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Heidari N, Hajikarim-Hamedani A, Heidari A, Ghane Y, Ashabi G, Zarrindast MR, Sadat-Shirazi MS. Alcohol: Epigenome alteration and inter/transgenerational effect. Alcohol 2024; 117:27-41. [PMID: 38508286 DOI: 10.1016/j.alcohol.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 03/22/2024]
Abstract
While DNA serves as the fundamental genetic blueprint for an organism, it is not a static entity. Gene expression, the process by which genetic information is utilized to create functional products like proteins, can be modulated by a diverse range of environmental factors. Epigenetic mechanisms, including DNA methylation, histone modification, and microRNAs, play a pivotal role in mediating the intricate interplay between the environment and gene expression. Intriguingly, alterations in the epigenome have the potential to be inherited across generations. Alcohol use disorder (AUD) poses significant health issues worldwide. Alcohol has the capability to induce changes in the epigenome, which can be inherited by offspring, thus impacting them even in the absence of direct alcohol exposure. This review delves into the impact of alcohol on the epigenome, examining how its effects vary based on factors such as the age of exposure (adolescence or adulthood), the duration of exposure (chronic or acute), and the specific sample collected (brain, blood, or sperm). The literature underscores that alcohol exposure can elicit diverse effects on the epigenome during different life stages. Furthermore, compelling evidence from human and animal studies demonstrates that alcohol induces alterations in epigenome content, affecting both the brain and blood. Notably, rodent studies suggest that these epigenetic changes can result in lasting phenotype alterations that extend across at least two generations. In conclusion, the comprehensive literature analysis supports the notion that alcohol exposure induces lasting epigenetic alterations, influencing the behavior and health of future generations. This knowledge emphasizes the significance of addressing the potential transgenerational effects of alcohol and highlights the importance of preventive measures to minimize the adverse impact on offspring.
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Affiliation(s)
- Nazila Heidari
- School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Amirhossein Heidari
- Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Yekta Ghane
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ghorbangol Ashabi
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad-Reza Zarrindast
- Department of Pharmacology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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2
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Ponzetti M, Rucci N, Falone S. RNA methylation and cellular response to oxidative stress-promoting anticancer agents. Cell Cycle 2023; 22:870-905. [PMID: 36648057 PMCID: PMC10054233 DOI: 10.1080/15384101.2023.2165632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
Disruption of the complex network that regulates redox homeostasis often underlies resistant phenotypes, which hinder effective and long-lasting cancer eradication. In addition, the RNA methylome-dependent control of gene expression also critically affects traits of cellular resistance to anti-cancer agents. However, few investigations aimed at establishing whether the epitranscriptome-directed adaptations underlying acquired and/or innate resistance traits in cancer could be implemented through the involvement of redox-dependent or -responsive signaling pathways. This is unexpected mainly because: i) the effectiveness of many anti-cancer approaches relies on their capacity to promote oxidative stress (OS); ii) altered redox milieu and reprogramming of mitochondrial function have been acknowledged as critical mediators of the RNA methylome-mediated response to OS. Here we summarize the current state of understanding on this topic, as well as we offer new perspectives that might lead to original approaches and strategies to delay or prevent the problem of refractory cancer and tumor recurrence.
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Affiliation(s)
- Marco Ponzetti
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L'Aquila, Italy
| | - Nadia Rucci
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L'Aquila, Italy
| | - Stefano Falone
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
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García-Eguren G, González-Ramírez M, Vizán P, Giró O, Vega-Beyhart A, Boswell L, Mora M, Halperin I, Carmona F, Gracia M, Casals G, Squarcia M, Enseñat J, Vidal O, Di Croce L, Hanzu FA. Glucocorticoid-induced Fingerprints on Visceral Adipose Tissue Transcriptome and Epigenome. J Clin Endocrinol Metab 2022; 107:150-166. [PMID: 34487152 DOI: 10.1210/clinem/dgab662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT Chronic glucocorticoid (GC) overexposure, resulting from endogenous Cushing's syndrome (CS) or exogenous GC therapy, causes several adverse outcomes, including persistent central fat accumulation associated with a low-grade inflammation. However, no previous multiomics studies in visceral adipose tissue (VAT) from patients exposed to high levels of unsuppressed GC during active CS or after remission are available yet. OBJECTIVE To determine the persistent VAT transcriptomic alterations and epigenetic fingerprints induced by chronic hypercortisolism. METHODS We employed a translational approach combining high-throughput data on endogenous CS patients and a reversible CS mouse model. We performed RNA sequencing and chromatin immunoprecipitation sequencing on histone modifications (H3K4me3, H3K27ac, and H3K27me3) to identify persistent transcriptional and epigenetic signatures in VAT produced during active CS and maintained after remission. RESULTS VAT dysfunction was associated with low-grade proinflammatory status, macrophage infiltration, and extracellular matrix remodeling. Most notably, chronic hypercortisolism caused a persistent circadian rhythm disruption in VAT through core clock genes modulation. Importantly, changes in the levels of 2 histone modifications associated to gene transcriptional activation (H3K4me3 and H3K27ac) correlated with the observed differences in gene expression during active CS and after CS remission. CONCLUSION We identified for the first time the persistent transcriptional and epigenetic signatures induced by hypercortisolism in VAT, providing a novel integrated view of molecular components driving the long-term VAT impairment associated with CS.
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Affiliation(s)
- Guillermo García-Eguren
- Group of Endocrine Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Mar González-Ramírez
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Pedro Vizán
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Oriol Giró
- Group of Endocrine Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Arturo Vega-Beyhart
- Group of Endocrine Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Laura Boswell
- Group of Endocrine Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Endocrinology and Nutrition Department, Hospital Clinic, Barcelona, Spain
| | - Mireia Mora
- Group of Endocrine Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Endocrinology and Nutrition Department, Hospital Clinic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Department of Medicine, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Irene Halperin
- Group of Endocrine Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Endocrinology and Nutrition Department, Hospital Clinic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Francisco Carmona
- Department of Medicine, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Gynecology and Obstetrics Department, Hospital Clínic, Barcelona, Spain
| | - Meritxell Gracia
- Department of Medicine, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Gynecology and Obstetrics Department, Hospital Clínic, Barcelona, Spain
| | - Gregori Casals
- Biomedical Diagnostics Centre, Hospital Clinic, Barcelona, Spain
| | - Mattia Squarcia
- Group of Endocrine Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Department of Radiology, Hospital Clínic, Barcelona, Spain
| | - Joaquim Enseñat
- Department of Medicine, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Endocrine Surgery Department, Hospital Clinic, Barcelona, Spain
| | - Oscar Vidal
- Department of Medicine, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Department of Neurosurgery, Hospital Clinic, Barcelona, Spain
| | - Luciano Di Croce
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Felicia A Hanzu
- Group of Endocrine Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Endocrinology and Nutrition Department, Hospital Clinic, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Department of Medicine, Faculty of Medicine, University of Barcelona, Barcelona, Spain
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Jin SW, Im JS, Park JH, Kim HG, Lee GH, Kim SJ, Kwack SJ, Kim KB, Chung KH, Lee BM, Kacew S, Jeong HG, Kim HS. Effects of tobacco compound 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) on the expression of epigenetically regulated genes in lung carcinogenesis. J Toxicol Environ Health A 2021; 84:1004-1019. [PMID: 34459362 DOI: 10.1080/15287394.2021.1965059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cigarette smoking is a major cause of lung cancer. Although tobacco smoking-induced genotoxicity has been well established, there is apparent lack of abundance functional epigenetic effects reported On cigarette smoke-induced lung carcinogenesis. The aim of this study was to determine effects of intratracheal administration of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) utilizing target gene expression DNA methylation patterns in lung tissues of mice following twice weekly for 8 weeks treatment. An unbiased approach where genomic regions was undertaken to assess early methylation changes within mouse pulmonary tissues. A methylated-CpG island recovery assay (MIRA) was performed to map the DNA methylome in lung tissues, with the position of methylated DNA determined using a Genome Analyzer (MIRA-SEQ). Alterations in epigenetic-regulated target genes were confirmed with quantitative reverse transcription-PCR, which revealed 35 differentially hypermethylated genes including Cdkn1C, Hsf4, Hnf1a, Cdx1, and Hoxa5 and 30 differentially hypomethylated genes including Ddx4, Piwi1, Mdm2, and Pce1 in NNK-exposed lung tissue compared with controls. The main pathway of these genes for mediating biological information was analyzed using the Kyoto Encyclopedia of Genes and Genomes database. Among them, Rssf1 and Mdm2 were closely associated with NNK-induced lung carcinogenesis. Taken together, our data provide valuable resources for detecting cigarette smoke-induced lung carcinogenesis.
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Affiliation(s)
- Sun Woo Jin
- College Of Pharmacy, Chungnam National University, Daejeon, Republic of Korea
| | - Jong Seung Im
- School Of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jae Hyeon Park
- School Of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Hyung Gyun Kim
- College Of Pharmacy, Chungnam National University, Daejeon, Republic of Korea
| | - Gi Ho Lee
- College Of Pharmacy, Chungnam National University, Daejeon, Republic of Korea
| | - Se Jong Kim
- College Of Pharmacy, Chungnam National University, Daejeon, Republic of Korea
| | - Seung Jun Kwack
- Department Of Biochemistry And Health Science, Changwon National University, Gyeongnam Republic of Korea
| | - Kyu-Bong Kim
- College Of Pharmacy, Dankook University, Chungnam, Republic of Korea
| | - Kyu Hyuck Chung
- School Of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Byung Mu Lee
- College Of Pharmacy, Chungnam National University, Daejeon, Republic of Korea
| | - Sam Kacew
- McLaughlin Centre for Population Health Risk Assessment, University Of Ottawa, Ottawa, ON, Canada
| | - Hye Gwang Jeong
- College Of Pharmacy, Chungnam National University, Daejeon, Republic of Korea
| | - Hyung Sik Kim
- School Of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
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5
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de la Fuente Revenga M, Zhu B, Guevara CA, Naler LB, Saunders JM, Zhou Z, Toneatti R, Sierra S, Wolstenholme JT, Beardsley PM, Huntley GW, Lu C, González-Maeso J. Prolonged epigenomic and synaptic plasticity alterations following single exposure to a psychedelic in mice. Cell Rep 2021; 37:109836. [PMID: 34686347 PMCID: PMC8582597 DOI: 10.1016/j.celrep.2021.109836] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 07/21/2021] [Accepted: 09/24/2021] [Indexed: 12/20/2022] Open
Abstract
Clinical evidence suggests that rapid and sustained antidepressant action can be attained with a single exposure to psychedelics. However, the biological substrates and key mediators of psychedelics' enduring action remain unknown. Here, we show that a single administration of the psychedelic DOI produces fast-acting effects on frontal cortex dendritic spine structure and acceleration of fear extinction via the 5-HT2A receptor. Additionally, a single dose of DOI leads to changes in chromatin organization, particularly at enhancer regions of genes involved in synaptic assembly that stretch for days after the psychedelic exposure. These DOI-induced alterations in the neuronal epigenome overlap with genetic loci associated with schizophrenia, depression, and attention deficit hyperactivity disorder. Together, these data support that epigenomic-driven changes in synaptic plasticity sustain psychedelics' long-lasting antidepressant action but also warn about potential substrate overlap with genetic risks for certain psychiatric conditions.
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MESH Headings
- Amphetamines/pharmacology
- Animals
- Behavior, Animal/drug effects
- Dendritic Spines/drug effects
- Dendritic Spines/metabolism
- Epigenesis, Genetic/drug effects
- Epigenome/drug effects
- Epigenomics
- Extinction, Psychological/drug effects
- Fear/drug effects
- Frontal Lobe/drug effects
- Frontal Lobe/metabolism
- Hallucinogens/pharmacology
- Male
- Mice, 129 Strain
- Mice, Inbred C57BL
- Mice, Knockout
- Neuronal Plasticity/drug effects
- Receptor, Serotonin, 5-HT2A/drug effects
- Receptor, Serotonin, 5-HT2A/genetics
- Receptor, Serotonin, 5-HT2A/metabolism
- Serotonin 5-HT2 Receptor Agonists/pharmacology
- Synapses/drug effects
- Synapses/metabolism
- Time Factors
- Mice
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Affiliation(s)
- Mario de la Fuente Revenga
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA; Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Bohan Zhu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Christopher A Guevara
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lynette B Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Justin M Saunders
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Zirui Zhou
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Rudy Toneatti
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Salvador Sierra
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Jennifer T Wolstenholme
- Department of Pharmacology and Toxicology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Patrick M Beardsley
- Department of Pharmacology and Toxicology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA; Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - George W Huntley
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Javier González-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA.
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6
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Wallén E, Auvinen P, Kaminen-Ahola N. The Effects of Early Prenatal Alcohol Exposure on Epigenome and Embryonic Development. Genes (Basel) 2021; 12:genes12071095. [PMID: 34356111 PMCID: PMC8303887 DOI: 10.3390/genes12071095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/05/2021] [Accepted: 07/15/2021] [Indexed: 12/15/2022] Open
Abstract
Prenatal alcohol exposure is one of the most significant causes of developmental disability in the Western world. Maternal alcohol consumption during pregnancy leads to an increased risk of neurological deficits and developmental abnormalities in the fetus. Over the past decade, several human and animal studies have demonstrated that alcohol causes alterations in epigenetic marks, including DNA methylation, histone modifications, and non-coding RNAs. There is an increasing amount of evidence that early pregnancy is a sensitive period for environmental-induced epigenetic changes. It is a dynamic period of epigenetic reprogramming, cell divisions, and DNA replication and, therefore, a particularly interesting period to study the molecular changes caused by alcohol exposure as well as the etiology of alcohol-induced developmental disorders. This article will review the current knowledge about the in vivo and in vitro effects of alcohol exposure on the epigenome, gene regulation, and the phenotype during the first weeks of pregnancy.
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7
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Wu R, Li S, Sargsyan D, Yin R, Kuo HC, Peter R, Wang L, Hudlikar R, Liu X, Kong AN. DNA methylome, transcriptome, and prostate cancer prevention by phenethyl isothiocyanate in TRAMP mice. Mol Carcinog 2021; 60:391-402. [PMID: 33848375 PMCID: PMC8201649 DOI: 10.1002/mc.23299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/28/2022]
Abstract
Epigenetics/epigenomics has been shown to be involved in carcinogenesis. However, how the epigenome would be altered in the transgenic adenocarcinoma of the mouse prostate (TRAMP) cancer model and the effect of cancer chemopreventive phytochemical phenethyl isothiocyanate (PEITC) on the epigenome in TRAMP mice are not known. PEITC has been reported to reduce the risk of many cancers including prostate cancer (PCa). In this study, male TRAMP mice were fed a control diet or diet containing 0.05% PEITC from 8 weeks to 16 weeks. The tumor incidence was reduced in the PEITC diet (0/6) as compared with the control diet (6/7). RNA-sequencing (RNA-seq) analyses on nontumor and tumor prostatic tissues revealed several pathways like cell cycle/Cdc42 signaling, inflammation, and cancer-related signaling, were activated in prostate tissues of TRAMP mice but were reversed or attenuated in TRAMP mice fed with PEITC diet. DNA CpG methyl-seq analyses showed that global methylation patterns of prostate samples from TRAMP mice were hugely different from those of wild-type mice. Dietary PEITC partially reversed the global methylation changes during prostatic carcinogenesis. Integration of RNA-seq and DNA methyl-seq analyses identified a list of genes, including Adgrb1 and Ebf4, with an inverse regulatory relationship between their RNA expression and CpG methylation. In summary, our current study demonstrates that alteration of the global epigenome in TRAMP prostate tumor and PEITC administration suppresses PCa carcinogenesis, impacts global CpG epigenome and transcriptome, and attenuates carcinogenic pathways like cell cycle arrest and inflammation. These results may provide insights and epigenetic markers/targets for PCa prevention and treatment in human PCa patients.
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Affiliation(s)
- Renyi Wu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Shanyi Li
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Davit Sargsyan
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ran Yin
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Hsiao-Chen Kuo
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Rebecca Peter
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Lujing Wang
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Rasika Hudlikar
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Xia Liu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ah-Ng Kong
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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Liu J, Liu J, Duan S, Liu L, Zhang G, Peng X. Reprogrammed Epigenetic Landscape-Prophesied Functions of Bioactive Polysaccharides in Alleviating Diseases: A Pilot Study of DNA Methylome Remodeling in Astragalus Polysaccharide (APS)-Improved Osteoporosis in a Rat Model. J Agric Food Chem 2020; 68:15449-15459. [PMID: 33320666 DOI: 10.1021/acs.jafc.0c06483] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
DNA methylation is an epigenetic event that plays critical roles in the pathogenesis, progression, and treatment of human diseases. In this study, we investigated the epigenetic mechanisms for Astragalus polysaccharide (APS)-improved osteoporosis in a rat model. The results showed that APS significantly changed the DNA methylome in colonic epithelia with great efficiency. Gene set enrichment analysis (GSEA) based on differentially methylated sites (DMSs) revealed that APS caused promoter DNA methylation changes of genes associated with calcium homeostasis, osteoclast/osteoblast balance, Wnt signaling, and hormone-related processes. Further analysis showed high consistency of APS-induced gene methylomic changes in colonic epithelia and its effects on diabetes, virus infection, and wound healing, which had been reported already. Moreover, we suggested new functions and the involved mechanisms of APS in heart disease, neurological disorder, reproductive problem, and olfactory dysfunction. In this study, we offered epigenetic mechanisms for APS-improved osteoporosis. More importantly, we proposed and proved a reliable method to explore the beneficial effects of bioactive polysaccharides by studying DNA methylation changes at nonfocal sites. We firmly believed the promising prospects of this method for its great efficiency, rapidness, and economy in exploring possible beneficial or therapeutic effects of functional macromolecules with one single experiment.
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Affiliation(s)
- Junsheng Liu
- Department of Food Science and Engineering, Jinan University, No. 601 West Huangpu Avenue, Guangzhou, Guangdong 510632, P. R. China
| | - Jun Liu
- Department of Food Science and Engineering, Jinan University, No. 601 West Huangpu Avenue, Guangzhou, Guangdong 510632, P. R. China
| | - Shan Duan
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, Guangdong 510642, P. R. China
| | - Liu Liu
- Department of Food Science and Engineering, Jinan University, No. 601 West Huangpu Avenue, Guangzhou, Guangdong 510632, P. R. China
| | - Guangwen Zhang
- Department of Food Science and Engineering, Jinan University, No. 601 West Huangpu Avenue, Guangzhou, Guangdong 510632, P. R. China
| | - Xichun Peng
- Department of Food Science and Engineering, Jinan University, No. 601 West Huangpu Avenue, Guangzhou, Guangdong 510632, P. R. China
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9
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Antoun E, Kitaba NT, Titcombe P, Dalrymple KV, Garratt ES, Barton SJ, Murray R, Seed PT, Holbrook JD, Kobor MS, Lin DTS, MacIsaac JL, Burdge GC, White SL, Poston L, Godfrey KM, Lillycrop KA. Maternal dysglycaemia, changes in the infant's epigenome modified with a diet and physical activity intervention in pregnancy: Secondary analysis of a randomised control trial. PLoS Med 2020; 17:e1003229. [PMID: 33151971 PMCID: PMC7643947 DOI: 10.1371/journal.pmed.1003229] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 10/06/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Higher maternal plasma glucose (PG) concentrations, even below gestational diabetes mellitus (GDM) thresholds, are associated with adverse offspring outcomes, with DNA methylation proposed as a mediating mechanism. Here, we examined the relationships between maternal dysglycaemia at 24 to 28 weeks' gestation and DNA methylation in neonates and whether a dietary and physical activity intervention in pregnant women with obesity modified the methylation signatures associated with maternal dysglycaemia. METHODS AND FINDINGS We investigated 557 women, recruited between 2009 and 2014 from the UK Pregnancies Better Eating and Activity Trial (UPBEAT), a randomised controlled trial (RCT), of a lifestyle intervention (low glycaemic index (GI) diet plus physical activity) in pregnant women with obesity (294 contol, 263 intervention). Between 27 and 28 weeks of pregnancy, participants had an oral glucose (75 g) tolerance test (OGTT), and GDM diagnosis was based on diagnostic criteria recommended by the International Association of Diabetes and Pregnancy Study Groups (IADPSG), with 159 women having a diagnosis of GDM. Cord blood DNA samples from the infants were interrogated for genome-wide DNA methylation levels using the Infinium Human MethylationEPIC BeadChip array. Robust regression was carried out, adjusting for maternal age, smoking, parity, ethnicity, neonate sex, and predicted cell-type composition. Maternal GDM, fasting glucose, 1-h, and 2-h glucose concentrations following an OGTT were associated with 242, 1, 592, and 17 differentially methylated cytosine-phosphate-guanine (dmCpG) sites (false discovery rate (FDR) ≤ 0.05), respectively, in the infant's cord blood DNA. The most significantly GDM-associated CpG was cg03566881 located within the leucine-rich repeat-containing G-protein coupled receptor 6 (LGR6) (FDR = 0.0002). Moreover, we show that the GDM and 1-h glucose-associated methylation signatures in the cord blood of the infant appeared to be attenuated by the dietary and physical activity intervention during pregnancy; in the intervention arm, there were no GDM and two 1-h glucose-associated dmCpGs, whereas in the standard care arm, there were 41 GDM and 160 1-h glucose-associated dmCpGs. A total of 87% of the GDM and 77% of the 1-h glucose-associated dmCpGs had smaller effect sizes in the intervention compared to the standard care arm; the adjusted r2 for the association of LGR6 cg03566881 with GDM was 0.317 (95% confidence interval (CI) 0.012, 0.022) in the standard care and 0.240 (95% CI 0.001, 0.015) in the intervention arm. Limitations included measurement of DNA methylation in cord blood, where the functional significance of such changes are unclear, and because of the strong collinearity between treatment modality and severity of hyperglycaemia, we cannot exclude that treatment-related differences are potential confounders. CONCLUSIONS Maternal dysglycaemia was associated with significant changes in the epigenome of the infants. Moreover, we found that the epigenetic impact of a dysglycaemic prenatal maternal environment appeared to be modified by a lifestyle intervention in pregnancy. Further research will be needed to investigate possible medical implications of the findings. TRIAL REGISTRATION ISRCTN89971375.
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Affiliation(s)
- Elie Antoun
- Biological Sciences, Institute of Developmental Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Negusse T. Kitaba
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Philip Titcombe
- MRC Lifecourse Epidemiology Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Kathryn V. Dalrymple
- Department of Women and Children’s Health, School of Life Course Sciences, King’s College London, London, United Kingdom
| | - Emma S. Garratt
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Trust, Southampton, United Kingdom
| | - Sheila J. Barton
- MRC Lifecourse Epidemiology Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Robert Murray
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Paul T. Seed
- Department of Women and Children’s Health, School of Life Course Sciences, King’s College London, London, United Kingdom
| | - Joanna D. Holbrook
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Michael S. Kobor
- BC Childrens Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - David TS Lin
- BC Childrens Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Julia L. MacIsaac
- BC Childrens Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Graham C. Burdge
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Sara L. White
- Department of Women and Children’s Health, School of Life Course Sciences, King’s College London, London, United Kingdom
| | - Lucilla Poston
- Department of Women and Children’s Health, School of Life Course Sciences, King’s College London, London, United Kingdom
| | - Keith M. Godfrey
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Trust, Southampton, United Kingdom
| | - Karen A. Lillycrop
- Biological Sciences, Institute of Developmental Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Trust, Southampton, United Kingdom
- * E-mail:
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Syding LA, Nickl P, Kasparek P, Sedlacek R. CRISPR/Cas9 Epigenome Editing Potential for Rare Imprinting Diseases: A Review. Cells 2020; 9:cells9040993. [PMID: 32316223 PMCID: PMC7226972 DOI: 10.3390/cells9040993] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/22/2022] Open
Abstract
Imprinting diseases (IDs) are rare congenital disorders caused by aberrant dosages of imprinted genes. Rare IDs are comprised by a group of several distinct disorders that share a great deal of homology in terms of genetic etiologies and symptoms. Disruption of genetic or epigenetic mechanisms can cause issues with regulating the expression of imprinted genes, thus leading to disease. Genetic mutations affect the imprinted genes, duplications, deletions, and uniparental disomy (UPD) are reoccurring phenomena causing imprinting diseases. Epigenetic alterations on methylation marks in imprinting control centers (ICRs) also alters the expression patterns and the majority of patients with rare IDs carries intact but either silenced or overexpressed imprinted genes. Canonical CRISPR/Cas9 editing relying on double-stranded DNA break repair has little to offer in terms of therapeutics for rare IDs. Instead CRISPR/Cas9 can be used in a more sophisticated way by targeting the epigenome. Catalytically dead Cas9 (dCas9) tethered with effector enzymes such as DNA de- and methyltransferases and histone code editors in addition to systems such as CRISPRa and CRISPRi have been shown to have high epigenome editing efficiency in eukaryotic cells. This new era of CRISPR epigenome editors could arguably be a game-changer for curing and treating rare IDs by refined activation and silencing of disturbed imprinted gene expression. This review describes major CRISPR-based epigenome editors and points out their potential use in research and therapy of rare imprinting diseases.
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Affiliation(s)
- Linn Amanda Syding
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
| | - Petr Nickl
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
| | - Petr Kasparek
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the CAS, v.v.i, 252 50 Vestec, Czech Republic
- Correspondence: ; Tel.: +420-325-873-243
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11
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Abstract
Interactions between hormones and epigenetic factors are key regulators of behaviour, but the mechanisms that underlie their effects are complex. Epigenetic factors can modify sensitivity to hormones by altering hormone receptor expression, and hormones can regulate epigenetic factors by recruiting epigenetic regulators to DNA. The bidirectional nature of this relationship is becoming increasingly evident and suggests that the ability of hormones to regulate certain forms of behaviour may depend on their ability to induce changes in the epigenome. Moreover, sex differences have been reported for several epigenetic modifications, and epigenetic factors are thought to regulate sexual differentiation of behaviour, although specific mechanisms remain to be understood. Indeed, hormone-epigenome interactions are highly complex and involve both canonical and non-canonical regulatory pathways that may permit for highly specific gene regulation to promote variable forms of behavioural adaptation.
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Affiliation(s)
- Jennet L Baumbach
- Department of Psychology, University of Toronto Mississauga, Mississauga, Canada
| | - Iva B Zovkic
- Department of Psychology, University of Toronto Mississauga, Mississauga, Canada.
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12
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Bansal A, Robles-Matos N, Wang PZ, Condon DE, Joshi A, Pinney SE. In utero Bisphenol A Exposure Is Linked with Sex Specific Changes in the Transcriptome and Methylome of Human Amniocytes. J Clin Endocrinol Metab 2020; 105:5571768. [PMID: 31536135 PMCID: PMC7046022 DOI: 10.1210/clinem/dgz037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/17/2019] [Indexed: 12/20/2022]
Abstract
CONTEXT Prenatal exposure to bisphenol A (BPA) is linked to obesity and diabetes but the molecular mechanisms driving these phenomena are not known. Alterations in deoxyribonucleic acid (DNA) methylation in amniocytes exposed to BPA in utero represent a potential mechanism leading to metabolic dysfunction later in life. OBJECTIVE To profile changes in genome-wide DNA methylation and expression in second trimester human amniocytes exposed to BPA in utero. DESIGN A nested case-control study was performed in amniocytes matched for offspring sex, maternal race/ethnicity, maternal age, gestational age at amniocentesis, and gestational age at birth. Cases had amniotic fluid BPA measuring 0.251 to 23.74 ng/mL. Sex-specific genome-wide DNA methylation analysis and RNA-sequencing (RNA-seq) were performed to determine differentially methylated regions (DMRs) and gene expression changes associated with BPA exposure. Ingenuity pathway analysis was performed to identify biologically relevant pathways enriched after BPA exposure. In silico Hi-C analysis identified potential chromatin interactions with DMRs. RESULTS There were 101 genes with altered expression in male amniocytes exposed to BPA (q < 0.05) in utero, with enrichment of pathways critical to hepatic dysfunction, collagen signaling and adipogenesis. Thirty-six DMRs were identified in male BPA-exposed amniocytes and 14 in female amniocyte analysis (q < 0.05). Hi-C analysis identified interactions between DMRs and 24 genes with expression changes in male amniocytes and 12 in female amniocytes (P < 0.05). CONCLUSION In a unique repository of human amniocytes exposed to BPA in utero, sex-specific analyses identified gene expression changes in pathways associated with metabolic disease and novel DMRs with potential distal regulatory functions.
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Affiliation(s)
- Amita Bansal
- Center for Research on Reproduction and Women’s Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicole Robles-Matos
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Program, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Paul Zhiping Wang
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Bioinformatics Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David E Condon
- Sanford Health, Sioux Falls, SD, USA
- Penn Bioinformatics Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Apoorva Joshi
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sara E Pinney
- Center for Research on Reproduction and Women’s Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Correspondence and Reprint Requests: Sara E. Pinney, Division of Endocrinology and Diabetes, Children’s Hospital Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA. E-mail:
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13
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Perera BP, Faulk C, Svoboda LK, Goodrich JM, Dolinoy DC. The role of environmental exposures and the epigenome in health and disease. Environ Mol Mutagen 2020; 61:176-192. [PMID: 31177562 PMCID: PMC7252203 DOI: 10.1002/em.22311] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 05/02/2023]
Abstract
The genetic material of every organism exists within the context of regulatory networks that govern gene expression, collectively called the epigenome. Epigenetics has taken center stage in the study of diseases such as cancer and diabetes, but its integration into the field of environmental health is still emerging. As the Environmental Mutagenesis and Genomics Society (EMGS) celebrates its 50th Anniversary this year, we have come together to review and summarize the seminal advances in the field of environmental epigenomics. Specifically, we focus on the role epigenetics may play in multigenerational and transgenerational transmission of environmentally induced health effects. We also summarize state of the art techniques for evaluating the epigenome, environmental epigenetic analysis, and the emerging field of epigenome editing. Finally, we evaluate transposon epigenetics as they relate to environmental exposures and explore the role of noncoding RNA as biomarkers of environmental exposures. Although the field has advanced over the past several decades, including being recognized by EMGS with its own Special Interest Group, recently renamed Epigenomics, we are excited about the opportunities for environmental epigenetic science in the next 50 years. Environ. Mol. Mutagen. 61:176-192, 2020. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Bambarendage P.U. Perera
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Christopher Faulk
- Department of Animal Sciences, University of Minnesota, St. Paul, Minnesota
| | - Laurie K. Svoboda
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
- Correspondence to: Dana C. Dolinoy, Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan.
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14
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Yang Y, Yin R, Wu R, Ramirez CN, Sargsyan D, Li S, Wang L, Cheng D, Wang C, Hudlikar R, Kuo HC, Lu Y, Kong AN. DNA methylome and transcriptome alterations and cancer prevention by triterpenoid ursolic acid in UVB-induced skin tumor in mice. Mol Carcinog 2019; 58:1738-1753. [PMID: 31237383 PMCID: PMC6722003 DOI: 10.1002/mc.23046] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/02/2019] [Accepted: 05/06/2019] [Indexed: 12/11/2022]
Abstract
Nonmelanoma skin cancers (NMSCs) are the most common type of skin cancers. Major risk factors for NMSCs include exposure to ultraviolet (UV) irradiation. Ursolic acid (UA) is a natural triterpenoid enriched in blueberries and herbal medicinal products, and possess anticancer activities. This study focuses on the impact of UA on epigenomic, genomic mechanisms and prevention of UVB-mediated NMSC. CpG methylome and RNA transcriptome alterations of early, promotion and late stages of UA treated on UVB-induced NMSC in SKH-1 hairless mice were conducted using CpG methyl-seq and RNA-seq. Samples were collected at weeks 2, 15, and 25, and integrated bioinformatic analyses were performed to identify key pathways and genes modified by UA against UVB-induced NMSC. Morphologically, UA significantly reduced NMSC tumor volume and tumor number. DNA methylome showed inflammatory pathways IL-8, NF-κB, and Nrf2 pathways were highly involved. Antioxidative stress master regulator Nrf2, cyclin D1, DNA damage, and anti-inflammatory pathways were induced by UA. Nrf2, cyclin D1, TNFrsf1b, and Mybl1 at early (2 weeks) and late (25 weeks) stages were identified and validated by quantitative polymerase chain reaction. In summary, integration of CpG methylome and RNA transcriptome studies show UA alters antioxidative, anti-inflammatory, and anticancer pathways in UVB-induced NMSC carcinogenesis. Particularly, UA appears to drive Nrf2 and its upstream/downstream genes, anti-inflammatory (at early stages) and cell cycle regulatory (both early and late stages) genes, of which might contribute to the overall chemopreventive effects of UVB-induced MNSC. This study may provide potential biomarkers/targets for chemoprevention of early stage of UVB-induced NMSC in human.
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Affiliation(s)
- Yuqing Yang
- Graduate Program in Pharmaceutical Science, Ernest Mario
School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ
08854, USA
- Department of Pharmaceutics, Ernest Mario School of
Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854,
USA
| | - Ran Yin
- Department of Pharmaceutics, Ernest Mario School of
Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854,
USA
| | - Renyi Wu
- Department of Pharmaceutics, Ernest Mario School of
Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854,
USA
| | - Christina N. Ramirez
- Center for Phytochemicals Epigenome Studies, Ernest Mario
School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ
08854, USA
- Cellular and Molecular Pharmacology Program, Rutgers Robert
Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Davit Sargsyan
- Department of Pharmaceutics, Ernest Mario School of
Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854,
USA
| | - Shanyi Li
- Department of Pharmaceutics, Ernest Mario School of
Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854,
USA
| | - Lujing Wang
- Graduate Program in Pharmaceutical Science, Ernest Mario
School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ
08854, USA
- Department of Pharmaceutics, Ernest Mario School of
Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854,
USA
| | - David Cheng
- Graduate Program in Pharmaceutical Science, Ernest Mario
School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ
08854, USA
- Department of Pharmaceutics, Ernest Mario School of
Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854,
USA
| | - Chao Wang
- Department of Pharmaceutics, Ernest Mario School of
Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854,
USA
| | - Rasika Hudlikar
- Department of Pharmaceutics, Ernest Mario School of
Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854,
USA
| | - Hsiao-Chen Kuo
- Graduate Program in Pharmaceutical Science, Ernest Mario
School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ
08854, USA
- Department of Pharmaceutics, Ernest Mario School of
Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854,
USA
| | - Yaoping Lu
- Center for Phytochemicals Epigenome Studies, Ernest Mario
School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ
08854, USA
- Department of Chemical Biology, Ernest Mario School of
Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854,
USA
| | - Ah-Ng Kong
- Department of Pharmaceutics, Ernest Mario School of
Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854,
USA
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15
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Howe CG, Zhou M, Wang X, Pittman GS, Thompson IJ, Campbell MR, Bastain TM, Grubbs BH, Salam MT, Hoyo C, Bell DA, Smith AD, Breton CV. Associations between Maternal Tobacco Smoke Exposure and the Cord Blood [Formula: see text] DNA Methylome. Environ Health Perspect 2019; 127:047009. [PMID: 31039056 PMCID: PMC6785223 DOI: 10.1289/ehp3398] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 02/20/2019] [Accepted: 03/05/2019] [Indexed: 05/16/2023]
Abstract
BACKGROUND Maternal tobacco smoke exposure has been associated with altered DNA methylation. However, previous studies largely used methylation arrays, which cover a small fraction of CpGs, and focused on whole cord blood. OBJECTIVES The current study examined the impact of in utero exposure to maternal tobacco smoke on the cord blood [Formula: see text] DNA methylome. METHODS The methylomes of 20 Hispanic white newborns ([Formula: see text] exposed to any maternal tobacco smoke in pregnancy; [Formula: see text] unexposed) from the Maternal and Child Health Study (MACHS) were profiled by whole-genome bisulfite sequencing (median coverage: [Formula: see text]). Statistical analyses were conducted using the Regression Analysis of Differential Methylation (RADMeth) program because it performs well on low-coverage data (minimizes false positives and negatives). RESULTS We found that 10,381 CpGs were differentially methylated by tobacco smoke exposure [neighbor-adjusted p-values that are additionally corrected for multiple testing based on the Benjamini-Hochberg method for controlling the false discovery rate (FDR) [Formula: see text]]. From these CpGs, RADMeth identified 557 differentially methylated regions (DMRs) that were overrepresented ([Formula: see text]) in important regulatory regions, including enhancers. Of nine DMRs that could be queried in a reduced representation bisulfite sequencing (RRBS) study of adult [Formula: see text] cells ([Formula: see text] smokers; [Formula: see text] nonsmokers), four replicated ([Formula: see text]). Additionally, a CpG in the promoter of SLC7A8 (percent methylation difference: [Formula: see text] comparing exposed to unexposed) replicated ([Formula: see text]) in an EPIC (Illumina) array study of cord blood [Formula: see text] cells ([Formula: see text] exposed to sustained maternal tobacco smoke; [Formula: see text] unexposed) and in a study of adult [Formula: see text] cells across two platforms (EPIC: [Formula: see text] smokers; [Formula: see text] nonsmokers; 450K: [Formula: see text] smokers; [Formula: see text] nonsmokers). CONCLUSIONS Maternal tobacco smoke exposure in pregnancy is associated with cord blood [Formula: see text] DNA methylation in key regulatory regions, including enhancers. While we used a method that performs well on low-coverage data, we cannot exclude the possibility that some results may be false positives. However, we identified a differentially methylated CpG in amino acid transporter SLC7A8 that is highly reproducible, which may be sensitive to cigarette smoke in both cord blood and adult [Formula: see text] cells. https://doi.org/10.1289/EHP3398.
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Affiliation(s)
- Caitlin G. Howe
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Meng Zhou
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Xuting Wang
- Immunity, Inflammation and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Dept. of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Gary S. Pittman
- Immunity, Inflammation and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Dept. of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Isabel J. Thompson
- Immunity, Inflammation and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Dept. of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Michelle R. Campbell
- Immunity, Inflammation and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Dept. of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Theresa M. Bastain
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Brendan H. Grubbs
- Department of Obstetrics and Gynecology, Keck School of Medicine, Los Angeles, California, USA
| | - Muhammad T. Salam
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Department of Psychiatry, Kern Medical, Bakersfield, California, USA
| | - Cathrine Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Douglas A. Bell
- Immunity, Inflammation and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Dept. of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Andrew D. Smith
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Carrie V. Breton
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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