1
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Rizavi HS, Gavin HE, Krishnan HR, Gavin DP, Sharma RP. Ethanol- and PARP-Mediated Regulation of Ribosome-Associated Long Non-Coding RNA (lncRNA) in Pyramidal Neurons. Noncoding RNA 2023; 9:72. [PMID: 37987368 PMCID: PMC10661276 DOI: 10.3390/ncrna9060072] [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: 07/14/2023] [Revised: 10/23/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023] Open
Abstract
Although, by definition, long noncoding RNAs (lncRNAs) are not translated, they are sometimes associated with ribosomes. In fact, some estimates suggest the existence of more than 50 K lncRNA molecules that could encode for small peptides. We examined the effects of an ethanol and Poly-ADP Ribose Polymerase (PARP) inhibitor (ABT-888) on ribosome-bound lncRNAs. Mice were administered via intraperitoneal injection (i.p.) either normal saline (CTL) or ethanol (EtOH) twice a day for four consecutive days. On the fourth day, a sub-group of mice administered with ethanol also received ABT-888 (EtOH+ABT). Ribosome-bound lncRNAs in CaMKIIα-expressing pyramidal neurons were measured using the Translating Ribosome Affinity Purification (TRAP) technique. Our findings show that EtOH altered the attachment of 107 lncRNA transcripts, while EtOH+ABT altered 60 lncRNAs. Among these 60 lncRNAs, 49 were altered by both conditions, while EtOH+ABT uniquely altered the attachment of 11 lncRNA transcripts that EtOH alone did not affect. To validate these results, we selected eight lncRNAs (Mir124-2hg, 5430416N02Rik, Snhg17, Snhg12, Snhg1, Mir9-3hg, Gas5, and 1110038B12Rik) for qRT-PCR analysis. The current study demonstrates that ethanol-induced changes in lncRNA attachment to ribosomes can be mitigated by the addition of the PARP inhibitor ABT-888.
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Affiliation(s)
- Hooriyah S. Rizavi
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA; (H.S.R.); (H.E.G.)
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL 60612, USA
| | - Hannah E. Gavin
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA; (H.S.R.); (H.E.G.)
| | - Harish R. Krishnan
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA;
| | - David P. Gavin
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA; (H.S.R.); (H.E.G.)
| | - Rajiv P. Sharma
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA; (H.S.R.); (H.E.G.)
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL 60612, USA
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2
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Methylation and expression of glucocorticoid receptor exon-1 variants and FKBP5 in teenage suicide-completers. Transl Psychiatry 2023; 13:53. [PMID: 36781843 PMCID: PMC9925759 DOI: 10.1038/s41398-023-02345-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 11/18/2022] [Accepted: 01/30/2023] [Indexed: 02/15/2023] Open
Abstract
A dysregulated hypothalamic-pituitary-adrenal (HPA) axis has repeatedly been demonstrated to play a fundamental role in psychiatric disorders and suicide, yet the mechanisms underlying this dysregulation are not clear. Decreased expression of the glucocorticoid receptor (GR) gene, which is also susceptible to epigenetic modulation, is a strong indicator of impaired HPA axis control. In the context of teenage suicide-completers, we have systematically analyzed the 5'UTR of the GR gene to determine the expression levels of all GR exon-1 transcript variants and their epigenetic state. We also measured the expression and the epigenetic state of the FK506-binding protein 51 (FKBP5/FKBP51), an important modulator of GR activity. Furthermore, steady-state DNA methylation levels depend upon the interplay between enzymes that promote DNA methylation and demethylation activities, thus we analyzed DNA methyltransferases (DNMTs), ten-eleven translocation enzymes (TETs), and growth arrest- and DNA-damage-inducible proteins (GADD45). Focusing on both the prefrontal cortex (PFC) and hippocampus, our results show decreased expression in specific GR exon-1 variants and a strong correlation of DNA methylation changes with gene expression in the PFC. FKBP5 expression is also increased in both areas suggesting a decreased GR sensitivity to cortisol binding. We also identified aberrant expression of DNA methylating and demethylating enzymes in both brain regions. These findings enhance our understanding of the complex transcriptional regulation of GR, providing evidence of epigenetically mediated reprogramming of the GR gene, which could lead to possible epigenetic influences that result in lasting modifications underlying an individual's overall HPA axis response and resilience to stress.
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3
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Domi E, Barchiesi R, Barbier E. Epigenetic Dysregulation in Alcohol-Associated Behaviors: Preclinical and Clinical Evidence. Curr Top Behav Neurosci 2023. [PMID: 36717533 DOI: 10.1007/7854_2022_410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Alcohol use disorder (AUD) is characterized by loss of control over intake and drinking despite harmful consequences. At a molecular level, AUD is associated with long-term neuroadaptations in key brain regions that are involved in reward processing and decision-making. Over the last decades, a great effort has been made to understand the neurobiological basis underlying AUD. Epigenetic mechanisms have emerged as an important mechanism in the regulation of long-term alcohol-induced gene expression changes. Here, we review the literature supporting a role for epigenetic processes in AUD. We particularly focused on the three most studied epigenetic mechanisms: DNA methylation, Histone modification and non-coding RNAs. Clinical studies indicate an association between AUD and DNA methylation both at the gene and global levels. Using behavioral paradigms that mimic some of the characteristics of AUD, preclinical studies demonstrate that changes in epigenetic mechanisms can functionally impact alcohol-associated behaviors. While many studies support a therapeutic potential for targeting epigenetic enzymes, more research is needed to fully understand their role in AUD. Identification of brain circuits underlying alcohol-associated behaviors has made major advances in recent years. However, there are very few studies that investigate how epigenetic mechanisms can affect these circuits or impact the neuronal ensembles that promote alcohol-associated behaviors. Studies that focus on the role of circuit-specific and cell-specific epigenetic changes for clinically relevant alcohol behaviors may provide new insights on the functional role of epigenetic processes in AUD.
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Affiliation(s)
- Esi Domi
- Department of Biomedical and Clinical Sciences, Center for Social and Affective Neuroscience, Linköping University, Linköping, Sweden
- School of Pharmacy, Pharmacology Unit, Center for Neuroscience, University of Camerino, Camerino, Italy
| | - Riccardo Barchiesi
- Department of Neuroscience, Waggoner Center for Alcohol and Alcohol Addiction Research, University of Texas at Austin, Austin, TX, USA
| | - Estelle Barbier
- Department of Biomedical and Clinical Sciences, Center for Social and Affective Neuroscience, Linköping University, Linköping, Sweden.
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4
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Jarczak J, Miszczak M, Radwanska K. Is DNA methylation in the brain a mechanism of alcohol use disorder? Front Behav Neurosci 2023; 17:957203. [PMID: 36778133 PMCID: PMC9908583 DOI: 10.3389/fnbeh.2023.957203] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 01/09/2023] [Indexed: 01/27/2023] Open
Abstract
Alcohol use disorder (AUD) is a worldwide problem. Unfortunately, the molecular mechanisms of alcohol misuse are still poorly understood, therefore successful therapeutic approaches are limited. Accumulating data indicate that the tendency for compulsive alcohol use is inherited, suggesting a genetic background as an important factor. However, the probability to develop AUD is also affected by life experience and environmental factors. Therefore, the epigenetic modifications that are altered over lifetime likely contribute to increased risk of alcohol misuse. Here, we review the literature looking for the link between DNA methylation in the brain, a common epigenetic modification, and AUD-related behaviors in humans, mice and rats. We sum up the main findings, identify the existing gaps in our knowledge and indicate future directions of the research.
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5
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Loe AKH, Francis R, Seo J, Du L, Wang Y, Kim JE, Hakim SW, Kim JE, He HH, Guo H, Kim TH. Uncovering the dosage-dependent roles of Arid1a in gastric tumorigenesis for combinatorial drug therapy. J Exp Med 2021; 218:211950. [PMID: 33822841 PMCID: PMC8034383 DOI: 10.1084/jem.20200219] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 01/20/2021] [Accepted: 03/05/2021] [Indexed: 12/25/2022] Open
Abstract
Gastric cancer (GC) is one of the most common deadly cancers in the world. Although patient genomic data have identified AT-rich interaction domain 1A (ARID1A), a key chromatin remodeling complex subunit, as the second most frequently mutated gene after TP53, its in vivo role and relationship to TP53 in gastric tumorigenesis remains unclear. Establishing a novel mouse model that reflects the ARID1A heterozygous mutations found in the majority of human GC cases, we demonstrated that Arid1a heterozygosity facilitates tumor progression through a global loss of enhancers and subsequent suppression of the p53 and apoptosis pathways. Moreover, mouse genetic and single-cell analyses demonstrated that the homozygous deletion of Arid1a confers a competitive disadvantage through the activation of the p53 pathway, highlighting its distinct dosage-dependent roles. Using this unique vulnerability of Arid1a mutated GC cells, our combined treatment with the epigenetic inhibitor, TP064, and the p53 agonist, Nutlin-3, inhibited growth of Arid1a heterozygous tumor organoids, providing a novel therapeutic option for GC.
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Affiliation(s)
- Adrian Kwan Ho Loe
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Roshane Francis
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jieun Seo
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China.,Tumor Marker Detection Engineering Laboratory of Shandong Province, Jinan, Shandong, China
| | - Yunshan Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China.,Tumor Marker Detection Engineering Laboratory of Shandong Province, Jinan, Shandong, China
| | - Ji-Eun Kim
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Shaheed W Hakim
- St. Joseph's Health Centre, Unity Health Toronto, Toronto, Ontario, Canada
| | - Jung-Eun Kim
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Haiyang Guo
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China.,Tumor Marker Detection Engineering Laboratory of Shandong Province, Jinan, Shandong, China.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Tae-Hee Kim
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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6
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Bohnsack JP, Pandey SC. Histone modifications, DNA methylation, and the epigenetic code of alcohol use disorder. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2020; 156:1-62. [PMID: 33461661 DOI: 10.1016/bs.irn.2020.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Alcohol use disorder (AUD) is a leading cause of morbidity and mortality. Despite AUD's substantial contributions to lost economic productivity and quality of life, there are only a limited number of approved drugs for treatment of AUD in the United States. This chapter will update progress made on the epigenetic basis of AUD, with particular focus on histone post-translational modifications and DNA methylation and how these two epigenetic mechanisms interact to contribute to neuroadaptive processes leading to initiation, maintenance and progression of AUD pathophysiology. We will also evaluate epigenetic therapeutic strategies that have arisen from preclinical models of AUD and epigenetic biomarkers that have been discovered in human populations with AUD.
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Affiliation(s)
- John Peyton Bohnsack
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Subhash C Pandey
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States; Jesse Brown VA Medical Center, Chicago, IL, United States; Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, United States.
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7
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Norepinephrine, neurodevelopment and behavior. Neurochem Int 2020; 135:104706. [PMID: 32092327 DOI: 10.1016/j.neuint.2020.104706] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/14/2020] [Accepted: 02/16/2020] [Indexed: 02/06/2023]
Abstract
Neurotransmitters play critical roles in the developing nervous system. Among the neurotransmitters, norepinephrine (NE) is in particular postulated to be an important regulator of brain development. NE is expressed during early stages of development and is known to regulate both the development of noradrenergic neurons and the development of target areas. NE participates in the shaping and the wiring of the nervous system during the critical periods of development, and perturbations in this process can alter the brain's developmental trajectory, which in turn can cause long-lasting and even permanent changes in the brain function and behavior later in life. Here we will briefly review evidence for the role of noradrenergic system in neurodevelopmental processes and will discuss about the potential disruptors of noradrenergic system during development and their behavioral consequences.
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8
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Sakharkar AJ, Kyzar EJ, Gavin DP, Zhang H, Chen Y, Krishnan HR, Grayson DR, Pandey SC. Altered amygdala DNA methylation mechanisms after adolescent alcohol exposure contribute to adult anxiety and alcohol drinking. Neuropharmacology 2019; 157:107679. [PMID: 31229451 PMCID: PMC6681823 DOI: 10.1016/j.neuropharm.2019.107679] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 06/08/2019] [Accepted: 06/18/2019] [Indexed: 01/04/2023]
Abstract
Binge drinking during adolescence increases the risk for neuropsychiatric disorders including alcoholism in adulthood. DNA methylation in post-mitotic neurons is an important epigenetic modification that plays a crucial role in neurodevelopment. We examined the effects of intermittent ethanol exposure during adolescence on adult behavior and whether DNA methylation changes provide a plausible explanation for the lasting effects of this developmental insult. One hour after last adolescent intermittent ethanol (AIE), growth arrest and DNA damage inducible protein 45 (Gadd45a, Gadd45b, and Gadd45g) mRNA expression was increased and DNA methyltransferase (DNMT) activity and Dnmt3b expression was decreased in the amygdala as compared to adolescent intermittent saline (AIS) rats. However, AIE rats 24 h after last exposure displayed increased DNMT activity but normalized Gadd45 and Dnmt3b mRNA expression compared to AIS rats. In adulthood, rats exposed to AIE show increased Dnmt3b mRNA expression and DNMT activity, along with decreased Gadd45g mRNA expression in the amygdala. DNA methylation of neuropeptide Y (Npy) and brain-derived neurotrophic factor (Bdnf) exon IV is increased in the AIE adult amygdala compared to AIS adult rats. Treatment with the DNMT inhibitor 5-azacytidine (5-azaC) at adulthood normalizes the AIE-induced DNA hypermethylation of Npy and Bdnf exon IV with concomitant reversal of AIE-induced anxiety-like and alcohol-drinking behaviors. These results suggest that binge-like ethanol exposure during adolescence leads to dysregulation in DNA methylation mechanisms in the amygdala which may contribute to behavioral phenotypes of anxiety and alcohol use in adulthood.
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Affiliation(s)
- Amul J Sakharkar
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, 60612, USA; Jesse Brown Veterans Affairs Medical Center, Chicago, IL, 60612, USA
| | - Evan J Kyzar
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, 60612, USA; Jesse Brown Veterans Affairs Medical Center, Chicago, IL, 60612, USA
| | - David P Gavin
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, 60612, USA; Jesse Brown Veterans Affairs Medical Center, Chicago, IL, 60612, USA
| | - Huaibo Zhang
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, 60612, USA; Jesse Brown Veterans Affairs Medical Center, Chicago, IL, 60612, USA
| | - Ying Chen
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Harish R Krishnan
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, 60612, USA; Jesse Brown Veterans Affairs Medical Center, Chicago, IL, 60612, USA
| | - Dennis R Grayson
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Subhash C Pandey
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, 60612, USA; Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, 60612, USA; Jesse Brown Veterans Affairs Medical Center, Chicago, IL, 60612, USA.
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9
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Saad MH, Rumschlag M, Guerra MH, Savonen CL, Jaster AM, Olson PD, Alazizi A, Luca F, Pique-Regi R, Schmidt CJ, Bannon MJ. Differentially expressed gene networks, biomarkers, long noncoding RNAs, and shared responses with cocaine identified in the midbrains of human opioid abusers. Sci Rep 2019; 9:1534. [PMID: 30733491 PMCID: PMC6367337 DOI: 10.1038/s41598-018-38209-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/21/2018] [Indexed: 12/21/2022] Open
Abstract
Opioid abuse is now the most common cause of accidental death in the US. Although opioids and most other drugs of abuse acutely increase signaling mediated by midbrain dopamine (DA)-synthesizing neurons, little is known about long-lasting changes in DA cells that may contribute to continued opioid abuse, craving, and relapse. A better understanding of the molecular and cellular bases of opioid abuse could lead to advancements in therapeutics. This study comprises, to our knowledge, the first unbiased examination of genome-wide changes in midbrain gene expression associated with human opioid abuse. Our analyses identified differentially expressed genes and distinct gene networks associated with opioid abuse, specific genes with predictive capability for subject assignment to the opioid abuse cohort, and genes most similarly affected in chronic opioid and cocaine abusers. We also identified differentially expressed long noncoding RNAs capable of regulating known drug-responsive protein-coding genes. Opioid-regulated genes identified in this study warrant further investigation as potential biomarkers and/or therapeutic targets for human substance abuse.
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Affiliation(s)
- Manal H Saad
- Wayne State University School of Medicine, Department of Pharmacology, Detroit, MI, 48201, USA
| | - Matthew Rumschlag
- Wayne State University School of Medicine, Department of Pharmacology, Detroit, MI, 48201, USA
| | - Michael H Guerra
- Wayne State University School of Medicine, Department of Pharmacology, Detroit, MI, 48201, USA
| | - Candace L Savonen
- Wayne State University School of Medicine, Department of Pharmacology, Detroit, MI, 48201, USA
| | - Alaina M Jaster
- Wayne State University School of Medicine, Department of Pharmacology, Detroit, MI, 48201, USA
| | - Philip D Olson
- Wayne State University School of Medicine, Department of Pharmacology, Detroit, MI, 48201, USA
| | - Adnan Alazizi
- Wayne State University School of Medicine, Center for Molecular Medicine & Genetics, Detroit, MI, 48201, USA.,Wayne State University School of Medicine, Department of Obstetrics and Gynecology, Detroit, MI, 48201, USA
| | - Francesca Luca
- Wayne State University School of Medicine, Center for Molecular Medicine & Genetics, Detroit, MI, 48201, USA.,Wayne State University School of Medicine, Department of Obstetrics and Gynecology, Detroit, MI, 48201, USA
| | - Roger Pique-Regi
- Wayne State University School of Medicine, Center for Molecular Medicine & Genetics, Detroit, MI, 48201, USA.,Wayne State University School of Medicine, Department of Obstetrics and Gynecology, Detroit, MI, 48201, USA
| | - Carl J Schmidt
- University of Michigan School of Medicine, Department of Pathology, Detroit, MI, 48109, USA
| | - Michael J Bannon
- Wayne State University School of Medicine, Department of Pharmacology, Detroit, MI, 48201, USA.
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10
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Gavin DP, Hashimoto JG, Lazar NH, Carbone L, Crabbe JC, Guizzetti M. Stable Histone Methylation Changes at Proteoglycan Network Genes Following Ethanol Exposure. Front Genet 2018; 9:346. [PMID: 30214456 PMCID: PMC6125400 DOI: 10.3389/fgene.2018.00346] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 08/09/2018] [Indexed: 12/14/2022] Open
Abstract
Alcohol use disorder (AUD) is a chronic mental illness in which patients often achieve protracted periods of abstinence prior to relapse. Epigenetic mechanisms may provide an explanation for the persisting gene expression changes that can be observed even after long periods of abstinence and may contribute to relapse. In this study, we examined two histone modifications, histone 3 lysine 4 tri-methylation (H3K4me3) and histone 3 lysine 27 tri-methylation (H3K27me3), in the prefrontal cortex of Withdrawal Seizure Resistant (WSR) mice 21 days after 72 h of ethanol vapor exposure. These histone modifications were selected because they are associated with active promoters (H3K4me3) and repressed gene expression in a euchromatic environment (H3K27me3). We performed a genome-wide analysis to identify differences in H3K4me3 and H3K27me3 levels in post-ethanol exposure vs. control mice by ChIP-seq. We detected a global reduction in H3K4me3 peaks and increase in H3K27me3 peaks in post-ethanol exposure mice compared to controls, these changes are consistent with persistent reductions in gene expression. Pathway analysis of genes displaying changes in H3K4me3 and H3K27me3 revealed enrichment for genes involved in proteoglycan and calcium signaling pathways, respectively. Microarray analysis of 7,683 genes and qPCR analysis identified eight genes displaying concordant regulation of gene expression and H3K4me3/H3K27me3. We also compared changes in H3K4me3 and/or H3K27me3 from our study with changes in gene expression in response to ethanol from published literature and we found that the expression of 52% of the genes with altered H3K4me3 binding and 40% of genes with H3K27me3 differences are altered by ethanol exposure. The chromatin changes associated with the 21-day post-exposure period suggest that this period is a unique state in the addiction cycle that differs from ethanol intoxication and acute withdrawal. These results provide insights into the enduring effects of ethanol on proteoglycan and calcium signaling genes in the brain.
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Affiliation(s)
- David P. Gavin
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL, United States
- Department of Psychiatry, Center for Alcohol Research in Epigenetics, University of Illinois at Chicago, Chicago, IL, United States
| | - Joel G. Hashimoto
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
| | - Nathan H. Lazar
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, United States
| | - Lucia Carbone
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, United States
| | - John C. Crabbe
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
| | - Marina Guizzetti
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
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11
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Vadigepalli R, Hoek JB. Introduction to the Virtual Issue Alcohol and Epigenetic Regulation: Do the Products of Alcohol Metabolism Drive Epigenetic Control of Gene Expression in Alcohol-Related Disorders? Alcohol Clin Exp Res 2018. [PMID: 29532481 DOI: 10.1111/acer.13630] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Rajanikanth Vadigepalli
- Department of Pathology, Anatomy & Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Jan B Hoek
- Department of Pathology, Anatomy & Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
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12
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Saha SK, Lee SB, Won J, Choi HY, Kim K, Yang GM, Dayem AA, Cho SG. Correlation between Oxidative Stress, Nutrition, and Cancer Initiation. Int J Mol Sci 2017; 18:E1544. [PMID: 28714931 PMCID: PMC5536032 DOI: 10.3390/ijms18071544] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 02/07/2023] Open
Abstract
Inadequate or excessive nutrient consumption leads to oxidative stress, which may disrupt oxidative homeostasis, activate a cascade of molecular pathways, and alter the metabolic status of various tissues. Several foods and consumption patterns have been associated with various cancers and approximately 30-35% of the cancer cases are correlated with overnutrition or malnutrition. However, several contradictory studies are available regarding the association between diet and cancer risk, which remains to be elucidated. Concurrently, oxidative stress is a crucial factor for cancer progression and therapy. Nutritional oxidative stress may be induced by an imbalance between antioxidant defense and pro-oxidant load due to inadequate or excess nutrient supply. Oxidative stress is a physiological state where high levels of reactive oxygen species (ROS) and free radicals are generated. Several signaling pathways associated with carcinogenesis can additionally control ROS generation and regulate ROS downstream mechanisms, which could have potential implications in anticancer research. Cancer initiation may be modulated by the nutrition-mediated elevation in ROS levels, which can stimulate cancer initiation by triggering DNA mutations, damage, and pro-oncogenic signaling. Therefore, in this review, we have provided an overview of the relationship between nutrition, oxidative stress, and cancer initiation, and evaluated the impact of nutrient-mediated regulation of antioxidant capability against cancer therapy.
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Affiliation(s)
- Subbroto Kumar Saha
- Department of Stem Cell and Regenerative Biotechnology, Incurable Disease Animal Model & Stem Cell Institute (IDASI), Konkuk University, Seoul 05029, Korea.
| | - Soo Bin Lee
- Department of Stem Cell and Regenerative Biotechnology, Incurable Disease Animal Model & Stem Cell Institute (IDASI), Konkuk University, Seoul 05029, Korea.
| | - Jihye Won
- Department of Stem Cell and Regenerative Biotechnology, Incurable Disease Animal Model & Stem Cell Institute (IDASI), Konkuk University, Seoul 05029, Korea.
| | - Hye Yeon Choi
- Department of Stem Cell and Regenerative Biotechnology, Incurable Disease Animal Model & Stem Cell Institute (IDASI), Konkuk University, Seoul 05029, Korea.
| | - Kyeongseok Kim
- Department of Stem Cell and Regenerative Biotechnology, Incurable Disease Animal Model & Stem Cell Institute (IDASI), Konkuk University, Seoul 05029, Korea.
| | - Gwang-Mo Yang
- Department of Stem Cell and Regenerative Biotechnology, Incurable Disease Animal Model & Stem Cell Institute (IDASI), Konkuk University, Seoul 05029, Korea.
| | - Ahmed Abdal Dayem
- Department of Stem Cell and Regenerative Biotechnology, Incurable Disease Animal Model & Stem Cell Institute (IDASI), Konkuk University, Seoul 05029, Korea.
| | - Ssang-Goo Cho
- Department of Stem Cell and Regenerative Biotechnology, Incurable Disease Animal Model & Stem Cell Institute (IDASI), Konkuk University, Seoul 05029, Korea.
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Ye J, Wu W, Li Y, Li L. Influences of the Gut Microbiota on DNA Methylation and Histone Modification. Dig Dis Sci 2017; 62:1155-1164. [PMID: 28341870 DOI: 10.1007/s10620-017-4538-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/09/2017] [Indexed: 12/12/2022]
Abstract
The gut microbiota is a vast ensemble of microorganisms inhabiting the mammalian gastrointestinal tract that can impact physiologic and pathologic processes. However, our understanding of the underlying mechanism for the dynamic interaction between host and gut microbiota is still in its infancy. The highly evolved epigenetic modifications allow hosts to reprogram the genome in response to environmental stimuli, which may play a key role in triggering multiple human diseases. In spite of increasing studies in gut microbiota and epigenetic modifications, the correlation between them has not been well elaborated. Here, we review current knowledge of gut microbiota impacts on epigenetic modifications, the major evidence of which centers on DNA methylation and histone modification of the immune system.
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Affiliation(s)
- Jianzhong Ye
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, 310003, China
| | - Wenrui Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, 310003, China
| | - Yating Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, 310003, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, 310003, China.
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14
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Tulisiak CT, Harris RA, Ponomarev I. DNA modifications in models of alcohol use disorders. Alcohol 2017; 60:19-30. [PMID: 27865607 DOI: 10.1016/j.alcohol.2016.11.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/03/2016] [Accepted: 11/05/2016] [Indexed: 02/07/2023]
Abstract
Chronic alcohol use and abuse result in widespread changes to gene expression, some of which contribute to the development of alcohol-use disorders (AUD). Gene expression is controlled, in part, by a group of regulatory systems often referred to as epigenetic factors, which includes, among other mechanisms, chemical marks made on the histone proteins around which genomic DNA is wound to form chromatin, and on nucleotides of the DNA itself. In particular, alcohol has been shown to perturb the epigenetic machinery, leading to changes in gene expression and cellular functions characteristic of AUD and, ultimately, to altered behavior. DNA modifications in particular are seeing increasing research in the context of alcohol use and abuse. To date, studies of DNA modifications in AUD have primarily looked at global methylation profiles in human brain and blood, gene-specific methylation profiles in animal models, methylation changes associated with prenatal ethanol exposure, and the potential therapeutic abilities of DNA methyltransferase inhibitors. Future studies may be aimed at identifying changes to more recently discovered DNA modifications, utilizing new methods to discriminate methylation profiles between cell types, thus clarifying how alcohol influences the methylomes of cell-type populations and how this may affect downstream processes. These studies and more in-depth probing of DNA methylation will be key to determining whether DNA-level epigenetic regulation plays a causative role in AUD and can thus be targeted for treatment of the disorder.
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Affiliation(s)
- Christopher T Tulisiak
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, 2500 Speedway, A4800, Austin, TX 78712, USA
| | - R Adron Harris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, 2500 Speedway, A4800, Austin, TX 78712, USA; The College of Pharmacy, The University of Texas at Austin, 2409 University Avenue, A1900, Austin, TX 78712, USA
| | - Igor Ponomarev
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, 2500 Speedway, A4800, Austin, TX 78712, USA; The College of Pharmacy, The University of Texas at Austin, 2409 University Avenue, A1900, Austin, TX 78712, USA.
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15
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Hashimoto JG, Gavin DP, Wiren KM, Crabbe JC, Guizzetti M. Prefrontal cortex expression of chromatin modifier genes in male WSP and WSR mice changes across ethanol dependence, withdrawal, and abstinence. Alcohol 2017; 60:83-94. [PMID: 28433423 PMCID: PMC5497775 DOI: 10.1016/j.alcohol.2017.01.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 12/20/2022]
Abstract
Alcohol-use disorder (AUD) is a relapsing disorder associated with excessive ethanol consumption. Recent studies support the involvement of epigenetic mechanisms in the development of AUD. Studies carried out so far have focused on a few specific epigenetic modifications. The goal of this project was to investigate gene expression changes of epigenetic regulators that mediate a broad array of chromatin modifications after chronic alcohol exposure, chronic alcohol exposure followed by 8 h withdrawal, and chronic alcohol exposure followed by 21 days of abstinence in Withdrawal-Resistant (WSR) and Withdrawal Seizure-Prone (WSP) selected mouse lines. We found that chronic vapor exposure to highly intoxicating levels of ethanol alters the expression of several chromatin remodeling genes measured by quantitative PCR array analyses. The identified effects were independent of selected lines, which, however, displayed baseline differences in epigenetic gene expression. We reported dysregulation in the expression of genes involved in histone acetylation, deacetylation, lysine and arginine methylation and ubiquitinationhylation during chronic ethanol exposure and withdrawal, but not after 21 days of abstinence. Ethanol-induced changes are consistent with decreased histone acetylation and with decreased deposition of the permissive ubiquitination mark H2BK120ub, associated with reduced transcription. On the other hand, ethanol-induced changes in the expression of genes involved in histone lysine methylation are consistent with increased transcription. The net result of these modifications on gene expression is likely to depend on the combination of the specific histone tail modifications present at a given time on a given promoter. Since alcohol does not modulate gene expression unidirectionally, it is not surprising that alcohol does not unidirectionally alter chromatin structure toward a closed or open state, as suggested by the results of this study.
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Affiliation(s)
- Joel G Hashimoto
- Department of Behavioral Neuroscience, Oregon Health & Science University, 3181 SW Sam Jackson Park Road L470, Portland, OR, 97239, United States; VA Portland Health Care System, 3710 SW US Veterans Hospital Rd, Portland, OR, 97239, United States
| | - David P Gavin
- Jesse Brown Veterans Affairs Medical Center, 820 South Damen Avenue (M/C 151), Chicago, IL, 60612, United States; Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL, 60612, United States
| | - Kristine M Wiren
- Department of Behavioral Neuroscience, Oregon Health & Science University, 3181 SW Sam Jackson Park Road L470, Portland, OR, 97239, United States; VA Portland Health Care System, 3710 SW US Veterans Hospital Rd, Portland, OR, 97239, United States
| | - John C Crabbe
- Department of Behavioral Neuroscience, Oregon Health & Science University, 3181 SW Sam Jackson Park Road L470, Portland, OR, 97239, United States; VA Portland Health Care System, 3710 SW US Veterans Hospital Rd, Portland, OR, 97239, United States
| | - Marina Guizzetti
- Department of Behavioral Neuroscience, Oregon Health & Science University, 3181 SW Sam Jackson Park Road L470, Portland, OR, 97239, United States; VA Portland Health Care System, 3710 SW US Veterans Hospital Rd, Portland, OR, 97239, United States.
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16
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Berkel TDM, Pandey SC. Emerging Role of Epigenetic Mechanisms in Alcohol Addiction. Alcohol Clin Exp Res 2017; 41:666-680. [PMID: 28111764 DOI: 10.1111/acer.13338] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/09/2017] [Indexed: 12/15/2022]
Abstract
Alcohol use disorder (AUD) is a complex brain disorder with an array of persistent behavioral and neurochemical manifestations. Both genetic and environmental factors are known to contribute to the development of AUD, and recent studies on alcohol exposure and subsequent changes in gene expression suggest the importance of epigenetic mechanisms. In particular, histone modifications and DNA methylation have emerged as important regulators of gene expression and associated phenotypes of AUD. Given the therapeutic potential of epigenetic targets, this review aims to summarize the role of epigenetic regulation in our current understanding of AUD by evaluating known epigenetic signatures of brain regions critical to addictive behaviors in both animal and human studies throughout various stages of AUD. More specifically, the effects of acute and chronic alcohol exposure, tolerance, and postexposure withdrawal on epigenetically induced changes to gene expression and synaptic plasticity within key brain regions and the associated behavioral phenotypes have been discussed. Understanding the contribution of epigenetic regulation to crucial signaling pathways may prove vital for future development of novel biomarkers and treatment agents in ameliorating or preventing AUD.
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Affiliation(s)
- Tiffani D M Berkel
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois.,Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
| | - Subhash C Pandey
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois.,Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois.,Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, Illinois
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17
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Kyzar EJ, Floreani C, Teppen TL, Pandey SC. Adolescent Alcohol Exposure: Burden of Epigenetic Reprogramming, Synaptic Remodeling, and Adult Psychopathology. Front Neurosci 2016; 10:222. [PMID: 27303256 PMCID: PMC4885838 DOI: 10.3389/fnins.2016.00222] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 05/06/2016] [Indexed: 12/22/2022] Open
Abstract
Adolescence represents a crucial phase of synaptic maturation characterized by molecular changes in the developing brain that shape normal behavioral patterns. Epigenetic mechanisms play an important role in these neuromaturation processes. Perturbations of normal epigenetic programming during adolescence by ethanol can disrupt these molecular events, leading to synaptic remodeling and abnormal adult behaviors. Repeated exposure to binge levels of alcohol increases the risk for alcohol use disorder (AUD) and comorbid psychopathology including anxiety in adulthood. Recent studies in the field clearly suggest that adolescent alcohol exposure causes widespread and persistent changes in epigenetic, neurotrophic, and neuroimmune pathways in the brain. These changes are manifested by altered synaptic remodeling and neurogenesis in key brain regions leading to adult psychopathology such as anxiety and alcoholism. This review details the molecular mechanisms underlying adolescent alcohol exposure-induced changes in synaptic plasticity and the development of alcohol addiction-related phenotypes in adulthood.
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Affiliation(s)
- Evan J Kyzar
- Department of Psychiatry, Center for Alcohol Research in Epigenetics, University of Illinois at ChicagoChicago, IL, USA; Jesse Brown Veterans Affairs Medical CenterChicago, IL, USA
| | - Christina Floreani
- Department of Psychiatry, Center for Alcohol Research in Epigenetics, University of Illinois at ChicagoChicago, IL, USA; Jesse Brown Veterans Affairs Medical CenterChicago, IL, USA
| | - Tara L Teppen
- Department of Psychiatry, Center for Alcohol Research in Epigenetics, University of Illinois at ChicagoChicago, IL, USA; Jesse Brown Veterans Affairs Medical CenterChicago, IL, USA
| | - Subhash C Pandey
- Department of Psychiatry, Center for Alcohol Research in Epigenetics, University of Illinois at ChicagoChicago, IL, USA; Jesse Brown Veterans Affairs Medical CenterChicago, IL, USA; Anatomy and Cell Biology, University of Illinois at ChicagoChicago, IL, USA
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