bari, Italy;
| | - Massimo Conese
- Department of Medical and Surgical Sciences, University of Foggia, Via Napoli 121, 71122 Foggia, Italy;
| | - Fiorentina Ascenzioni
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, Via dei Sardi 70, 00185 Roma, Italy;
- Correspondence: (F.A.); (M.L.)
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, Viale Regina Elena 324, 00161 Roma, Italy; (S.P.); (G.T.); (F.C.); (S.M.B.)
- Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, Viale Regina Elena 291, 00161 Roma, Italy
- Correspondence: (F.A.); (M.L.)
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5
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Li X, Bu S, Pan RR, Zhou C, Qu K, Ying X, Zhong J, Xiao J, Yuan Q, Zhang S, Tipton L, Wang Y, Deng Y, Duan S. The values of AHCY and CBS promoter methylation on the diagnosis of cerebral infarction in Chinese Han population. BMC Med Genomics 2020; 13:163. [PMID: 33138824 PMCID: PMC7607831 DOI: 10.1186/s12920-020-00798-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 09/16/2020] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The goal of our study is to investigate whether the methylation levels of AHCY and CBS promoters are related to the risk of cerebral infarction by detecting the methylation level of AHCY and CBS genes. METHODS We extracted peripheral venous blood from 152 patients with cerebral infarction and 152 gender- and age-matched healthy controls, and determined methylation levels of AHCY and CBS promoters using quantitative methylation-specific polymerase chain reaction. We used the percentage of methylation reference (PMR) to indicate gene methylation level. RESULTS We compared the promoter methylation levels of two genes (AHCY and CBS) in peripheral blood DNA between the cerebral infarction case group and the control group. Our study showed no significant difference in AHCY promoter methylation between case and control. Subgroup analysis by gender showed that the methylation level of AHCY in males in the case group was lower than that in the control group, but the difference was not statistically significant in females. In a subgroup analysis by age, there was no significant difference in the AHCY methylation level between the case and control in the young group (≤44 years old). However, the level of AHCY gene methylation in the middle-aged group (45-59 years old) was significantly higher and the aged group (≥60 years old) was significantly lower than that in the control groups. However, CBS promoter methylation levels were significantly lower in the case group than in the control group (median PMR: 70.20% vs 104.10%, P = 3.71E-10). In addition, the CBS methylation levels of males and females in the case group were significantly lower than those in the control group (male: 64.33% vs 105%, P = 2.667E-08; female: 78.05% vs 102.8%, P = 0.003). We also found that the CBS levels in the young (23-44), middle-aged (45-59), and older (60-90) groups were significantly lower than those in the control group (young group: 69.97% vs 114.71%; P = 0.015; middle-aged group: 56.04% vs 91.71%; P = 6.744E-06; older group: 81.6% vs 119.35%; P = 2.644E-04). Our ROC curve analysis of CBS hypomethylation showed an area under the curve of 0.713, a sensitivity of 67.4%, and a specificity of 74.0%. CONCLUSION Our study suggests that hypomethylation of the CBS promoter may be closely related to the risk of cerebral infarction and may be used as a non-invasive diagnostic biomarker for cerebral infarction.
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Affiliation(s)
- Xiaodong Li
- Department of Neurology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450006, Henan, China
| | - Shufang Bu
- Department of Neurology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, 450006, Henan, China
| | - Ran Ran Pan
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Cong Zhou
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Kun Qu
- Department of Neurology, the 960th of Hospital of PLA, Zibo, 255330, Shandong, China
| | - Xiuru Ying
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Jie Zhong
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Jianhao Xiao
- Department of Neurology, the Second Affiliated Hospital, Zhengzhou University, Zhengzhou, 450014, Henan, China
| | - Qian Yuan
- Department of Neurology, the Second Affiliated Hospital, Zhengzhou University, Zhengzhou, 450014, Henan, China
| | - Simiao Zhang
- Department of Neurology, the Second Affiliated Hospital, Zhengzhou University, Zhengzhou, 450014, Henan, China
| | - Laura Tipton
- Bioinformatics Core, Department of Complementary and Integrative Medicine and John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, 96822, USA
| | - Yunliang Wang
- Department of Neurology, the Second Affiliated Hospital, Zhengzhou University, Zhengzhou, 450014, Henan, China.
| | - Youping Deng
- Bioinformatics Core, Department of Complementary and Integrative Medicine and John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, 96822, USA.
| | - Shiwei Duan
- School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China.
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6
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Monti N, Cavallaro RA, Stoccoro A, Nicolia V, Scarpa S, Kovacs GG, Fiorenza MT, Lucarelli M, Aronica E, Ferrer I, Coppedè F, Troen AM, Fuso A. CpG and non-CpG Presenilin1 methylation pattern in course of neurodevelopment and neurodegeneration is associated with gene expression in human and murine brain. Epigenetics 2020; 15:781-799. [PMID: 32019393 PMCID: PMC7518704 DOI: 10.1080/15592294.2020.1722917] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 01/14/2020] [Accepted: 01/20/2020] [Indexed: 12/26/2022] Open
Abstract
The Presenilin1 (PSEN1) gene encodes the catalytic peptide of the γ-secretase complex, a key enzyme that cleaves the amyloid-β protein precursor (AβPP), to generate the amyloid-β (Aβ) peptides, involved in Alzheimer's Disease (AD). Other substrates of the γ-secretase, such as E-cadherin and Notch1, are involved in neurodevelopment and haematopoiesis. Gene-specific DNA methylation influences PSEN1 expression in AD animal models. Here we evaluated canonical and non-canonical cytosine methylation patterns of the PSEN1 5'-flanking during brain development and AD progression, in DNA extracted from the frontal cortex of AD transgenic mice (TgCRND8) and post-mortem human brain. Mapping CpG and non-CpG methylation revealed different methylation profiles in mice and humans. PSEN1 expression only correlated with DNA methylation in adult female mice. However, in post-mortem human brain, lower methylation, both at CpG and non-CpG sites, correlated closely with higher PSEN1 expression during brain development and in disease progression. PSEN1 methylation in blood DNA was significantly lower in AD patients than in controls. The present study is the first to demonstrate a temporal correlation between dynamic changes in PSEN1 CpG and non-CpG methylation patterns and mRNA expression during neurodevelopment and AD neurodegeneration. These observations were made possible by the use of an improved bisulphite methylation assay employing primers that are not biased towards non-CpG methylation. Our findings deepen the understanding of γ-secretase regulation and support the hypothesis that epigenetic changes can promote the pathophysiology of AD. Moreover, they suggest that PSEN1 DNA methylation in peripheral blood may provide a biomarker for AD.
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Affiliation(s)
- Noemi Monti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
- Department of Surgery “P. Valdoni”, Sapienza University of Rome, Rome, Italy
| | | | - Andrea Stoccoro
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
| | - Vincenzina Nicolia
- Department of Surgery “P. Valdoni”, Sapienza University of Rome, Rome, Italy
| | - Sigfrido Scarpa
- Department of Surgery “P. Valdoni”, Sapienza University of Rome, Rome, Italy
| | - Gabor G. Kovacs
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Maria Teresa Fiorenza
- Department of Psychology, Division of Neuroscience, Sapienza University of Rome, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
- Pasteur Institute Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Eleonora Aronica
- Department of (Neuro) Pathology, Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Isidre Ferrer
- Neuropathology, Service of Pathology, Bellvitge University Hospital, Barcelona, Spain
- CIBERNED, Hospitalet De Llobregat, University of Barcelona, Barcelona, Spain
| | - Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
| | - Aron M. Troen
- Nutrition and Brain Health Laboratory, the Institute of Biochemistry Food and Nutrition Science, the Robert H. Smith Faculty of Agriculture Food and the Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Andrea Fuso
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
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7
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Tarashi S, Badi SA, Moshiri A, Ebrahimzadeh N, Fateh A, Vaziri F, Aazami H, Siadat SD, Fuso A. The inter-talk between Mycobacterium tuberculosis and the epigenetic mechanisms. Epigenomics 2020; 12:455-469. [PMID: 32267165 DOI: 10.2217/epi-2019-0187] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Epigenetics regulate gene function without any alteration in the DNA sequence. The epigenetics represent one of the most important regulators in different cellular processes and have initially been developed in microorganisms as a protective strategy. The evaluation of the epigenetic mechanisms is also important in achieving an efficient control strategy in tuberculosis (TB). TB is one of the most significant epidemiological concerns in human history. Despite several in vivo and in vitro studies that have evaluated different epigenetic modifications in TB, many aspects of the association between epigenetics and TB are not fully understood. The current paper is aimed at reviewing our knowledge on histone modifications and DNA methylation modifications, as well as miRNAs regulation in TB.
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Affiliation(s)
- Samira Tarashi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Mycobacteriology & Pulmonary Research Department, Pasteur Institute of Iran, Tehran, Iran
| | - Sara Ahmadi Badi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Mycobacteriology & Pulmonary Research Department, Pasteur Institute of Iran, Tehran, Iran
| | - Arfa Moshiri
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Gastroenterology & Liver Diseases Research Center, Research Institute for Gastroenterology & Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Laboratory of Molecular Medicine, IRCCS Institute Giannina Gaslini, Genova, Italy
| | - Nayereh Ebrahimzadeh
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Mycobacteriology & Pulmonary Research Department, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Mycobacteriology & Pulmonary Research Department, Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Mycobacteriology & Pulmonary Research Department, Pasteur Institute of Iran, Tehran, Iran
| | - Hossein Aazami
- Endocrinology & Metabolism Research Center, Endocrinology & Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Davar Siadat
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Mycobacteriology & Pulmonary Research Department, Pasteur Institute of Iran, Tehran, Iran.,Endocrinologyand Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Andrea Fuso
- Department of Experimental Medicine, Sapienza University of Rome, Italy
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8
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Fuso A, Raia T, Orticello M, Lucarelli M. The complex interplay between DNA methylation and miRNAs in gene expression regulation. Biochimie 2020; 173:12-16. [PMID: 32061806 DOI: 10.1016/j.biochi.2020.02.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/11/2020] [Indexed: 12/12/2022]
Abstract
The short, non-coding RNAs, also called microRNAs (miRNAs) can bind complementary sequences on cellular mRNAs. The consequence of this binding is generally the degradation of mRNA and the inhibition of its translation. For this reason, miRNAs are included among the epigenetic factors acting as a modulator of gene expression. How miRNAs expression is, in turn, regulated is still the object of active investigation, but DNA methylation, another epigenetic modification, seems to play a central role in this sense. The "one-carbon" metabolism is responsible for the metabolic regulation of trans-methylation reactions and, therefore, DNA methylation. For this reason, to investigate the possible correlations between alterations of the one-carbon metabolism and differential DNA methylation sounds interesting. Moreover, recent evidence indicates that, vice-versa, miRNAs are associated with DNA methylation modulation, in a mutual cross-talk. The present review will discuss the interplay between miRNAs and DNA methylation and its fall-out on gene expression regulation.
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Affiliation(s)
- Andrea Fuso
- Dept. of Experimental Medicine, Sapienza University of Rome, Rome, Italy.
| | - Tiziana Raia
- Dept. of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Michela Orticello
- Dept. of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Marco Lucarelli
- Dept. of Experimental Medicine, Sapienza University of Rome, Rome, Italy; Pasteur Institute Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
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9
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Ma WR, Xu P, Liu ZJ, Zhou J, Gu LK, Zhang J, Deng DJ. Impact of GFRA1 gene reactivation by DNA demethylation on prognosis of patients with metastatic colon cancer. World J Gastroenterol 2020; 26:184-198. [PMID: 31988584 PMCID: PMC6962434 DOI: 10.3748/wjg.v26.i2.184] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/14/2019] [Accepted: 12/23/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The expression of the membrane receptor protein GFRA1 is frequently upregulated in many cancers, which can promote cancer development by activating the classic RET-RAS-ERK and RET-RAS-PI3K-AKT pathways. Several therapeutic anti-GFRA1 antibody-drug conjugates are under development. Demethylation (or hypomethylation) of GFRA1 CpG islands (dmGFRA1) is associated with increased gene expression and metastasis risk of gastric cancer. However, it is unknown whether dmGFRA1 affects the metastasis of other cancers, including colon cancer (CC).
AIM To study whether dmGFRA1 is a driver for CC metastasis and GFRA1 is a potential therapeutic target.
METHODS CC and paired surgical margin tissue samples from 144 inpatients and normal colon mucosal biopsies from 21 noncancer patients were included in this study. The methylation status of GFRA1 islands was determined by MethyLight and denaturing high-performance liquid chromatography and bisulfite-sequencing. Kaplan-Meier analysis was used to explore the effect of dmGFRA1 on the survival of CC patients. Impacts of GFRA1 on CC cell proliferation and migration were evaluated by a battery of biological assays in vitro and in vivo. The phosphorylation of AKT and ERK proteins was examined by Western blot analysis.
RESULTS The proportion of dmGFRA1 in CC, surgical margin, and normal colon tissues by MethyLight was 68.4%, 73.4%, and 35.9% (median; nonparametric test, P = 0.001 and < 0.001), respectively. Using the median value of dmGFRA1 peak area proportion as the cutoff, the proportion of dmGFRA1-high samples was much higher in poorly differentiated CC samples than in moderately or well-differentiated samples (92.3%% vs 55.8%, Chi-square test, P = 0.002) and significantly higher in CC samples with distant metastasis than in samples without (77.8% vs 46.0%, P = 0.021). The overall survival of patients with dmGFRA1-low CC was significantly longer than that of patients with dmGFRA1-high CC (adjusted hazard ratio = 0.49, 95% confidence interval: 0.24-0.98), especially for 89 CC patients with metastatic CC (adjusted hazard ratio = 0.41, 95% confidence interval: 0.18-0.91). These data were confirmed by the mining results from TCGA datasets. Furthermore, GFRA1 overexpression significantly promoted the proliferation/invasion of RKO and HCT116 cells and the growth of RKO cells in nude mice but did not affect their migration. GFRA1 overexpression markedly increased the phosphorylation levels of AKT and ERK proteins, two key molecules in two classic GFRA1 downstream pathways.
CONCLUSION GFRA1 expression is frequently reactivated by DNA demethylation in CC tissues and is significantly associated with a poor prognosis in patients with CC, especially those with metastatic CC. GFRA1 can promote the proliferation/growth of CC cells, probably by the activation of AKT and ERK pathways. GFRA1 might be a therapeutic target for CC patients, especially those with metastatic potential.
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Affiliation(s)
- Wan-Ru Ma
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100143, China
| | - Peng Xu
- Shihezi University School of Medicine, Shihezi 832000, Xinjiang Uygur Autonomous Region, China
- Morphological Center of Basic Medical School of Xinjiang Medical University, Urumqi 830011, Xinjiang Uygur Autonomous Region, China
| | - Zhao-Jun Liu
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100143, China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100143, China
| | - Lian-Kun Gu
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100143, China
| | - Jun Zhang
- Shihezi University School of Medicine, Shihezi 832000, Xinjiang Uygur Autonomous Region, China
| | - Da-Jun Deng
- Key Laboratory of Carcinogenesis and Translational Research (MOE/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing 100143, China
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10
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Active Demethylation of Non-CpG Moieties in Animals: A Neglected Research Area. Int J Mol Sci 2019; 20:ijms20246272. [PMID: 31842376 PMCID: PMC6940975 DOI: 10.3390/ijms20246272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 11/17/2022] Open
Abstract
The functional role of cytosine methylation in the CpG moieties of DNA, is well established in several biological functions. The interplay between CpG methylation and hypomethylation is a well-known mechanism of modulation of gene expression. However, the role of non-CpG methylation and active dynamics of demethylation is not clearly recognized. Although some evidence exists of a role of active non-CpG demethylation in the fast dynamics of transcriptional activation in animals, few studies deal with this topic. At present, active demethylation of non-CpG moieties is a neglected research area, in spite of the promise of significant novelties.
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11
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Cosentino L, Vigli D, Medici V, Flor H, Lucarelli M, Fuso A, De Filippis B. Methyl-CpG binding protein 2 functional alterations provide vulnerability to develop behavioral and molecular features of post-traumatic stress disorder in male mice. Neuropharmacology 2019; 160:107664. [PMID: 31175878 DOI: 10.1016/j.neuropharm.2019.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 05/30/2019] [Accepted: 06/05/2019] [Indexed: 10/26/2022]
Abstract
Post-traumatic stress disorder (PTSD) is a mental disorder characterized by symptoms of persistent anxiety arising after exposure to traumatic events. Stress susceptibility due to a complex interplay between genetic and environmental factors plays a major role in the disease etiology, although biological underpinnings have not been clarified. We hypothesized that aberrant functionality of the methyl-CpG binding protein 2 (MECP2), a master regulator of experience-dependent epigenetic programming, confers susceptibility to develop PTSD-like symptomatology in the aftermath of traumatic events. Transgenic male mice expressing a truncated form of MeCP2 protein (MeCP2-308) were exposed at adulthood to a trauma in the form of high-intensity footshocks. The presence and duration of PTSD-like symptoms were assessed and compared to those of trauma-exposed wild type littermates and MeCP2-308 mice subjected to a mild stressor. The effects of fluoxetine, a prime pharmacological PTSD treatment, on PTSD-like symptomatology were also explored. Trauma-exposed MeCP2-308 mice showed long-lasting hyperresponsiveness to both correct and incorrect predictors of the trauma and persistent increased avoidance of trauma-related cues. Traumatized MeCP2-308 mice also displayed abnormal post-traumatic plasma levels of the stress hormone corticosterone and altered peripheral gene expression mirroring that of PTSD patients. Fluoxetine improved PTSD-like symptoms in trauma-exposed MeCP2-308 mice. These findings provide evidence that MeCP2 dysfunction results in increased susceptibility to develop PTSD-like symptoms after trauma exposure, and identify trauma-exposed MeCP2-308 mice as a new tool to investigate the underpinnings of PTSD vulnerability.
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Affiliation(s)
- Livia Cosentino
- Center for Behavioral Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy
| | - Daniele Vigli
- Center for Behavioral Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy
| | - Vanessa Medici
- Center for Behavioral Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy
| | - Herta Flor
- Department of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Ruprecht-Karls-University Heidelberg, Mannheim, Germany
| | - Marco Lucarelli
- Department of Experimental Medicine, Sapienza University of Rome, Italy; Pasteur Institute Cenci Bolognetti Foundation, Sapienza University of Rome, Italy
| | - Andrea Fuso
- Department of Experimental Medicine, Sapienza University of Rome, Italy
| | - Bianca De Filippis
- Center for Behavioral Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy.
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12
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Fuso A, Lucarelli M. CpG and Non-CpG Methylation in the Diet–Epigenetics–Neurodegeneration Connection. Curr Nutr Rep 2019; 8:74-82. [DOI: 10.1007/s13668-019-0266-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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13
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Involvement of sperm acetylated histones and the nuclear isoform of Glutathione peroxidase 4 in fertilization. J Cell Physiol 2017; 233:3093-3104. [DOI: 10.1002/jcp.26146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/11/2017] [Indexed: 12/30/2022]
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14
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Fuso A, Ferraguti G, Scarpa S, Ferrer I, Lucarelli M. Disclosing bias in bisulfite assay: MethPrimers underestimate high DNA methylation. PLoS One 2015; 10:e0118318. [PMID: 25692551 PMCID: PMC4333220 DOI: 10.1371/journal.pone.0118318] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 01/14/2015] [Indexed: 01/18/2023] Open
Abstract
Discordant results obtained in bisulfite assays using MethPrimers (PCR primers designed using MethPrimer software or assuming that non-CpGs cytosines are non methylated) versus primers insensitive to cytosine methylation lead us to hypothesize a technical bias. We therefore used the two kinds of primers to study different experimental models and methylation statuses. We demonstrated that MethPrimers negatively select hypermethylated DNA sequences in the PCR step of the bisulfite assay, resulting in CpG methylation underestimation and non-CpG methylation masking, failing to evidence differential methylation statuses. We also describe the characteristics of “Methylation-Insensitive Primers” (MIPs), having degenerated bases (G/A) to cope with the uncertain C/U conversion. As CpG and non-CpG DNA methylation patterns are largely variable depending on the species, developmental stage, tissue and cell type, a variable extent of the bias is expected. The more the methylome is methylated, the greater is the extent of the bias, with a prevalent effect of non-CpG methylation. These findings suggest a revision of several DNA methylation patterns so far documented and also point out the necessity of applying unbiased analyses to the increasing number of epigenomic studies.
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Affiliation(s)
- Andrea Fuso
- Dept. of Psychology, Sapienza University of Rome, Rome, Italy; European Center for Brain Research (CERC)/IRCCS Santa Lucia Foundation, Rome, Italy
| | - Giampiero Ferraguti
- Dept. of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Rome, Italy
| | - Sigfrido Scarpa
- Dept. of Surgery "P. Valdoni", Sapienza University of Rome, Rome, Italy
| | - Isidre Ferrer
- Institute of Neuropathology, IDIBELL-Bellvitge University Hospital and University of Barcelona, CIBERNED, L'Hospitalet de Llobregat, Spain
| | - Marco Lucarelli
- Dept. of Cellular Biotechnologies and Hematology, Sapienza University of Rome, Rome, Italy; Pasteur Institute, Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
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15
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Ehara T, Kamei Y, Takahashi M, Yuan X, Kanai S, Tamura E, Tanaka M, Yamazaki T, Miura S, Ezaki O, Suganami T, Okano M, Ogawa Y. Role of DNA methylation in the regulation of lipogenic glycerol-3-phosphate acyltransferase 1 gene expression in the mouse neonatal liver. Diabetes 2012; 61:2442-50. [PMID: 22721968 PMCID: PMC3447899 DOI: 10.2337/db11-1834] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 04/19/2012] [Indexed: 12/17/2022]
Abstract
The liver is a major organ of lipid metabolism, which is markedly changed in response to physiological nutritional demand; however, the regulation of hepatic lipogenic gene expression in early life is largely unknown. In this study, we show that expression of glycerol-3-phosphate acyltransferase 1 (GPAT1; Gpam), a rate-limiting enzyme of triglyceride biosynthesis, is regulated in the mouse liver by DNA methylation, an epigenetic modification involved in the regulation of a diverse range of biological processes in mammals. In the neonatal liver, DNA methylation of the Gpam promoter, which is likely to be induced by Dnmt3b, inhibited recruitment of the lipogenic transcription factor sterol regulatory element-binding protein-1c (SREBP-1c), whereas in the adult, decreased DNA methylation resulted in active chromatin conformation, allowing recruitment of SREBP-1c. Maternal overnutrition causes decreased Gpam promoter methylation with increased GPAT1 expression and triglyceride content in the pup liver, suggesting that environmental factors such as nutritional conditions can affect DNA methylation in the liver. This study is the first detailed analysis of the DNA-methylation-dependent regulation of the triglyceride biosynthesis gene Gpam, thereby providing new insight into the molecular mechanism underlying the epigenetic regulation of metabolic genes and thus metabolic diseases.
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Affiliation(s)
- Tatsuya Ehara
- Department of Molecular Medicine and Metabolism, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Functional Food Research Department, Food Science and Technology Institute, Morinaga Milk Industry Co., Ltd., Kanagawa, Japan
| | - Yasutomi Kamei
- Department of Molecular Medicine and Metabolism, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Organ Network and Metabolism, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Mayumi Takahashi
- Department of Molecular Medicine and Metabolism, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Xunmei Yuan
- Department of Molecular Medicine and Metabolism, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sayaka Kanai
- Department of Molecular Medicine and Metabolism, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Erina Tamura
- Department of Molecular Medicine and Metabolism, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Miyako Tanaka
- Department of Molecular Medicine and Metabolism, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Organ Network and Metabolism, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomomi Yamazaki
- Nutritional Science Program, National Institute of Health and Nutrition, Tokyo, Japan
| | - Shinji Miura
- Nutritional Science Program, National Institute of Health and Nutrition, Tokyo, Japan
| | - Osamu Ezaki
- Nutritional Science Program, National Institute of Health and Nutrition, Tokyo, Japan
| | - Takayoshi Suganami
- Department of Molecular Medicine and Metabolism, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masaki Okano
- Laboratory for Mammalian Epigenetic Studies, Center for Developmental Biology, RIKEN, Kobe, Japan
| | - Yoshihiro Ogawa
- Department of Molecular Medicine and Metabolism, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- Global Center of Excellence Program, International Research Center for Molecular Science in Tooth and Bone Diseases, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
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16
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Fuso A, Ferraguti G, Grandoni F, Ruggeri R, Scarpa S, Strom R, Lucarelli M. Early demethylation of non-CpG, CpC-rich, elements in the myogenin 5'-flanking region: a priming effect on the spreading of active demethylation. Cell Cycle 2010; 9:3965-76. [PMID: 20935518 DOI: 10.4161/cc.9.19.13193] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The dynamic changes and structural patterns of DNA methylation of genes without CpG islands are poorly characterized. The relevance of CpG to the non-CpG methylation equilibrium in transcriptional repression is unknown. In this work, we analyzed the DNA methylation pattern of the 5'-flanking of the myogenin gene, a positive regulator of muscle differentiation with no CpG island and low CpG density, in both C2C12 muscle satellite cells and embryonic muscle. Embryonic brain was studied as a non-expressing tissue. High levels of both CpG and non-CpG methylation were observed in non-expressing experimental conditions. Both CpG and non-CpG methylation rapidly dropped during muscle differentiation and myogenin transcriptional activation, with an active demethylation dynamics. Non-CpG demethylation occurred more rapidly than CpG demethylation. Demethylation spread from initially highly methylated short CpC-rich elements to a virtually unmethylated status. These short elements have a high CpC content and density, share some motifs and largely coincide with putative recognition sequences of some differentiation-related transcription factors. Our findings point to a dynamically controlled equilibrium between CpG and non-CpG active demethylation in the transcriptional control of tissue-specific genes. The short CpC-rich elements are new structural features of the methylation machinery, whose functions may include priming the complete demethylation of a transcriptionally crucial DNA region.
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Affiliation(s)
- Andrea Fuso
- Department of Surgery P. Valdoni, Sapienza University of Rome, Italy
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17
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Fuso A, Nicolia V, Pasqualato A, Fiorenza MT, Cavallaro RA, Scarpa S. Changes in Presenilin 1 gene methylation pattern in diet-induced B vitamin deficiency. Neurobiol Aging 2009; 32:187-99. [PMID: 19329227 DOI: 10.1016/j.neurobiolaging.2009.02.013] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Revised: 01/14/2009] [Accepted: 02/13/2009] [Indexed: 02/06/2023]
Abstract
We have previously shown that a nutritional model of B vitamin deficiency and homocysteine cycle alteration could lead to increased amyloid β deposition, due to PSEN1 and BACE over-expression and consequent increase in secretase activity. We hypothesize that nutritional factors causing homocysteine cycle alterations (i.e. hyperhomocysteinemia) could induce sequence-specific DNA hypomethylation and "aberrant" gene activation. Aim of present study was to analyze the methylation pattern of PSEN1 promoter in SK-N-BE neuroblastoma cells and TgCRND8 mice, in a B vitamin (folate, B12 and B6) deficiency paradigm. PSEN1 methylation status has been evaluated through bisulphite modification and genomic sequencing. We demonstrate that B vitamin deficiency induces hypomethylation of specific CpG moieties in the 5'-flanking region; S-adenosylmethionine has been supplemented as methyl donor to reverse this effect. PSEN1 promoter methylation status is correlated with gene expression. These findings pinpoint a direct relationship between B vitamin-dependent alteration of homocysteine cycle and DNA methylation and also indicate that PSEN1 promoter is regulated by methylation of specific CpG moieties.
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Affiliation(s)
- Andrea Fuso
- Dept. of Surgery "P. Valdoni", Sapienza Università di Roma, Via Antonio Scarpa, 14 - 00161, Roma, Italy
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18
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Lenz B, Bleich S, Beutler S, Schlierf B, Schwager K, Reulbach U, Kornhuber J, Bönsch D. Homocysteine regulates expression of Herp by DNA methylation involving the AARE and CREB binding sites. Exp Cell Res 2006; 312:4049-55. [PMID: 17020760 DOI: 10.1016/j.yexcr.2006.09.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Revised: 08/28/2006] [Accepted: 09/07/2006] [Indexed: 01/28/2023]
Abstract
Herp (homocysteine-induced endoplasmic reticulum protein) is an ER-resident membrane protein, which has a ubiquitin-like domain at its N-terminus. Expression of Herp protein is up-regulated in response to ER stress, including homocysteine. Herp stabilizes neuronal Ca(2+) homeostasis and is involved in improving the balance of the folding capacity and protein loading in the ER. In patients with alcoholism, we observed a significant decrease in Herp mRNA expression, and an increase of Herp promoter DNA methylation, which was associated with elevated homocysteine levels. Therefore, we studied the mechanism of Herp CpG islands regulation by luciferase assays and mRNA analysis in neuronal SH-SY5Y (human neuroblastoma cell line) and HEK 293T (human embryonic kidney 293T) cells. Acute homocysteine treatment caused transient demethylation of the Herp promoter and an increase in Herp mRNA level. Global DNA methylation was increased over the following 48 h period. We identified the transcription factor binding site AARE (amino acid response element) by mutational analysis involved in Herp induction in SH-SY5Y cells, and the more significant role of the CREB binding site (cyclic AMP response element-binding protein) compared to AARE in HEK 293T cells. Stimulation with SAM (S-adenosyl methionine) and homocysteine led to an increase in Herp promoter methylation, which correlated to an acute decrease in luciferase expression in SAM, but not in homocysteine stimulated cells. Complete methylation of the CpG islands resulted in suppressed gene expression.
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Affiliation(s)
- Bernd Lenz
- Department of Psychiatry and Psychotherapy, Friedrich-Alexander-University of Erlangen-Nuremberg, Germany
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