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Doan TNA, Cowley JM, Phillips AL, Briffa JF, Leemaqz SY, Burton RA, Romano T, Wlodek ME, Bianco-Miotto T. Imprinted gene alterations in the kidneys of growth restricted offspring may be mediated by a long non-coding RNA. Epigenetics 2024; 19:2294516. [PMID: 38126131 PMCID: PMC10761017 DOI: 10.1080/15592294.2023.2294516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Altered epigenetic mechanisms have been previously reported in growth restricted offspring whose mothers experienced environmental insults during pregnancy in both human and rodent studies. We previously reported changes in the expression of the DNA methyltransferase Dnmt3a and the imprinted genes Cdkn1c (Cyclin-dependent kinase inhibitor 1C) and Kcnq1 (Potassium voltage-gated channel subfamily Q member 1) in the kidney tissue of growth restricted rats whose mothers had uteroplacental insufficiency induced on day 18 of gestation, at both embryonic day 20 (E20) and postnatal day 1 (PN1). To determine the mechanisms responsible for changes in the expression of these imprinted genes, we investigated DNA methylation of KvDMR1, an imprinting control region (ICR) that includes the promoter of the antisense long non-coding RNA Kcnq1ot1 (Kcnq1 opposite strand/antisense transcript 1). Kcnq1ot1 expression decreased by 51% in growth restricted offspring compared to sham at PN1. Interestingly, there was a negative correlation between Kcnq1ot1 and Kcnq1 in the E20 growth restricted group (Spearman's ρ = 0.014). No correlation was observed between Kcnq1ot1 and Cdkn1c expression in either group at any time point. Additionally, there was a 11.25% decrease in the methylation level at one CpG site within KvDMR1 ICR. This study, together with others in the literature, supports that long non-coding RNAs may mediate changes seen in tissues of growth restricted offspring.
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Affiliation(s)
- Thu N. A. Doan
- School of Agriculture, Food and Wine, & Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - James M. Cowley
- School of Agriculture, Food and Wine, & Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Aaron L. Phillips
- School of Agriculture, Food and Wine, & Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Jessica F. Briffa
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, Australia
| | - Shalem Y. Leemaqz
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
- SAHMRI Women and Kids, South Australian Health & Medical Research Institute, Adelaide, South Australia, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Rachel A. Burton
- School of Agriculture, Food and Wine, & Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Tania Romano
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, Australia
| | - Mary E. Wlodek
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, Victoria, Australia
- Department of Obstetrics and Gynaecology, The University of Melbourne, Parkville, Victoria, Australia
| | - Tina Bianco-Miotto
- School of Agriculture, Food and Wine, & Waite Research Institute, University of Adelaide, Adelaide, South Australia, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
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Tyagi SC, Pushpakumar S, Sen U, Akinterinwa OE, Zheng Y, Mokshagundam SPL, Kalra DK, Singh M. Role of circadian clock system in the mitochondrial trans-sulfuration pathway and tissue remodeling. Can J Physiol Pharmacol 2024; 102:105-115. [PMID: 37979203 DOI: 10.1139/cjpp-2023-0186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2023]
Abstract
Previous studies from our laboratory revealed that the gaseous molecule hydrogen sulfide (H2S), a metabolic product of epigenetics, involves trans-sulfuration pathway for ensuring metabolism and clearance of homocysteine (Hcy) from body, thereby mitigating the skeletal muscle's pathological remodeling. Although the master circadian clock regulator that is known as brain and muscle aryl hydrocarbon receptor nuclear translocator like protein 1 (i.e., BMAL 1) is associated with S-adenosylhomocysteine hydrolase (SAHH) and Hcy metabolism but how trans-sulfuration pathway is influenced by the circadian clock remains unexplored. We hypothesize that alterations in the functioning of circadian clock during sleep and wake cycle affect skeletal muscle's biology. To test this hypothesis, we measured serum matrix metalloproteinase (MMP) activities using gelatin gels for analyzing the MMP-2 and MMP-9. Further, employing casein gels, we also studied MMP-13 that is known to be influenced by the growth arrest and DNA damage-45 (GADD45) protein during sleep and wake cycle. The wild type and cystathionine β synthase-deficient (CBS-/+) mice strains were treated with H2S and subjected to measurement of trans-sulfuration factors from skeletal muscle tissues. The results suggested highly robust activation of MMPs in the wake mice versus sleep mice, which appears somewhat akin to the "1-carbon metabolic dysregulation", which takes place during remodeling of extracellular matrix during muscular dystrophy. Interestingly, the levels of trans-sulfuration factors such as CBS, cystathionine γ lyase (CSE), methyl tetrahydrofolate reductase (MTHFR), phosphatidylethanolamine N-methyltransferase (PEMT), and Hcy-protein bound paraoxonase 1 (PON1) were attenuated in CBS-/+ mice. However, treatment with H2S mitigated the attenuation of the trans-sulfuration pathway. In addition, levels of mitochondrial peroxisome proliferator-activated receptor-gamma coactivator 1-α (PGC 1-α) and mitofusin-2 (MFN-2) were significantly improved by H2S intervention. Our findings suggest participation of the circadian clock in trans-sulfuration pathway that affects skeletal muscle remodeling and mitochondrial regeneration.
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Affiliation(s)
- Suresh C Tyagi
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Sathnur Pushpakumar
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Utpal Sen
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Oluwaseun E Akinterinwa
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Yuting Zheng
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Sri Prakash L Mokshagundam
- Division of Endocrinology, Metabolism and Diabetes and Robley Rex VA Medical Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Dinesh K Kalra
- Division of Cardiovascular Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Mahavir Singh
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY 40202, USA
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Ehrlich M, Ehrlich KC, Lacey M, Baribault C, Sen S, Estève PO, Pradhan S. Epigenetics of Genes Preferentially Expressed in Dissimilar Cell Populations: Myoblasts and Cerebellum. EPIGENOMES 2024; 8:4. [PMID: 38390894 PMCID: PMC10885033 DOI: 10.3390/epigenomes8010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
While studying myoblast methylomes and transcriptomes, we found that CDH15 had a remarkable preference for expression in both myoblasts and cerebellum. To understand how widespread such a relationship was and its epigenetic and biological correlates, we systematically looked for genes with similar transcription profiles and analyzed their DNA methylation and chromatin state and accessibility profiles in many different cell populations. Twenty genes were expressed preferentially in myoblasts and cerebellum (Myob/Cbl genes). Some shared DNA hypo- or hypermethylated regions in myoblasts and cerebellum. Particularly striking was ZNF556, whose promoter is hypomethylated in expressing cells but highly methylated in the many cell populations that do not express the gene. In reporter gene assays, we demonstrated that its promoter's activity is methylation sensitive. The atypical epigenetics of ZNF556 may have originated from its promoter's hypomethylation and selective activation in sperm progenitors and oocytes. Five of the Myob/Cbl genes (KCNJ12, ST8SIA5, ZIC1, VAX2, and EN2) have much higher RNA levels in cerebellum than in myoblasts and displayed myoblast-specific hypermethylation upstream and/or downstream of their promoters that may downmodulate expression. Differential DNA methylation was associated with alternative promoter usage for Myob/Cbl genes MCF2L, DOK7, CNPY1, and ANK1. Myob/Cbl genes PAX3, LBX1, ZNF556, ZIC1, EN2, and VAX2 encode sequence-specific transcription factors, which likely help drive the myoblast and cerebellum specificity of other Myob/Cbl genes. This study extends our understanding of epigenetic/transcription associations related to differentiation and may help elucidate relationships between epigenetic signatures and muscular dystrophies or cerebellar-linked neuropathologies.
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Affiliation(s)
- Melanie Ehrlich
- Tulane Cancer Center, Hayward Human Genetics Center, Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Kenneth C Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
| | - Michelle Lacey
- Department of Mathematics, Tulane University, New Orleans, LA 70118, USA
| | - Carl Baribault
- Information Technology, Tulane University, New Orleans, LA 70118, USA
| | - Sagnik Sen
- Genome Biology Division, New England Biolabs, Ipswich, MA 01938, USA
| | | | - Sriharsa Pradhan
- Genome Biology Division, New England Biolabs, Ipswich, MA 01938, USA
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Tyagi SC, Pushpakumar S, Sen U, Mokshagundam SPL, Kalra DK, Saad MA, Singh M. COVID-19 Mimics Pulmonary Dysfunction in Muscular Dystrophy as a Post-Acute Syndrome in Patients. Int J Mol Sci 2022; 24:ijms24010287. [PMID: 36613731 PMCID: PMC9820572 DOI: 10.3390/ijms24010287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/12/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Although progressive wasting and weakness of respiratory muscles are the prominent hallmarks of Duchenne muscular dystrophy (DMD) and long-COVID (also referred as the post-acute sequelae of COVID-19 syndrome); however, the underlying mechanism(s) leading to respiratory failure in both conditions remain unclear. We put together the latest relevant literature to further understand the plausible mechanism(s) behind diaphragm malfunctioning in COVID-19 and DMD conditions. Previously, we have shown the role of matrix metalloproteinase-9 (MMP9) in skeletal muscle fibrosis via a substantial increase in the levels of tumor necrosis factor-α (TNF-α) employing a DMD mouse model that was crossed-bred with MMP9-knockout (MMP9-KO or MMP9-/-) strain. Interestingly, recent observations from clinical studies show a robust increase in neopterin (NPT) levels during COVID-19 which is often observed in patients having DMD. What seems to be common in both (DMD and COVID-19) is the involvement of neopterin (NPT). We know that NPT is generated by activated white blood cells (WBCs) especially the M1 macrophages in response to inducible nitric oxide synthase (iNOS), tetrahydrobiopterin (BH4), and tetrahydrofolate (FH4) pathways, i.e., folate one-carbon metabolism (FOCM) in conjunction with epigenetics underpinning as an immune surveillance protection. Studies from our laboratory, and others researching DMD and the genetically engineered humanized (hACE2) mice that were administered with the spike protein (SP) of SARS-CoV-2 revealed an increase in the levels of NPT, TNF-α, HDAC, IL-1β, CD147, and MMP9 in the lung tissue of the animals that were subsequently accompanied by fibrosis of the diaphragm depicting a decreased oscillation phenotype. Therefore, it is of interest to understand how regulatory processes such as epigenetics involvement affect DNMT, HDAC, MTHFS, and iNOS that help generate NPT in the long-COVID patients.
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Affiliation(s)
- Suresh C. Tyagi
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Sathnur Pushpakumar
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Utpal Sen
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Sri Prakash L. Mokshagundam
- Division of Endocrinology, Metabolism and Diabetes and Robley Rex VA Medical Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Dinesh K. Kalra
- Division of Cardiovascular Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Mohamed A. Saad
- Division of Pulmonary, Critical Care and Sleep Disorders Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Mahavir Singh
- Department of Physiology, School of Medicine, University of Louisville, Louisville, KY 40202, USA
- Correspondence: or
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Long non-coding RNA NR2F2-AS1: its expanding oncogenic roles in tumor progression. Hum Cell 2022; 35:1355-1363. [PMID: 35796938 DOI: 10.1007/s13577-022-00733-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/01/2022] [Indexed: 11/04/2022]
Abstract
Long non-coding RNA (LncRNA) is a new type of non-coding RNA whose transcription is more than 200 nucleotides in length and can be up to 100 kb. The crucial regulatory function of lncRNAs in different cellular processes is now notable in many human diseases, especially in different steps of tumorigenesis, making them clinically significant. This research tried to collect all evidence obtained so far regarding Nuclear Receptor subfamily 2 group F member 2 Antisense RNA 1 (NR2F2-AS1) to explore its role in carcinogenesis and molecular mechanism in several cancers. Collecting evidence value an oncogenic role for NR2F2-AS1, whose dysregulation changes the status for cancerous cells to gain the supremacy toward cellular proliferation, dissemination, and ultimately migration. The NR2F2-AS1 acts as competitive endogenous RNA (ceRNA) and contains several microRNA response elements (MREs) for different microRNAs involved in various pathways such as PI3K/AKT, Wnt/β-catenin, and TGF-β. This clinically makes NR2F2-AS1 a remarkable lncRNA which contributes to cancer progression and invasion and perhaps could be a candidate as a prognostic marker or even a therapeutic target.
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Age-Related DNA Methylation in Normal Kidney Tissue Identifies Epigenetic Cancer Risk Susceptibility Loci in the ANKRD34B and ZIC1 Genes. Int J Mol Sci 2022; 23:ijms23105327. [PMID: 35628134 PMCID: PMC9141100 DOI: 10.3390/ijms23105327] [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: 03/21/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 02/01/2023] Open
Abstract
Both age-dependent and age-independent alteration of DNA methylation in human tissues are functionally associated with the development of many malignant and non-malignant human diseases. TCGA-KIRC data were biometrically analyzed to identify new loci with age-dependent DNA methylation that may contribute to tumor risk in normal kidney tissue. ANKRD34B and ZIC1 were evaluated as candidate genes by pyrosequencing of 539 tissues, including 239 normal autopsy, 157 histopathologically tumor-adjacent normal, and 143 paired tumor kidney samples. All candidate CpG loci demonstrated a strong correlation between relative methylation levels and age (R = 0.70−0.88, p < 2 × 10−16) and seven out of 10 loci were capable of predicting chronological age in normal kidney tissues, explaining 84% of the variance (R = 0.92). Moreover, significantly increased age-independent methylation was found for 9 out of 10 CpG loci in tumor-adjacent tissues, compared to normal autopsy tissues (p = 0.001−0.028). Comparing tumor and paired tumor-adjacent tissues revealed two patient clusters showing hypermethylation, one cluster without significant changes in methylation, and a smaller cluster demonstrating hypomethylation in the tumors (p < 1 × 10−10). Taken together, our results show the presence of additional methylation risk factors besides age for renal cancer in normal kidney tissue. Concurrent tumor-specific hypermethylation suggests a subset of these loci are candidates for epigenetic renal cancer susceptibility.
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Dietary Restriction and Rapamycin Affect Brain Aging in Mice by Attenuating Age-Related DNA Methylation Changes. Genes (Basel) 2022; 13:genes13040699. [PMID: 35456505 PMCID: PMC9030181 DOI: 10.3390/genes13040699] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/02/2022] [Accepted: 04/13/2022] [Indexed: 02/07/2023] Open
Abstract
The fact that dietary restriction (DR) and long-term rapamycin treatment (RALL) can ameliorate the aging process has been reported by many researchers. As the interface between external and genetic factors, epigenetic modification such as DNA methylation may have latent effects on the aging rate at the molecular level. To understand the mechanism behind the impacts of dietary restriction and rapamycin on aging, DNA methylation and gene expression changes were measured in the hippocampi of different-aged mice. Examining the single-base resolution of DNA methylation, we discovered that both dietary restriction and rapamycin treatment can maintain DNA methylation in a younger state compared to normal-aged mice. Through functional enrichment analysis of genes in which DNA methylation or gene expression can be affected by DR/RALL, we found that DR/RALL may retard aging through a relationship in which DNA methylation and gene expression work together not only in the same gene but also in the same biological process. This study is instructive for understanding the maintenance of DNA methylation by DR/RALL in the aging process, as well as the role of DR and RALL in the amelioration of aging.
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Ehrlich M. Risks and rewards of big-data in epigenomics research: an interview with Melanie Ehrlich. Epigenomics 2022; 14:351-358. [PMID: 35255735 DOI: 10.2217/epi-2022-0056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Melanie Ehrlich, PhD, is a professor in the Tulane Cancer Center, the Tulane Center for Medical Bioinformatics and Genomics and the Hayward Human Genetics Program at Tulane Medical School, New Orleans, LA. She obtained her PhD in molecular biology in 1971 from the State University of New York at Stony Brook and completed postdoctoral research at Albert Einstein College of Medicine in 1972. She has been working on various aspects of epigenetics, starting with DNA methylation, since 1973. Her group made many first findings about DNA methylation (see below). For example, in 1982 and 1983, in collaboration with Charles Gehrke at the University of Missouri, she was the first to report tissue-specific and cancer-specific differences in overall DNA methylation in humans. In 1985, Xian-Yang Zhang and Richard Wang in her lab discovered a class of human DNA sequences specifically hypomethylated in sperm. In 1998, her group was the first to describe extensive losses of DNA methylation in pericentromeric and centromeric DNA repeats in human cancer. Her lab's many publications on the prevalence of both DNA hypermethylation and hypomethylation in the same cancers brought needed balance to our understanding of the epigenetics of cancer and to its clinical implications [1]. Besides working on cancer epigenetics, her research group has helped elucidate cytogenetic and gene expression abnormalities in the immunodeficiency, centromeric and facial anomalies (ICF) syndrome, a rare recessive disease often caused by mutations in DNMT3B. Her group also studied the epigenetics and transcriptomics of facioscapulohumeral muscular dystrophy (FSHD), whose disease locus is a tandem 3.3-kb repeat at subtelomeric 4q (that happens to be hypomethylated in ICF DNA [2]). Her study of FSHD has taken her in the direction of muscle (skeletal muscle, heart and aorta) epigenetics [3-6]. Recently, she has led research that applies epigenetics much more rigorously than usual to the evaluation of genetic variants from genome-wide association studies (GWAS) of osteoporosis and obesity. In continued collaboration with Sriharsa Pradhan at New England Biolabs and Michelle Lacey at Tulane University, she has compared 5-hydroxymethylcytosine and 5-methylcytosine clustering in various human tissues [7] and is studying myoblast methylomes that they generated by a new high-resolution enzymatic technique (enzymatic methyl-seq).
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Affiliation(s)
- Melanie Ehrlich
- Tulane Cancer Center, Center for Medical Bioinformatics & Genomics, & Hayward Genetics Center, Tulane University, New Orleans, LA 70112, USA
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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Xiao K, Zhu H, Zhu X, Liu Z, Wang Y, Pu W, Guan P, Hu J. Overexpression of PsoRPM3, an NBS-LRR gene isolated from myrobalan plum, confers resistance to Meloidogyne incognita in tobacco. PLANT MOLECULAR BIOLOGY 2021; 107:129-146. [PMID: 34596818 DOI: 10.1007/s11103-021-01185-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGES We reported an NBS-LRR gene, PsoRPM3, is highly expressed following RKN infection, initiating an HR response that promotes plant resistance. Meloidogyne spp. are root-knot nematodes (RKNs) that cause substantial economic losses worldwide. Screening for resistant tree resources and identifying plant resistance genes is currently the most effective way to prevent RKN infestations. Here, we cloned a novel TIR-NB-LRR-type resistance gene, PsoRPM3, from Xinjiang wild myrobalan plum (Prunus sogdiana Vassilcz.) and demonstrated that its protein product localized to the nucleus. In response to Meloidogyne incognita infection, PsoRPM3 gene expression levels were significantly higher in resistant myrobalan plum plants compared to susceptible plants. We investigated this difference, discovering that the - 309 to - 19 bp region of the susceptible PsoRPM3 promoter was highly methylated. Indeed, heterologous expression of PsoRPM3 significantly enhanced the resistance of susceptible tobacco plants to M. incognita. Moreover, transient expression of PsoRPM3 induced a hypersensitive response in tobacco, whereas RNAi-mediated silencing of PsoRPM3 in transgenic tobacco reduced this hypersensitive response. Several hypersensitive response marker genes were considerably up-regulated in resistant myrobalan plum plants when compared with susceptible counterparts inoculated with M. incognita. PsoPR1a (a SA marker gene), PsoPR2 (a JA marker gene), and PsoACS6 (an ET signaling marker gene) were all more highly expressed in resistant than in susceptible plants. Together, these results support a model in which PsoRPM3 is highly expressed following RKN infection, initiating an HR response that promotes plant resistance through activated salicylic acid, jasmonic acid, and ethylene signaling pathways.
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Affiliation(s)
- Kun Xiao
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
| | - Haifeng Zhu
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
| | - Xiang Zhu
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
- Institute of Laboratory Animal Science, Guizhou University of Traditional Chinese, Guiyang, China
| | - Zhenhua Liu
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
| | - Yan Wang
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
| | - Wenjiang Pu
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
| | - Pingyin Guan
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China
| | - Jianfang Hu
- Laboratory of Fruit Physiology and Molecular Biology, China Agricultural University, Beijing, China.
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Epigenetic Changes in Gestational Diabetes Mellitus. Int J Mol Sci 2021; 22:ijms22147649. [PMID: 34299269 PMCID: PMC8303885 DOI: 10.3390/ijms22147649] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/30/2021] [Accepted: 07/14/2021] [Indexed: 12/30/2022] Open
Abstract
Gestational diabetes mellitus (GDM) is defined as carbohydrate intolerance that appears or is for the first time diagnosed during pregnancy. It can lead to many complications in the mother and in the offspring, so diagnostics and management of GDM are important to avoid adverse pregnancy outcomes. Epigenetic studies revealed the different methylation status of genes in pregnancies with GDM compared to pregnancies without GDM. A growing body of evidence shows that the GDM can affect not only the course of the pregnancy, but also the development of the offspring, thus contributing to long-term effects and adverse health outcomes of the progeny. Epigenetic changes occur through histone modification, DNA methylation, and disrupted function of non-coding ribonucleic acid (ncRNA) including microRNAs (miRNAs). In this review, we focus on the recent knowledge about epigenetic changes in GDM. The analysis of this topic may help us to understand pathophysiological mechanisms in GDM and find a solution to prevent their consequences.
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Abstract
Substance use disorders (SUDs) are chronic brain diseases characterized by transitions from recreational to compulsive drug use and aberrant drug craving that persists for months to years after abstinence is achieved. The transition to compulsive drug use implies that plasticity is occurring, altering the physiology of the brain to precipitate addicted states. Epigenetic phenomena represent a varied orchestra of transcriptional tuning mechanisms that, in response to environmental stimuli, create and maintain gene expression-mediated physiological outcomes. Therefore, epigenetic mechanisms represent a convergent regulatory framework through which the plasticity required to achieve an addicted state can arise and then persist long after drug use has ended. In the first section, we will introduce basic concepts in epigenetics, such as chromatin architecture, histones and their posttranslational modifications, DNA methylation, noncoding RNAs, and transcription factors, along with methods for their investigation. We will then examine the implications of these mechanisms in SUDs, with a particular focus on cocaine-mediated neuroepigenetic plasticity across multiple behavioral models of addiction.
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Affiliation(s)
- Andrew F Stewart
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Sasha L Fulton
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Ian Maze
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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Combined prenatal Lactobacillus reuteri and ω-3 supplementation synergistically modulates DNA methylation in neonatal T helper cells. Clin Epigenetics 2021; 13:135. [PMID: 34193262 PMCID: PMC8247185 DOI: 10.1186/s13148-021-01115-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/15/2021] [Indexed: 02/08/2023] Open
Abstract
Background Environmental exposures may alter DNA methylation patterns of T helper cells. As T helper cells are instrumental for allergy development, changes in methylation patterns may constitute a mechanism of action for allergy preventive interventions. While epigenetic effects of separate perinatal probiotic or ω-3 fatty acid supplementation have been studied previously, the combined treatment has not been assessed. We aimed to investigate epigenome-wide DNA methylation patterns from a sub-group of children in an on-going randomised double-blind placebo-controlled allergy prevention trial using pre- and postnatal combined Lactobacillus reuteri and ω-3 fatty acid treatment. To this end, > 866000 CpG sites (MethylationEPIC 850K array) in cord blood CD4+ T cells were examined in samples from all four study arms (double-treatment: n = 18, single treatments: probiotics n = 16, ω-3 n = 15, and double placebo: n = 14). Statistical and bioinformatic analyses identified treatment-associated differentially methylated CpGs and genes, which were used to identify putatively treatment-induced network modules. Pathway analyses inferred biological relevance, and comparisons were made to an independent allergy data set. Results Comparing the active treatments to the double placebo group, most differentially methylated CpGs and genes were hypermethylated, possibly suggesting induction of transcriptional inhibition. The double-treated group showed the largest number of differentially methylated CpGs, of which many were unique, suggesting synergy between interventions. Clusters within the double-treated network module consisted of immune-related pathways, including T cell receptor signalling, and antigen processing and presentation, with similar pathways revealed for the single-treatment modules. CpGs derived from differential methylation and network module analyses were enriched in an independent allergy data set, particularly in the double-treatment group, proposing treatment-induced DNA methylation changes as relevant for allergy development. Conclusion Prenatal L. reuteri and/or ω-3 fatty acid treatment results in hypermethylation and affects immune- and allergy-related pathways in neonatal T helper cells, with potentially synergistic effects between the interventions and relevance for allergic disease. Further studies need to address these findings on a transcriptional level, and whether the results associate to allergy development in the children. Understanding the role of DNA methylation in regulating effects of perinatal probiotic and ω-3 interventions may provide essential knowledge in the development of efficacious allergy preventive strategies. Trial registration ClinicalTrials.gov, ClinicalTrials.gov-ID: NCT01542970. Registered 27th of February 2012—Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT01542970. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01115-4.
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14
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Liu S, An G, Cao Q, Li T, Jia X, Lei L. The miR-106b/NR2F2-AS1/PLEKHO2 Axis Regulates Migration and Invasion of Colorectal Cancer through the MAPK Pathway. Int J Mol Sci 2021; 22:ijms22115877. [PMID: 34070923 PMCID: PMC8198404 DOI: 10.3390/ijms22115877] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 12/27/2022] Open
Abstract
Increasing numbers of miRNAs have been observed as oncogenes or tumor suppressors in colorectal cancer (CRC). It was recently reported that hsa-miR-106b-5p (miR-106b) promoted CRC cell migration and invasion. However, there were also studies showing contradictory results. Therefore, in the present study, we further explore the role of miR-106b and its downstream networks in the carcinogenesis of CRC. We observed that the expression of miR-106b is significantly increased in Pan-Cancer and CRC tissues compared with normal tissues from The Cancer Genome Atlas (TCGA) database. Furthermore, we used Transwell, Cell Counting Kit-8, and colony formation assays to clarify that miR-106b promotes the migratory, invasive, and proliferative abilities of CRC cells. For the first time, we systematically screened the target mRNAs and lncRNAs of miR-106b using TCGA database and the bioinformatics algorithms. Dual-luciferase reporter assay confirmed that NR2F2-AS1 and PLEKHO2 are the direct targets of miR-106b. Furthermore, NR2F2-AS1 acts as a competing endogenous RNA (ceRNA) to regulate PLEKHO2 expression by sponging miR-106b. The results of Gene set enrichment analysis (GSEA) and Western blot indicated that they play important roles in CRC progression by regulating MAPK pathway. Thus, miR-106b/NR2F2-AS1/PLEKHO2/MAPK signaling axis may suggest the potential usage in CRC treatment.
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Affiliation(s)
- Shuzhen Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, School of Medicine, Northwest University, Ministry of Education, Xi’an 710069, China; (S.L.); (G.A.); (Q.C.); (T.L.)
| | - Guoyan An
- Key Laboratory of Resource Biology and Biotechnology in Western China, School of Medicine, Northwest University, Ministry of Education, Xi’an 710069, China; (S.L.); (G.A.); (Q.C.); (T.L.)
| | - Qing Cao
- Key Laboratory of Resource Biology and Biotechnology in Western China, School of Medicine, Northwest University, Ministry of Education, Xi’an 710069, China; (S.L.); (G.A.); (Q.C.); (T.L.)
| | - Tong Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, School of Medicine, Northwest University, Ministry of Education, Xi’an 710069, China; (S.L.); (G.A.); (Q.C.); (T.L.)
| | - Xinyu Jia
- Health Science Center, Xi’an Jiaotong University, Xi’an 710049, China;
| | - Lei Lei
- Key Laboratory of Resource Biology and Biotechnology in Western China, School of Medicine, Northwest University, Ministry of Education, Xi’an 710069, China; (S.L.); (G.A.); (Q.C.); (T.L.)
- Correspondence:
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15
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Luo X, Schwartz J, Baccarelli A, Liu Z. Testing cell-type-specific mediation effects in genome-wide epigenetic studies. Brief Bioinform 2021; 22:bbaa131. [PMID: 32632436 PMCID: PMC8138838 DOI: 10.1093/bib/bbaa131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/19/2020] [Accepted: 05/27/2020] [Indexed: 12/12/2022] Open
Abstract
Epigenome-wide mediation analysis aims to identify DNA methylation CpG sites that mediate the causal effects of genetic/environmental exposures on health outcomes. However, DNA methylations in the peripheral blood tissues are usually measured at the bulk level based on a heterogeneous population of white blood cells. Using the bulk level DNA methylation data in mediation analysis might cause confounding bias and reduce study power. Therefore, it is crucial to get fine-grained results by detecting mediation CpG sites in a cell-type-specific way. However, there is a lack of methods and software to achieve this goal. We propose a novel method (Mediation In a Cell-type-Specific fashion, MICS) to identify cell-type-specific mediation effects in genome-wide epigenetic studies using only the bulk-level DNA methylation data. MICS follows the standard mediation analysis paradigm and consists of three key steps. In step1, we assess the exposure-mediator association for each cell type; in step 2, we assess the mediator-outcome association for each cell type; in step 3, we combine the cell-type-specific exposure-mediator and mediator-outcome associations using a multiple testing procedure named MultiMed [Sampson JN, Boca SM, Moore SC, et al. FWER and FDR control when testing multiple mediators. Bioinformatics 2018;34:2418-24] to identify significant CpGs with cell-type-specific mediation effects. We conduct simulation studies to demonstrate that our method has correct FDR control. We also apply the MICS procedure to the Normative Aging Study and identify nine DNA methylation CpG sites in the lymphocytes that might mediate the effect of cigarette smoking on the lung function.
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Affiliation(s)
- Xiangyu Luo
- Institute of Statistics and Big Data, Renmin University of China, Beijing, China
| | - Joel Schwartz
- Department of Environmental Health, Harvard University, Boston, MA, USA
| | - Andrea Baccarelli
- Leon Hess Professor in the Department of Environmental Health Sciences, Columbia University, New York City, NY, USA
| | - Zhonghua Liu
- Department of Statistics and Actuarial Science, University of Hong Kong, Hong Kong SAR, China
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16
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Chen X, Huang NX, Cheng YJ, Cai QY, Tian YP, Chen XS, Xiao L. DNA Hypermethylation Induced by L-Methionine Leads to Oligodendroglial and Myelin Deficits and Schizophrenia-Like Behaviors in Adolescent Mice. Front Neurosci 2021; 15:659853. [PMID: 33958986 PMCID: PMC8095669 DOI: 10.3389/fnins.2021.659853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/23/2021] [Indexed: 12/29/2022] Open
Abstract
Increasing evidence has demonstrated that in addition to dysfunction of neuronal circuitry, oligodendroglial dysfunction and/or disruption of white matter integrity are found in the brains of patients with schizophrenia. DNA methylation, a well-established risk factor for schizophrenia, has been demonstrated to cause neuronal dysfunction; however, whether dysregulation of DNA methylation contributes to oligodendroglial/myelin deficits in the pathogenesis of schizophrenia remains unclear. In the present study, by using L-methionine-treated mice, we confirmed that mice with DNA hypermethylation exhibited an anxious phenotype, impaired sociability, and sensorimotor gating deficits. Notably, DNA hypermethylation in oligodendroglial cells led to dysregulation of multiple oligodendroglia-specific transcription factors, which indicated disruption of the transcriptional architecture. Furthermore, DNA hypermethylation caused a reduction of oligodendroglial lineage cells and myelin integrity in the frontal white matter of mice. Taken together, these results indicate that DNA hypermethylation leads to oligodendroglial and/or myelin deficits, which may, at least in part, contribute to schizophrenia-like behaviors in mice. This study provides new insights into the possibility that precise modulation of DNA methylation status in oligodendroglia could be beneficial for the white matter pathology in schizophrenia.
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Affiliation(s)
- Xianjun Chen
- Department of Histology and Embryology, Institute of Brain and Intelligence, Army Medical University (Third Military Medical University), Chongqing, China.,Department of Physiology, Research Center of Neuroscience, College of Basic Medical Science, Chongqing Medical University, Chongqing, China
| | - Nan-Xin Huang
- Department of Histology and Embryology, Institute of Brain and Intelligence, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yong-Jie Cheng
- Department of Histology and Embryology, Institute of Brain and Intelligence, Army Medical University (Third Military Medical University), Chongqing, China
| | - Qi-Yan Cai
- Department of Histology and Embryology, Institute of Brain and Intelligence, Army Medical University (Third Military Medical University), Chongqing, China
| | - Yan-Ping Tian
- Department of Histology and Embryology, Institute of Brain and Intelligence, Army Medical University (Third Military Medical University), Chongqing, China
| | - Xing-Shu Chen
- Department of Histology and Embryology, Institute of Brain and Intelligence, Army Medical University (Third Military Medical University), Chongqing, China.,Key Laboratory of Extreme Environmental Medicine, Ministry of Education, Department of Military Medical Geography, Army Medical Training Base, Army Medical University (Third Military Medical University), Chongqing, China
| | - Lan Xiao
- Department of Histology and Embryology, Institute of Brain and Intelligence, Army Medical University (Third Military Medical University), Chongqing, China
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17
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Electrochemically detecting DNA methylation in the EN1 gene promoter: implications for understanding ageing and disease. Biosci Rep 2021; 40:226876. [PMID: 33135722 PMCID: PMC7670582 DOI: 10.1042/bsr20202571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/29/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
There is a growing need for biomarkers which predict age-onset pathology. Although this is challenging, the methylome offers significant potential. Cancer is associated with the hypermethylation of many gene promoters, among which are developmental genes. Evolutionary theory suggests developmental genes arbitrate early-late life trade-offs, causing epimutations that increase disease vulnerability. Such genes could predict age-related disease. The aim of this work was to optimise an electrochemical procedure for the future investigation of a broad range of ageing-related pathologies. An electrochemical approach, which adopted three analytical techniques, was used to investigate DNA methylation in the engrailed-1 (EN1) gene promoter. Using synthetic single-stranded DNA, one technique was able to detect DNA at concentrations as low as 10 nM, with methylation status distinguishable at concentrations >25 nM. A negative correlation could be observed between % methylation of a heterogeneous solution and the key electrochemical parameter, charge transfer resistance (Rct; r = -0.982, P<0.01). The technique was applied to the breast cancer cell line Michigan Cancer Foundation-7 (MCF-7), where a similar correlation was observed (r = -0.965, P<0.01). These results suggest electrochemistry can effectively measure DNA methylation at low concentrations of DNA. This has implications for the future detection of age-related disease.
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18
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Karamat U, Ejaz S. Overexpression of RAD50 is the Marker of Poor Prognosis and Drug Resistance in Breast Cancer Patients. Curr Cancer Drug Targets 2021; 21:163-176. [PMID: 33038913 DOI: 10.2174/1568009620666201009125507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The prevalence of breast cancer is increasing at an alarming rate and thus demands exploration of the most relevant diagnostic biomarkers. RAD50 is a cancer susceptibility gene that encodes a DNA damage repairing protein. Its role in breast cancer as clinico-pathological specific biomarker has yet to be explored. OBJECTIVE This study was aimed to investigate the RAD50 expression and its promoter's methylation level variations in breast invasive carcinoma patients having different clinico-pathological features. This study further explored the mutational spectrum of RAD50 and the correlation of its expression with the survival of patients and the effectiveness of drugs used for treatment. METHODS Enrichment analysis of RAD50 was accomplished using the platform of GeneCards. The information regarding RAD50 expression, its promoter methylation and impact on survival of patient was retrieved from TCGA and CPTAC databases. However, the effect of RAD50 expression on tumor's response to various drugs was deduced through the analysis of CCLE and genomic of GDSC dataset. RESULTS The promoter hyper-methylation and elevated expression of RAD50 was documented in various subgroups of breast invasive carcinoma. The subjects having low/medium expression levels were observed to survive longer than patients exhibiting high expression of RAD50 except for post-menopausal subjects. The frequency of missense mutations was higher in RAD50 than truncating mutations. Most of the drugs were found to have a positive correlation with RAD50 expression. CONCLUSION The status of RAD50 promoter's methylation inversely correlates with the expression level of RAD50. While RAD50 is overexpressed in breast cancer patients and thus makes tumor resistant against many anti-cancer drugs.
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Affiliation(s)
- Uzma Karamat
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), Faculty of Science, The Islamia University of Bahwalpur, Bahwalpur, Pakistan
| | - Samina Ejaz
- Department of Biochemistry, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), Faculty of Science, The Islamia University of Bahawalpur, Bahwalpur, Pakistan
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19
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Gardini ES, Chen GG, Fiacco S, Mernone L, Willi J, Turecki G, Ehlert U. Differential ESR1 Promoter Methylation in the Peripheral Blood-Findings from the Women 40+ Healthy Aging Study. Int J Mol Sci 2020; 21:E3654. [PMID: 32455834 PMCID: PMC7279168 DOI: 10.3390/ijms21103654] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/16/2020] [Accepted: 05/19/2020] [Indexed: 12/16/2022] Open
Abstract
Background Estrogen receptor α (ERα) contributes to maintaining biological processes preserving health during aging. DNA methylation changes of ERα gene (ESR1) were established as playing a direct role in the regulation of ERα levels. In this study, we hypothesized decreased DNA methylation of ESR1 associated with postmenopause, lower estradiol (E2) levels, and increased age among healthy middle-aged and older women. Methods We assessed DNA methylation of ESR1 promoter region from dried blood spots (DBSs) and E2 from saliva samples in 130 healthy women aged 40-73 years. Results We found that postmenopause and lower E2 levels were associated with lower DNA methylation of a distal regulatory region, but not with DNA methylation of proximal promoters. Conclusion Our results indicate that decreased methylation of ESR1 cytosine-phosphate-guanine island (CpGI) shore may be associated with conditions of lower E2 in older healthy women.
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Affiliation(s)
- Elena S. Gardini
- Clinical Psychology and Psychotherapy, Department of Psychology, University of Zurich, 8050 Zurich, Switzerland; (E.S.G.); (S.F.); (L.M.); (J.W.)
- University Research Priority Program (URPP) Dynamics of Healthy Aging, University of Zurich, 8050 Zurich, Switzerland
| | - Gary G. Chen
- Douglas Hospital Research Center, McGill University, Montreal, QC H4H 1R3, Canada; (G.G.C.); (G.T.)
| | - Serena Fiacco
- Clinical Psychology and Psychotherapy, Department of Psychology, University of Zurich, 8050 Zurich, Switzerland; (E.S.G.); (S.F.); (L.M.); (J.W.)
- University Research Priority Program (URPP) Dynamics of Healthy Aging, University of Zurich, 8050 Zurich, Switzerland
| | - Laura Mernone
- Clinical Psychology and Psychotherapy, Department of Psychology, University of Zurich, 8050 Zurich, Switzerland; (E.S.G.); (S.F.); (L.M.); (J.W.)
- University Research Priority Program (URPP) Dynamics of Healthy Aging, University of Zurich, 8050 Zurich, Switzerland
| | - Jasmine Willi
- Clinical Psychology and Psychotherapy, Department of Psychology, University of Zurich, 8050 Zurich, Switzerland; (E.S.G.); (S.F.); (L.M.); (J.W.)
- University Research Priority Program (URPP) Dynamics of Healthy Aging, University of Zurich, 8050 Zurich, Switzerland
| | - Gustavo Turecki
- Douglas Hospital Research Center, McGill University, Montreal, QC H4H 1R3, Canada; (G.G.C.); (G.T.)
| | - Ulrike Ehlert
- Clinical Psychology and Psychotherapy, Department of Psychology, University of Zurich, 8050 Zurich, Switzerland; (E.S.G.); (S.F.); (L.M.); (J.W.)
- University Research Priority Program (URPP) Dynamics of Healthy Aging, University of Zurich, 8050 Zurich, Switzerland
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20
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Yang J, Bashkenova N, Zang R, Huang X, Wang J. The roles of TET family proteins in development and stem cells. Development 2020; 147:147/2/dev183129. [PMID: 31941705 DOI: 10.1242/dev.183129] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ten-eleven translocation (TET) methylcytosine dioxygenases are enzymes that catalyze the demethylation of 5-methylcytosine on DNA. Through global and site-specific demethylation, they regulate cell fate decisions during development and in embryonic stem cells by maintaining pluripotency or by regulating differentiation. In this Primer, we provide an updated overview of TET functions in development and stem cells. We discuss the catalytic and non-catalytic activities of TETs, and their roles as epigenetic regulators of both DNA and RNA hydroxymethylation, highlighting how TET proteins function in regulating gene expression at both the transcriptional and post-transcriptional levels.
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Affiliation(s)
- Jihong Yang
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nazym Bashkenova
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ruge Zang
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA.,Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xin Huang
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development, Columbia University Irving Medical Center, New York, NY 10032, USA
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21
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Wu M, Li X, Zhang C, Zhang C, Qian D, Ma J, Cai M, Tang L, Cheng H, Shen C, Chen G, Zheng X, Zhang X, Zhou F. DNA methylation profile of psoriatic skins from different body locations. Epigenomics 2019; 11:1613-1625. [PMID: 31701765 DOI: 10.2217/epi-2018-0225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: To understand whether the anatomical location of origin plays a role in shaping the DNA methylation (DNAm) landscape of psoriatic skins. Patients & methods: A number of 108 psoriatic and 57 control skin samples were grouped based on their anatomical locations. Two group t-tests were used to identify those differentially methylated sites and regions. Target region methylation loci were validated by bisulfate conversion sequencing. The correlations of DNAm with pathological features, DNAm and gene expression were also interrogated. Results: Our analysis revealed 315 location-specific differentially methylated sites for back, 291 for the extremities and 801 for abdomen. Moreover, we observed that the extremity-specific loci cg21942490 located on HOXA9 is associated with hyperkeratosis. We further observed that HOXA5 and KIAA1949 are differential methylation regions. Conclusion: Our study shown evidence of anatomical location-dependent DNAm pattern in psoriasis skins, and thus provided new insights into the pathogenesis of this disease.
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Affiliation(s)
- Mingshun Wu
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Xueying Li
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Chaowen Zhang
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Chuanliang Zhang
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Danfeng Qian
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Jie Ma
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Minglong Cai
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Lili Tang
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Hui Cheng
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Changbing Shen
- Department of Dermatology, China-Japan Friendship Hospital, Beijing 100029, PR China
| | - Gang Chen
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Xiaodong Zheng
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
| | - Xuejun Zhang
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,Department of Dermatology, Institute of Dermatology, Huashan Hospital, Fudan University, Shanghai 200040, PR China
| | - Fusheng Zhou
- Department of Dermatology, Institute of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, PR China.,The Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei 230032, PR China
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Gu X, Guo XK, Chen BH, Gao XJ, Chen F, Liu Q. Prognostic and clinicopathological value of ZIC1 in patients with cervical squamous cell carcinoma. Oncol Lett 2019; 18:6621-6627. [PMID: 31788119 PMCID: PMC6865731 DOI: 10.3892/ol.2019.11007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/30/2019] [Indexed: 01/05/2023] Open
Abstract
The aim of the present study was to analyze the differences in zinc finger of the cerebellum 1 (ZIC1) expression between cervical cancer tissue, precancer tissue and normal cervical tissue to determine its clinicopathological and prognostic value in cervical squamous cell carcinoma (CSCC). Reverse transcription-quantitative PCR was used to determine the mRNA expression levels of ZIC1 in 569 fresh-frozen biopsy tissues, and immunohistochemistry was performed to detect ZIC1 protein expression in 80 CSCC tissues and 320 cervical intraepithelial neoplasia (CIN) grade III samples. The association of ZIC1 expression with the clinicopathological characteristics of CSCC was then analyzed using Cox regression analysis, and Kaplan-Meier curves were used to analyze the prognostic value. The level of ZIC1 mRNA expression in CSCC was significantly lower compared with normal cervical tissues and CIN I–III tissues (P<0.001). There was a negative correlation between ZIC1 immunoreactivity score (IRS) in CSCC tissue and adjacent noncancerous tissue (R=−0.279; P=0.012); the mean IRS of ZIC1 in CSCC tissue was 5.36±3.48, which was significantly lower compared with the corresponding adjacent noncancerous tissues (11.31±5.68; P<0.001) and CIN III samples (10.42±1.54; P<0.001). In addition, expression of ZIC1 was negatively associated with International Federation of Gynecology and Obstetrics (FIGO) stage (P=0.027) and lymph node metastasis (P<0.001). In Cox regression analysis, ZIC1 expression [hazard ratio (HR), 0.61; 95% confidence interval (CI), 0.40–0.92; P=0.018), FIGO staging (HR, 3.55; 95% CI, 2.35–5.37; P<0.001) and lymph node metastasis (HR, 2.50; 95% CI, 1.62–3.86; P<0.001) were three independent prognostic factors of overall survival. Furthermore, ZIC1 expression was also associated with disease-free survival (P=0.003). These results suggest that ZIC1 expression in CSCC may be lower than in normal cervical tissues or CIN tissues, and high expression of ZIC1 may be negatively associated with FIGO stage and lymph node metastasis. Therefore, ZIC1 may be a promising biomarker for the prognosis of CSCC.
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Affiliation(s)
- Xing Gu
- Department of Gynecology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu 215300, P.R. China
| | - Xue-Ke Guo
- Department of Gynecology, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Bi-Hui Chen
- Department of Gynecology, Kunshan Hospital of Traditional Chinese Medicine, Kunshan, Jiangsu 215300, P.R. China
| | - Xiao-Jiao Gao
- Department of Pathology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu 215300, P.R. China
| | - Fang Chen
- Department of Pathology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu 215300, P.R. China
| | - Qin Liu
- Department of Gynecology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, Jiangsu 215300, P.R. China
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Paredes-Céspedes DM, Herrera-Moreno JF, Bernal-Hernández YY, Medina-Díaz IM, Salazar AM, Ostrosky-Wegman P, Barrón-Vivanco BS, Rojas-García AE. Pesticide Exposure Modifies DNA Methylation of Coding Region of WRAP53α, an Antisense Sequence of p53, in a Mexican Population. Chem Res Toxicol 2019; 32:1441-1448. [PMID: 31243981 DOI: 10.1021/acs.chemrestox.9b00153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The influence of pesticide exposure in alteration of DNA methylation patterns of specific genes is still limited, specifically in natural antisense transcripts (NAT), such as the WRAP53α gene. The aim of this study was to determine the methylation of the WRAP53α gene in mestizo and indigenous populations as well as its relationship with internal (age, sex, and body mass index) and external factors (pesticide exposure and micronutrient intake). A cross-sectional study was conducted including 91 mestizo individuals without occupational exposure to pesticides, 164 mestizo urban sprayers and 189 indigenous persons without occupational exposure to pesticides. Acute pesticide exposure was evaluated by measurement of urinary dialkylphosphate (DAP) concentration by gas chromatograph coupled to a mass spectrometer. Anthropometric characteristics, unhealthy habits, and chronic pesticide exposure were assessed using a structured questionnaire. The frequency of macro- and micronutrient intake was determined using SNUT software. DNA methylation of the WRAP53α gene was determined by pyrosequencing of bisulfite-modified DNA. The mestizo sprayers group had the higher values of %5mC. In addition, this group had the most DAP urinary concentration with respect to the indigenous and reference groups. Bivariate analysis showed an association between %5mC of the WRAP53α gene with micronutrient intake and pesticide exposure in mestizo sprayers, whereas changes in %5mC of the WRAP53α gene was associated with body mass index in the indigenous group. These data suggest that the %5mC of the WRAP53α gene can be influenced by pesticide exposure and ethnicity in the study population, and changes in the WRAP53α gene might cause an important cell process disturbance.
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Affiliation(s)
- Diana M Paredes-Céspedes
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado , Universidad Autónoma de Nayarit , 63155, Ciudad de la Cultura s/n. Col. Centro, C.P. 63000 , Tepic , Nayarit , México.,Posgrado en Ciencias Biológico Agropecuarias , Unidad Académica de Agricultura , Km. 9 Carretera Tepic-Compostela, Xalisco , Nayarit , México
| | - José F Herrera-Moreno
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado , Universidad Autónoma de Nayarit , 63155, Ciudad de la Cultura s/n. Col. Centro, C.P. 63000 , Tepic , Nayarit , México.,Posgrado en Ciencias Biológico Agropecuarias , Unidad Académica de Agricultura , Km. 9 Carretera Tepic-Compostela, Xalisco , Nayarit , México
| | - Yael Y Bernal-Hernández
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado , Universidad Autónoma de Nayarit , 63155, Ciudad de la Cultura s/n. Col. Centro, C.P. 63000 , Tepic , Nayarit , México
| | - Irma M Medina-Díaz
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado , Universidad Autónoma de Nayarit , 63155, Ciudad de la Cultura s/n. Col. Centro, C.P. 63000 , Tepic , Nayarit , México
| | - Ana M Salazar
- Instituto de Investigaciones Biomédicas , Universidad Nacional Autónoma de México (UNAM) , P.O. Box 70228, Ciudad Universitaria, México DF 04510 , México
| | - Patricia Ostrosky-Wegman
- Instituto de Investigaciones Biomédicas , Universidad Nacional Autónoma de México (UNAM) , P.O. Box 70228, Ciudad Universitaria, México DF 04510 , México
| | - Briscia S Barrón-Vivanco
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado , Universidad Autónoma de Nayarit , 63155, Ciudad de la Cultura s/n. Col. Centro, C.P. 63000 , Tepic , Nayarit , México
| | - Aurora E Rojas-García
- Laboratorio de Contaminación y Toxicología Ambiental, Secretaría de Investigación y Posgrado , Universidad Autónoma de Nayarit , 63155, Ciudad de la Cultura s/n. Col. Centro, C.P. 63000 , Tepic , Nayarit , México
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24
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Abstract
Increasing numbers of studies implicate abnormal DNA methylation in cancer and many non-malignant diseases. This is consistent with numerous findings about differentiation-associated changes in DNA methylation at promoters, enhancers, gene bodies, and sites that control higher-order chromatin structure. Abnormal increases or decreases in DNA methylation contribute to or are markers for cancer formation and tumour progression. Aberrant DNA methylation is also associated with neurological diseases, immunological diseases, atherosclerosis, and osteoporosis. In this review, I discuss DNA hypermethylation in disease and its interrelationships with normal development as well as proposed mechanisms for the origin of and pathogenic consequences of disease-associated hypermethylation. Disease-linked DNA hypermethylation can help drive oncogenesis partly by its effects on cancer stem cells and by the CpG island methylator phenotype (CIMP); atherosclerosis by disease-related cell transdifferentiation; autoimmune and neurological diseases through abnormal perturbations of cell memory; and diverse age-associated diseases by age-related accumulation of epigenetic alterations.
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Affiliation(s)
- Melanie Ehrlich
- Tulane Cancer Center and Tulane Center for Bioinformatics and Genomics, Tulane University Health Sciences Center , New Orleans , LA , USA
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25
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Lacey M, Baribault C, Ehrlich KC, Ehrlich M. Data showing atherosclerosis-associated differentially methylated regions are often at enhancers. Data Brief 2019; 23:103812. [PMID: 31372457 PMCID: PMC6660590 DOI: 10.1016/j.dib.2019.103812] [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: 01/30/2019] [Revised: 02/22/2019] [Accepted: 02/26/2019] [Indexed: 12/22/2022] Open
Abstract
Atherosclerosis involves phenotypic modulation and transdifferentiation of vascular smooth muscle cells (SMCs). Data are given in tabular or figure format that illustrate genome-wide DNA methylation alterations in atherosclerotic vs. control aorta (athero DMRs). Data based upon publicly available chromatin state profiles are also shown for normal aorta, monocyte, and skeletal muscle tissue-specific DMRs and for aorta-specific chromatin features (enhancer chromatin, promoter chromatin, repressed chromatin, actively transcribed chromatin). Athero hypomethylated and hypermethylated DMRs as well as epigenetic and transcription profiles are described for the following genes: ACTA2, MYH10, MYH11 (SMC-associated genes); SMAD3 (a signaling gene for SMCs and other cell types); CD79B and SH3BP2 (leukocyte-associated genes); and TBX20 and genes in the HOXA, HOXB, HOXC, and HOXD clusters (T-box and homeobox developmental genes). The data reveal strong correlations between athero hypermethylated DMRs and regions of enhancer chromatin in aorta, which are discussed in the linked research article “Atherosclerosis-associated differentially methylated regions can reflect the disease phenotype and are often at enhancers” (M. Lacey et al., 2019).
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Key Words
- Atherosclerosis
- DMR, differentially methylated region
- DNA methylation
- Differentially methylated regions (DMRs)
- Enhancers
- GO, gene ontology
- Monocytes
- PBMC, peripheral blood mononuclear cells
- PMD, percent methylation difference
- SkM, skeletal muscle
- Smooth muscle
- athero hypermeth DMR, atherosclerosis-associated hypermethylated DMR
- athero hypometh DMR, atherosclerosis-associated hypomethylated DMR
- ctl, control
- enh, enhancer chromatin
- mod, moderate
- prom, promoter chromatin
- repr, repressed
- txn chromatin, chromatin with the histone marks of actively transcribed chromatin
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Affiliation(s)
- Michelle Lacey
- Tulane Cancer Center, Tulane University Health Sciences Center, LA 70112, USA.,Department of Mathematics, Tulane University, New Orleans, LA 70118, USA
| | - Carl Baribault
- Tulane Cancer Center, Tulane University Health Sciences Center, LA 70112, USA
| | - Kenneth C Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, USA
| | - Melanie Ehrlich
- Tulane Cancer Center, Tulane University Health Sciences Center, LA 70112, USA.,Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, USA.,Hayward Genetics Center, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
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26
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Lacey M, Baribault C, Ehrlich KC, Ehrlich M. Atherosclerosis-associated differentially methylated regions can reflect the disease phenotype and are often at enhancers. Atherosclerosis 2018; 280:183-191. [PMID: 30529831 DOI: 10.1016/j.atherosclerosis.2018.11.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/05/2018] [Accepted: 11/22/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND AND AIMS Atherosclerosis is a widespread and complicated disease involving phenotypic modulation and transdifferentiation of vascular smooth muscle cells (SMCs), the predominant cells in aorta, as well as changes in endothelial cells and infiltrating monocytes. Alterations in DNA methylation are likely to play central roles in these phenotypic changes, just as they do in normal differentiation and cancer. METHODS We examined genome-wide DNA methylation changes in atherosclerotic aorta using more stringent criteria for differentially methylated regions (DMRs) than in previous studies and compared these DMRs to tissue-specific epigenetic features. RESULTS We found that disease-linked hypermethylated DMRs account for 85% of the total atherosclerosis-associated DMRs and often overlap aorta-associated enhancer chromatin. These hypermethylated DMRs were associated with functionally different sets of genes compared to atherosclerosis-linked hypomethylated DMRs. The extent and nature of the DMRs could not be explained as direct effects of monocyte/macrophage infiltration. Among the known atherosclerosis- and contractile SMC-related genes that exhibited hypermethylated DMRs at aorta enhancer chromatin were ACTA2 (aorta α2 smooth muscle actin), ELN (elastin), MYOCD (myocardin), C9orf3 (miR-23b and miR-27b host gene), and MYH11 (smooth muscle myosin). Our analyses also suggest a role in atherosclerosis for developmental transcription factor genes having little or no previous association with atherosclerosis, such as NR2F2 (COUP-TFII) and TBX18. CONCLUSIONS We provide evidence for atherosclerosis-linked DNA methylation changes in aorta SMCs that might help minimize or reverse the standard contractile character of many of these cells by down-modulating aorta SMC-related enhancers, thereby facilitating pro-atherosclerotic phenotypic changes in many SMCs.
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Affiliation(s)
- Michelle Lacey
- Tulane Cancer Center, Tulane University Health Sciences Center, LA, 70112, USA; Department of Mathematics, Tulane University, New Orleans, LA, 70118, USA
| | - Carl Baribault
- Tulane Cancer Center, Tulane University Health Sciences Center, LA, 70112, USA
| | - Kenneth C Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, USA
| | - Melanie Ehrlich
- Tulane Cancer Center, Tulane University Health Sciences Center, LA, 70112, USA; Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, USA; Hayward Genetics Center, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA.
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27
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Kumar R, Jain V, Kushwah N, Dheer A, Mishra KP, Prasad D, Singh SB. Role of DNA Methylation in Hypobaric Hypoxia-Induced Neurodegeneration and Spatial Memory Impairment. Ann Neurosci 2018; 25:191-200. [PMID: 31000957 DOI: 10.1159/000490368] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/24/2018] [Indexed: 12/19/2022] Open
Abstract
Hypobaric hypoxia (HH) is a major stress factor that is associated with physiological, biochemical, molecular and genomic alterations. Brain is the organ that reacts sensitively to oxygen deprivation, which leads to oxidative stress and cognitive function impairment. Our previous studies have reported that downregulation of brain derived neurotrophic factor (BDNF) leads to neurodegeneration and memory impairment. The aim of the present study was to investigate the effect of HH exposure on DNA methylation and its regulation in BDNF expression, neurodegeneration and spatial memory impairment. For this purpose, Sprague Dawley rats were exposed to HH at a simulated altitude of 25,000 feet for 14 days. Real-time polymerase chain reaction was used for transcriptional expression of DNA Methyltransferases (DNMTs) including DNMT1, DNMT3a and -DNMT3b, and immunoblotting was used for the translational expression of DNMT1, DNMT3a, DNMT3b, Methyl CpG binding protein 2 (MeCP2), pMeCP2 and BDNF in rat hippocampus. Additionally, neuronal morphology alteration and neurodegeneration in CA1 region of hippocampus were investigated though Cresyl violet (CV) staining and Fluoro-Jade C staining respectively. Results obtained suggested that HH exposure increased the expression of DNMT1 DNMT3b at the mRNA as well as protein level, whereas no significant change was observed in the level of DNMT3a. Furthermore, the level of pMeCP2 and BDNF were significantly decreased; however, the expression level of MeCP2 was significantly increased. The CV and Fluoro-Jade C-positive cells were significantly enhanced in the CA1 region of hippocampus in the HH exposed group as compared to unexposed rats. Thus, the present study concluded that HH decreases neuronal activation by the upregulation of DNA methylation and MeCP2 and decreased the expression of pMeCP2, which result in the downregulation of BDNF. The decreased BDNF expression is associated with neuronal loss and spatial memory impairment. This study highlights that DNMT inhibition could be an important therapeutic target for neurodegenerative diseases.
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Affiliation(s)
- Rahul Kumar
- Neurobiology Division, Defence Institute of Physiology and Allied Science (DIAPS), DRDO, New Delhi, India
| | - Vishal Jain
- Neurophysiology Division, Defence Institute of Physiology and Allied Science (DIAPS), DRDO, New Delhi, India
| | - Neetu Kushwah
- Neurobiology Division, Defence Institute of Physiology and Allied Science (DIAPS), DRDO, New Delhi, India
| | - Aastha Dheer
- Neurobiology Division, Defence Institute of Physiology and Allied Science (DIAPS), DRDO, New Delhi, India
| | - Kamla Prasad Mishra
- Directorate General Life Sciences, Defence research Development Organisation (DRDO), Government of India, DRDO Bhawan, Rajaji Marg, New Delhi, India
| | - Dipti Prasad
- Neurobiology Division, Defence Institute of Physiology and Allied Science (DIAPS), DRDO, New Delhi, India
| | - Shashi Bala Singh
- Directorate General Life Sciences, Defence research Development Organisation (DRDO), Government of India, DRDO Bhawan, Rajaji Marg, New Delhi, India
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