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Brampton C, Pomozi V, Le Corre Y, Zoll J, Kauffenstein G, Ma C, Hoffmann PR, Martin L, Le Saux O. Bone Marrow-Derived ABCC6 Is an Essential Regulator of Ectopic Calcification In Pseudoxanthoma Elasticum. J Invest Dermatol 2024; 144:1772-1783.e3. [PMID: 38367909 PMCID: PMC11260544 DOI: 10.1016/j.jid.2024.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/31/2023] [Accepted: 01/26/2024] [Indexed: 02/19/2024]
Abstract
Physiological calcification of soft tissues is a common occurrence in aging and various acquired and inherited disorders. ABCC6 sequence variations cause the calcification phenotype of pseudoxanthoma elasticum (PXE) as well as some cases of generalized arterial calcification of infancy, which is otherwise caused by defective ENPP1. ABCC6 is primarily expressed in the liver, which has given the impression that the liver is central to the pathophysiology of PXE/generalized arterial calcification of infancy. The emergence of inflammation as a contributor to the calcification in PXE suggested that peripheral tissues play a larger role than expected. In this study, we investigated whether bone marrow-derived ABCC6 contributes to the calcification in PXE. In Abcc6‒/‒ mice, we observed prevalent mineralization in several lymph nodes and surrounding connective tissues and an extensive network of lymphatic vessels within vibrissae, a calcified tissue in Abcc6‒/‒ mice. Furthermore, we found evidence of lymphangiogenesis in patients with PXE and mouse skin, suggesting an inflammatory process. Finally, restoring wild-type bone marrow in Abcc6‒/‒ mice produced a significant reduction of calcification, suggesting that the liver alone is not sufficient to fully inhibit mineralization. With evidence that ABCC6 is expressed in lymphocytes, we suggest that the adaptative immune system and inflammation largely contribute to the calcification in PXE/generalized arterial calcification of infancy.
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Affiliation(s)
- Christopher Brampton
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA; Bio-Rad Laboratories, Hercules, California, USA
| | - Viola Pomozi
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA; Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences Centre of Excellence, Budapest, Hungary
| | - Yannick Le Corre
- PXE National Reference Center (MAGEC Nord), University Hospital of Angers, Angers, France
| | - Janna Zoll
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA
| | - Gilles Kauffenstein
- UMR INSERM 1260, Nano Regenerative Medicine, University of Strasbourg, Strasbourg, France
| | - Chi Ma
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA
| | - Peter R Hoffmann
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA
| | - Ludovic Martin
- PXE National Reference Center (MAGEC Nord), University Hospital of Angers, Angers, France; CNRS 6015, UMR INSERM U1083, MITOVASC Laboratory, University of Angers, Angers, France
| | - Olivier Le Saux
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA.
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Barzegar S, Pirouzpanah S. Zinc finger proteins and ATP-binding cassette transporter-dependent multidrug resistance. Eur J Clin Invest 2024; 54:e14120. [PMID: 37930002 DOI: 10.1111/eci.14120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 07/12/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Multidrug resistance (MDR) remains a significant challenge in cancer treatment, leading to poor clinical outcomes. Dysregulation of ATP-binding cassette (ABC) transporters has been identified as a key contributor to MDR. Zinc finger proteins (ZNPs) are key regulators of transcription and have emerged as potential contributors to cancer drug resistance. Bridging the knowledge gap between ZNPs and MDR is essential to understand a source of heterogeneity in cancer treatment. This review sought to elucidate how different ZNPs modulate the transcriptional regulation of ABC genes, contributing to resistance to cancer therapies. METHODS The search was conducted using PubMed, Google Scholar, EMBASE and Web of Science. RESULTS In addition to ABC-blockers, the transcriptional features regulated by ZNP are expected to play a role in reversing ABC-mediated MDR and predicting the efficacy of anticancer treatments. Among the ZNP-induced epithelial to mesenchymal transition, SNAIL, SLUG and Zebs have been identified as important factors in promoting MDR through activation of ATM, NFκB and PI3K/Akt pathways, exposing the metabolism to potential ZNP-MDR interactions. Additionally, nuclear receptors, such as VDR, ER and PXR have been found to modulate certain ABC regulations. Other C2H2-type zinc fingers, including Kruppel-like factors, Gli and Sp also have the potential to contribute to MDR. CONCLUSION Besides reviewing evidence on the effects of ZNP dysregulation on ABC-related chemoresistance in malignancies, significant markers of ZNP functions are discussed to highlight the clinical implications of gene-to-gene and microenvironment-to-gene interactions on MDR prospects. Future research on ZNP-derived biomarkers is crucial for addressing heterogeneity in cancer therapy.
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Affiliation(s)
- Sanaz Barzegar
- Shahid Madani Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saeed Pirouzpanah
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Sun Y, Wiese M, Hmadi R, Karayol R, Seyfferth J, Martinez Greene JA, Erdogdu NU, Deboutte W, Arrigoni L, Holz H, Renschler G, Hirsch N, Foertsch A, Basilicata MF, Stehle T, Shvedunova M, Bella C, Pessoa Rodrigues C, Schwalb B, Cramer P, Manke T, Akhtar A. MSL2 ensures biallelic gene expression in mammals. Nature 2023; 624:173-181. [PMID: 38030723 PMCID: PMC10700137 DOI: 10.1038/s41586-023-06781-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
In diploid organisms, biallelic gene expression enables the production of adequate levels of mRNA1,2. This is essential for haploinsufficient genes, which require biallelic expression for optimal function to prevent the onset of developmental disorders1,3. Whether and how a biallelic or monoallelic state is determined in a cell-type-specific manner at individual loci remains unclear. MSL2 is known for dosage compensation of the male X chromosome in flies. Here we identify a role of MSL2 in regulating allelic expression in mammals. Allele-specific bulk and single-cell analyses in mouse neural progenitor cells revealed that, in addition to the targets showing biallelic downregulation, a class of genes transitions from biallelic to monoallelic expression after MSL2 loss. Many of these genes are haploinsufficient. In the absence of MSL2, one allele remains active, retaining active histone modifications and transcription factor binding, whereas the other allele is silenced, exhibiting loss of promoter-enhancer contacts and the acquisition of DNA methylation. Msl2-knockout mice show perinatal lethality and heterogeneous phenotypes during embryonic development, supporting a role for MSL2 in regulating gene dosage. The role of MSL2 in preserving biallelic expression of specific dosage-sensitive genes sets the stage for further investigation of other factors that are involved in allelic dosage compensation in mammalian cells, with considerable implications for human disease.
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Affiliation(s)
- Yidan Sun
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Meike Wiese
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Raed Hmadi
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Remzi Karayol
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Janine Seyfferth
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Juan Alfonso Martinez Greene
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Niyazi Umut Erdogdu
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ward Deboutte
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Laura Arrigoni
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Herbert Holz
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Gina Renschler
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Naama Hirsch
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Arion Foertsch
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Thomas Stehle
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Maria Shvedunova
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Chiara Bella
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Bjoern Schwalb
- Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Britsemmer JH, Krause C, Taege N, Geißler C, Lopez-Alcantara N, Schmidtke L, Naujack AM, Wagner J, Wolter S, Mann O, Kirchner H. Fatty Acid Induced Hypermethylation in the Slc2a4 Gene in Visceral Adipose Tissue Is Associated to Insulin-Resistance and Obesity. Int J Mol Sci 2023; 24:ijms24076417. [PMID: 37047391 PMCID: PMC10094548 DOI: 10.3390/ijms24076417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/16/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
De novo lipogenesis (DNL) in visceral adipose tissue (VAT) is associated with systemic insulin sensitivity. DNL in VAT is regulated through ChREBP activity and glucose uptake through Glut4 (encoded by Slc2a4). Slc2a4 expression, ChREBP activity, and DNL are decreased in obesity, the underlying cause however remains unidentified. We hypothesize that increased DNA methylation in an enhancer region of Slc2a4 decreases Slc2a4 expression in obesity and insulin resistance. We found that SLC2A4 expression in VAT of morbidly obese subjects with high HbA1c (>6.5%, n = 35) is decreased, whereas DNA methylation is concomitantly increased compared to morbidly obese subjects with low HbA1c (≤6.5%, n = 65). In diet-induced obese (DIO) mice, DNA methylation of Slc2a4 persistently increases with the onset of obesity and insulin resistance, while gene expression progressively decreases. The regulatory impact of DNA methylation in the investigated enhancer region on SLC2A4 gene expression was validated with a reporter gene assay. Additionally, treatment of 3T3 pre-adipocytes with palmitate/oleate during differentiation decreased DNA methylation and increased Slc2a4 expression. These findings highlight a potential regulation of Slc2a4 by DNA methylation in VAT, which is induced by fatty acids and may play a role in the progression of obesity and insulin resistance in humans.
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Camerota M, Davis JM, Dansereau LM, Oliveira EL, Padbury JF, Lester BM. Effects of Pharmacologic Treatment for Neonatal Abstinence Syndrome on DNA Methylation and Neurobehavior: A Prospective Cohort Study. J Pediatr 2022; 243:21-26. [PMID: 34971656 PMCID: PMC8960328 DOI: 10.1016/j.jpeds.2021.12.057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/17/2021] [Accepted: 12/19/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To determine whether pharmacologic treatment for neonatal abstinence syndrome (NAS) is associated with changes in DNA methylation (DNAm) of the mu-opioid receptor gene (OPRM1) and improvements in neonatal neurobehavior. STUDY DESIGN Buccal swabs were collected from 37 neonates before and after morphine treatment for NAS. Genomic DNA was extracted, and DNAm was examined at 4 cytosine-phosphate-guanine (CpG) sites within the OPRM1 gene. Assessment with the NICU Network Neurobehavioral Scales (NNNS) was also performed before and after NAS treatment. Changes in DNAm (DNAmpost-tx - DNAmpre-tx) and NNNS summary scores (NNNSpost-tx - NNNSpre-tx) were then calculated. Path analysis was used to examine associations among pharmacologic treatment (length of treatment [LOT] and total dose of morphine), changes in DNAm, and changes in NNNS summary scores. RESULTS DNAm was significantly decreased from pretreatment to post-treatment at 1 of 4 CpG sites within the OPRM1 gene. Neonates also demonstrated decreased excitability, hypertonia, lethargy, signs of stress and abstinence, and increased quality of movement and regulation from pretreatment to post-treatment. Longer LOT and higher morphine dose were associated with greater decreases in DNAm; greater decreases in DNAm were associated with greater decreases in excitability and hypertonia on the NNNS. CONCLUSIONS Pharmacologic treatment of NAS is associated with decreased DNAm of the OPRM1 gene and improved neonatal neurobehavior. Epigenetic changes may play a role in these changes in neonatal neurobehavior.
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Affiliation(s)
- Marie Camerota
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI; Department of Pediatrics, Women and Infants Hospital, Providence, RI.
| | - Jonathan M. Davis
- Department of Pediatrics, Tufts Children’s Hospital and the Tufts Clinical and Translational Science Institute, Boston, MA, USA
| | - Lynne M. Dansereau
- Department of Pediatrics, Women and Infants Hospital, Providence, RI, USA
| | - Erica L. Oliveira
- Department of Pediatrics, Women and Infants Hospital, Providence, RI, USA
| | - James F. Padbury
- Department of Pediatrics, Women and Infants Hospital, Providence, RI, USA
| | - Barry M. Lester
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI, USA,Department of Pediatrics, Women and Infants Hospital, Providence, RI, USA
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Shimada BK, Pomozi V, Zoll J, Kuo S, Martin L, Le Saux O. ABCC6, Pyrophosphate and Ectopic Calcification: Therapeutic Solutions. Int J Mol Sci 2021; 22:ijms22094555. [PMID: 33925341 PMCID: PMC8123679 DOI: 10.3390/ijms22094555] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/11/2022] Open
Abstract
Pathological (ectopic) mineralization of soft tissues occurs during aging, in several common conditions such as diabetes, hypercholesterolemia, and renal failure and in certain genetic disorders. Pseudoxanthoma elasticum (PXE), a multi-organ disease affecting dermal, ocular, and cardiovascular tissues, is a model for ectopic mineralization disorders. ABCC6 dysfunction is the primary cause of PXE, but also some cases of generalized arterial calcification of infancy (GACI). ABCC6 deficiency in mice underlies an inducible dystrophic cardiac calcification phenotype (DCC). These calcification diseases are part of a spectrum of mineralization disorders that also includes Calcification of Joints and Arteries (CALJA). Since the identification of ABCC6 as the “PXE gene” and the development of several animal models (mice, rat, and zebrafish), there has been significant progress in our understanding of the molecular genetics, the clinical phenotypes, and pathogenesis of these diseases, which share similarities with more common conditions with abnormal calcification. ABCC6 facilitates the cellular efflux of ATP, which is rapidly converted into inorganic pyrophosphate (PPi) and adenosine by the ectonucleotidases NPP1 and CD73 (NT5E). PPi is a potent endogenous inhibitor of calcification, whereas adenosine indirectly contributes to calcification inhibition by suppressing the synthesis of tissue non-specific alkaline phosphatase (TNAP). At present, therapies only exist to alleviate symptoms for both PXE and GACI; however, extensive studies have resulted in several novel approaches to treating PXE and GACI. This review seeks to summarize the role of ABCC6 in ectopic calcification in PXE and other calcification disorders, and discuss therapeutic strategies targeting various proteins in the pathway (ABCC6, NPP1, and TNAP) and direct inhibition of calcification via supplementation by various compounds.
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Affiliation(s)
- Briana K Shimada
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96817, USA
| | - Viola Pomozi
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 1117 Budapest, Hungary
| | - Janna Zoll
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96817, USA
| | - Sheree Kuo
- Department of Pediatrics, Kapi'olani Medical Center for Women and Children, University of Hawaii, Honolulu, HI 96826, USA
| | - Ludovic Martin
- PXE Consultation Center, MAGEC Reference Center for Rare Skin Diseases, Angers University Hospital, 49100 Angers, France
- BNMI, CNRS 6214/INSERM 1083, University Bretagne-Loire, 49100 Angers, France
| | - Olivier Le Saux
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96817, USA
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Taryma-Lesniak O, Sokolowska KE, Wojdacz TK. Short history of 5-methylcytosine: from discovery to clinical applications. J Clin Pathol 2021; 74:692-696. [PMID: 33431485 DOI: 10.1136/jclinpath-2020-206922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 12/22/2020] [Accepted: 12/27/2020] [Indexed: 12/15/2022]
Abstract
Covalent modifications of nucleotides in genetic material have been known from the beginning of the last century. Currently, one of those modifications referred to as DNA methylation, is impacting personalised medicine both as a treatment target and a biomarker source for clinical disease management. In this short review, we describe landmark discoveries that led to the elucidation of the DNA methylation importance in the cell's physiology and clarification of its role as one of the major processes in disease pathology. We also describe turning points in the development of methodologies to study this modification, which ultimately resulted in the development of in-vitro diagnostic kits targeting disease related DNA methylation changes as biomarkers.
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Affiliation(s)
- Olga Taryma-Lesniak
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Szczecin, Zachodniopomorskie, Poland
| | - Katarzyna Ewa Sokolowska
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Szczecin, Zachodniopomorskie, Poland
| | - Tomasz Kazimierz Wojdacz
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Szczecin, Zachodniopomorskie, Poland
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Krause C, Geißler C, Tackenberg H, El Gammal AT, Wolter S, Spranger J, Mann O, Lehnert H, Kirchner H. Multi-layered epigenetic regulation of IRS2 expression in the liver of obese individuals with type 2 diabetes. Diabetologia 2020; 63:2182-2193. [PMID: 32710190 PMCID: PMC7476982 DOI: 10.1007/s00125-020-05212-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 04/30/2020] [Indexed: 12/15/2022]
Abstract
AIMS/HYPOTHESIS IRS2 is an important molecular switch that mediates insulin signalling in the liver. IRS2 dysregulation is responsible for the phenomenon of selective insulin resistance that is observed in type 2 diabetes. We hypothesise that epigenetic mechanisms are involved in the regulation of IRS2 in the liver of obese and type 2 diabetic individuals. METHODS DNA methylation of seven CpG sites was studied by bisulphite pyrosequencing and mRNA and microRNA (miRNA) expression was assessed by quantitative real-time PCR in liver biopsies of 50 obese non-diabetic and 31 obese type 2 diabetic participants, in a cross-sectional setting. Methylation-sensitive luciferase assays and electrophoretic mobility shift assays were performed. Furthermore, HepG2 cells were treated with insulin and high glucose concentrations to induce miRNA expression and IRS2 downregulation. RESULTS We found a significant downregulation of IRS2 expression in the liver of obese individuals with type 2 diabetes (0.84 ± 0.08-fold change; p = 0.0833; adjusted p value [pa] = 0.0417; n = 31) in comparison with non-diabetic obese participants (n = 50). This downregulation correlated with hepatic IRS2 DNA methylation at CpG5. Additionally, CpG6, which is located in intron 1 of IRS2, was hypomethylated in type 2 diabetes; this site spans the sterol regulatory element binding transcription factor 1 (SREBF1) recognition motif, which likely acts as transcriptional repressor. The adjacent polymorphism rs4547213 (G>A) was significantly associated with DNA methylation at a specificity-protein-1 (SP1) binding site (CpG3). Moreover, DNA methylation of cg25924746, a CpG site located in the shore region of the IRS2 promoter-associated CpG island, was increased in the liver of individuals with type 2 diabetes, as compared with those without diabetes. A second epigenetic mechanism, upregulation of hepatic miRNA hsa-let-7e-5p (let-7e-5p) in obese individuals with type 2 diabetes (n = 29) vs non-diabetic obese individuals (n = 49) (1.2 ± 0.08-fold change; p = 0.0332; pa = 0.0450), is likely to act synergistically with altered IRS2 DNA methylation to decrease IRS2 expression. Mechanistic in vitro experiments demonstrated an acute upregulation of let-7e-5p expression and simultaneous IRS2 downregulation in a liver (HepG2) cell line upon hyperinsulinaemic and hyperglycaemic conditions. CONCLUSIONS/INTERPRETATION Our study highlights a new multi-layered epigenetic network that could be involved in subtle dysregulation of IRS2 in the liver of individuals with type 2 diabetes. This might lead to fine-tuning of IRS2 expression and is likely to be supplementary to the already known factors regulating IRS2 expression. Thereby, our findings could support the discovery of new diagnostic and therapeutic strategies for type 2 diabetes. Graphical abstract.
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Affiliation(s)
- Christin Krause
- First Department of Medicine, Division of Epigenetics and Metabolism, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Cathleen Geißler
- First Department of Medicine, Division of Epigenetics and Metabolism, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Heidi Tackenberg
- First Department of Medicine, Division of Epigenetics and Metabolism, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Alexander T El Gammal
- Department of General, Visceral and Thoracic Surgery, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Wolter
- Department of General, Visceral and Thoracic Surgery, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Joachim Spranger
- Department of Endocrinology and Metabolism, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Oliver Mann
- Department of General, Visceral and Thoracic Surgery, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Hendrik Lehnert
- First Department of Medicine, Division of Epigenetics and Metabolism, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Henriette Kirchner
- First Department of Medicine, Division of Epigenetics and Metabolism, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany.
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Tahira AC, Barbosa AR, Feltrin AS, Gastaldi VD, de Toledo VHC, de Carvalho Pereira JG, Lisboa BCG, de Souza Reis VN, dos Santos ACF, Maschietto M, Brentani H. Putative contributions of the sex chromosome proteins SOX3 and SRY to neurodevelopmental disorders. Am J Med Genet B Neuropsychiatr Genet 2019; 180:390-414. [PMID: 30537354 PMCID: PMC6767407 DOI: 10.1002/ajmg.b.32704] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 12/12/2022]
Abstract
The male-biased prevalence of certain neurodevelopmental disorders and the sex-biased outcomes associated with stress exposure during gestation have been previously described. Here, we hypothesized that genes distinctively targeted by only one or both homologous proteins highly conserved across therian mammals, SOX3 and SRY, could induce sexual adaptive changes that result in a differential risk for neurodevelopmental disorders. ChIP-seq/chip data showed that SOX3/SRY gene targets were expressed in different brain cell types in mice. We used orthologous human genes in rodent genomes to extend the number of SOX3/SRY set (1,721). These genes were later found to be enriched in five modules of coexpressed genes during the early and mid-gestation periods (FDR < 0.05), independent of sexual hormones. Genes with differential expression (24, p < 0.0001) and methylation (40, p < 0.047) between sexes were overrepresented in this set. Exclusive SOX3 or SRY target genes were more associated with the late gestational and postnatal periods. Using autism as a model sex-biased disorder, the SOX3/SRY set was enriched in autism gene databases (FDR ≤ 0.05), and there were more de novo variations from the male autism spectrum disorder (ASD) samples under the SRY peaks compared to the random peaks (p < 0.024). The comparison of coexpressed networks of SOX3/SRY target genes between male autism and control samples revealed low preservation in gene modules related to stress response (99 genes) and neurogenesis (78 genes). This study provides evidence that while SOX3 is a regulatory mechanism for both sexes, the male-exclusive SRY also plays a role in gene regulation, suggesting a potential mechanism for sex bias in ASD.
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Affiliation(s)
- Ana Carolina Tahira
- LIM23, Instituto de Psiquiatria, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao PauloSao PauloSPBrazil
| | - André Rocha Barbosa
- LIM23, Instituto de Psiquiatria, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao PauloSao PauloSPBrazil
- Inter‐institutional Grad Program on BioinformaticsUniversity of São PauloSão PauloSPBrazil
| | | | - Vinicius Daguano Gastaldi
- LIM23, Instituto de Psiquiatria, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao PauloSao PauloSPBrazil
| | - Victor Hugo Calegari de Toledo
- LIM23, Instituto de Psiquiatria, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao PauloSao PauloSPBrazil
| | | | - Bianca Cristina Garcia Lisboa
- LIM23, Instituto de Psiquiatria, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao PauloSao PauloSPBrazil
| | - Viviane Neri de Souza Reis
- LIM23, Instituto de Psiquiatria, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao PauloSao PauloSPBrazil
| | - Ana Cecília Feio dos Santos
- LIM23, Instituto de Psiquiatria, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao PauloSao PauloSPBrazil
- Laboratório de Pesquisas Básicas em Malária – EntomologiaSeção de Parasitologia – Instituto Evandro Chagas/SVS/MSAnanindeuaPABrazil
| | - Mariana Maschietto
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasSPBrazil
| | - Helena Brentani
- LIM23, Instituto de Psiquiatria, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao PauloSao PauloSPBrazil
- Inter‐institutional Grad Program on BioinformaticsUniversity of São PauloSão PauloSPBrazil
- Instituto de Psiquiatria, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao PauloSPBrazil
- National Institute of Developmental Psychiatry for Children and Adolescents (INPD)Sao PauloSPBrazil
- Faculdade de Medicina FMUSPUniversidade de Sao PauloSao PauloSPBrazil
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10
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Feng W, Zhou L, Wang H, Hu Z, Wang X, Fu J, Wang A, Liu JF. Functional analysis of DNA methylation of the PACSIN1 promoter in pig peripheral blood mononuclear cells. J Cell Biochem 2018; 120:10118-10127. [PMID: 30537176 DOI: 10.1002/jcb.28295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 10/22/2018] [Indexed: 12/19/2022]
Abstract
DNA methylation plays essential roles in regulating the activity of genes and may contribute to understanding the potential epigenetic biomarkers response to viruses. To explore the function of DNA methylation of protein kinase C and casein kinase substrate in neurons 1 (PACSNI1) promoter, herein we performed the bisulfite sequencing polymerase chain reaction and Western blot analysis to verify hypermethylation and downregulation of PACSIN1 expression in peripheral blood mononuclear cells of pig as the vitro model. Promoter methylation could reduce the transcriptional activity of the PACSIN1 gene potentially by affecting the binding of transcription factor Sp1. In addition, downregulation of the PACSIN1 gene expression could facilitate the production of interleukin-6 (IL-6), IL-8, tumor necrosis factor α, and NECAP2. The comprehensive analysis of PACSIN1 methylation and its function will help us to understand the gene to be served as an important candidate gene in pig for disease resistance breeding and aid in the identification of potential epigenetic biomarkers associated with responsiveness to viruses.
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Affiliation(s)
- Wen Feng
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lei Zhou
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haifei Wang
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China.,Department of Animal Genetics, Breeding and Reproduction and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhengzheng Hu
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaomei Wang
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jianlian Fu
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Aiguo Wang
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding; Department of Animal genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, China
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11
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J J, Vanisree AJ, Ravisankar S, K R. Site specific hypermethylation of CpGs in Connexin genes 30, 26 and 43 in different grades of glioma and attenuated levels of their mRNAs. Int J Neurosci 2018; 129:273-282. [PMID: 30280947 DOI: 10.1080/00207454.2018.1526802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
AIM Gliomas, the intracranial tumours are considered the deadliest malignancies. The gap junctional Connexins (Cxs) that maintain cellular homeostasis perform a unique function in glial tumour suppression. However, the differential methylation patterns of Cxs were not revealed in glioma so far. The current study attempts to categorise promoter methylation of Cx30 and Cx26 and intron methylation of Cx43 in different grades of human glioma. MATERIALS AND METHODS About 85 glioma patients with pathologically confirmed grades and 15 control brain tissues were recruited in the study. Bisulphite-PCR-Single Stranded Conformation analysis(SSCA), Bisulphite sequencing and MeDIP-qPCR were carried out to assess methylation status and Cx mRNA levels were also analysed to evaluate the effect of methylation. RESULTS We found that promoter CpG islands(CpGs) reside in Sp1 and Ap2 sites of Cx30 and 26 were hypermethylated in high grades (HG) of glioma rather than low grades. The input % of both was significantly increased (p < 0.03) in progressive grades. Interestingly, Cx43 could exhibit a significant increase (p < 0.05) in input % only in grade IV. While, Cx30 and 26 mRNAs were downregulated according to their methylation status in progressive fashion with grades, Cx43 was downregulated irrespective of intron methylation. CONCLUSION Thus, we suggest that the sites and extent of methylation of Cxs (30 and 26 but not in 43) are found to be altered. In different grades of glioma can provide better appreciation of the grade of the patient and might help in strategies based on epigenetic approaches.
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Affiliation(s)
- Jayalakshmi J
- a Department of Biochemistry , University of Madras , Chennai , Tamilnadu , India
| | | | - Shantha Ravisankar
- b Department of Neuropathology , Tamilnadu Multispeciality Hospital , Chennai , Tamilnadu , India
| | - Rama K
- c Department of Neuropathology , Madras Medical College and Government General hospital , Chennai , Tamilnadu , India
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12
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Hu XQ, Chen M, Dasgupta C, Xiao D, Huang X, Yang S, Zhang L. Chronic hypoxia upregulates DNA methyltransferase and represses large conductance Ca2+-activated K+ channel function in ovine uterine arteries. Biol Reprod 2018; 96:424-434. [PMID: 28203702 DOI: 10.1095/biolreprod.116.145946] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/23/2016] [Accepted: 12/19/2016] [Indexed: 01/06/2023] Open
Abstract
Chronic hypoxia during gestation suppresses large-conductance Ca2+-activated K+ (BKCa) channel function and impedes uterine arterial adaptation to pregnancy. This study tested the hypothesis that chronic hypoxia has a direct effect in upregulating DNA methyltransferase (DNMT) and epigenetically repressing BKCa channel beta-1 subunit (KCNMB1) expression in uterine arteries. Resistance-sized uterine arteries were isolated from near-term pregnant sheep maintained at ∼300 m above sea level or animals acclimatized to high-altitude (3,801 m) hypoxia for 110 days during gestation. For ex vivo hypoxia treatment, uterine arteries from normoxic animals were treated with 21.0% O2 or 10.5% O2 for 48 h. High-altitude hypoxia significantly upregulated DNMT3b expression and enzyme activity in uterine arteries. Similarly, ex vivo hypoxia treatment upregulated DNMT3b expression and enzyme activity that was blocked by a DNMT inhibitor 5-aza-2'-deoxycytidine (5-Aza). Of importance, 5-Aza inhibited hypoxia-induced hypermethylation of specificity protein (SP) 1 binding site at the KCNMB1 promoter and restored transcription factor binding to the KCNMB1 promoter, resulting in the recovery of KCNMB1 gene expression in uterine arteries. Furthermore, 5-Aza blocked the effect of hypoxia and rescued BKCa channel activity and reversed hypoxia-induced decrease in BKCa channel-mediated relaxations and increase in myogenic tone of uterine arteries. Collectively, these results suggest that chronic hypoxia during gestation upregulates DNMT expression and activity, resulting in hypermethylation and repression of KCNMB1 gene and BKCa channel function, impeding uterine arterial adaptation to pregnancy.
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Affiliation(s)
- Xiang-Qun Hu
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California, USA
| | - Man Chen
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California, USA
| | - Chiranjib Dasgupta
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California, USA
| | - Daliao Xiao
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California, USA
| | - Xiaohui Huang
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California, USA
| | - Shumei Yang
- Department of Chemistry and Biochemistry, California State University, San Bernardino, California, USA
| | - Lubo Zhang
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California, USA
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13
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Wachman EM, Hayes MJ, Shrestha H, Nikita FNU, Nolin A, Hoyo L, Daigle K, Jones HE, Nielsen DA. Epigenetic variation in OPRM1
gene in opioid-exposed mother-infant dyads. GENES BRAIN AND BEHAVIOR 2018; 17:e12476. [DOI: 10.1111/gbb.12476] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/02/2018] [Accepted: 03/20/2018] [Indexed: 12/17/2022]
Affiliation(s)
- E. M. Wachman
- Department of Pediatrics; Boston Medical Center; Boston Massachusetts
| | - M. J. Hayes
- Department of Psychology; Graduate School of Biomedical Sciences & Engineering, University of Maine; Orono Maine
| | - H. Shrestha
- Department of Pediatrics; Boston Medical Center; Boston Massachusetts
| | - F. N. U. Nikita
- Boston University School of Public Health; Boston Massachusetts
| | - A. Nolin
- Boston University School of Medicine; Boston Massachusetts
| | - L. Hoyo
- Boston University School of Medicine; Boston Massachusetts
| | - K. Daigle
- Department of Adolescent and Young Adult Medicine; Boston Children's Hospital; Boston Massachusetts
| | - H. E. Jones
- UNC Horizons, Department of Obstetrics and Gynecology; University of North Carolina at Chapel Hill; Chapel Hill North Carolina
- Department of Psychiatry and Behavioral Sciences and Obstetrics and Gynecology; School of Medicine, Johns Hopkins University; Baltimore Maryland
- Department of Obstetrics and Gynecology; School of Medicine, Johns Hopkins University; Baltimore Maryland
| | - D. A. Nielsen
- Menninger Department of Psychiatry and Behavioral Sciences; Baylor College of Medicine; Houston Texas
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14
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Yao L, Gu J, Mao Y, Zhang X, Wang X, Jin C, Fu D, Li J. Dynamic quantitative detection of ABC transporter family promoter methylation by MS-HRM for predicting MDR in pancreatic cancer. Oncol Lett 2018; 15:5602-5610. [PMID: 29552197 PMCID: PMC5840752 DOI: 10.3892/ol.2018.8041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 09/01/2017] [Indexed: 12/11/2022] Open
Abstract
The main focus of the present study was to evaluate whether ABC transporter family promoter methylation predicted multidrug resistance in gemcitabine-resistant cancer cell lines (BxPC-3/Gem and PANC-1/Gem). Using low concentrations of gemcitabine, the cell lines acquired drug resistance with different initial gemcitabine concentrations. A novel technology, methylation-sensitive high-resolution melting, was used to monitor the dynamic changes of ABC transporter family promoter methylation, including ATP binding cassette subfamily B member 1 (ABCB1), ATP binding cassette subfamily C (ABCC) and ATP binding cassette subfamily G member 2 (ABCG2) mRNA expression. It was revealed that, with elevation of initial gemcitabine concentration, expression of ABCB1, ABCC and ABCG2 mRNA and corresponding downstream proteins was increased while promoter methylation was decreased. These discoveries indicate that promoter methylation of ABCB1, ABCC and ABCG2 may be a valuable indicator of drug-resistance characteristics in BxPC-3/Gem and PANC-1/Gem cells via quantitative and simultaneous detection. These results also implied that MDR in pancreatic cancer not only arises from gene mutation, but also originates from promoter methylation.
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Affiliation(s)
- Lie Yao
- Department of Pancreatic Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Jichun Gu
- Department of Pancreatic Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Yishen Mao
- Department of Clinical Medicine, Fudan University, Shanghai 200082, P.R. China
| | - Xinju Zhang
- Central Laboratory, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Xiaoyi Wang
- Department of Pancreatic Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Chen Jin
- Department of Pancreatic Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Deliang Fu
- Department of Pancreatic Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
| | - Ji Li
- Department of Pancreatic Surgery, Huashan Hospital, Fudan University, Shanghai 200040, P.R. China
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15
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Alisch RS, Van Hulle C, Chopra P, Bhattacharyya A, Zhang SC, Davidson RJ, Kalin NH, Goldsmith HH. A multi-dimensional characterization of anxiety in monozygotic twin pairs reveals susceptibility loci in humans. Transl Psychiatry 2017; 7:1282. [PMID: 29225348 PMCID: PMC5802687 DOI: 10.1038/s41398-017-0047-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/13/2017] [Indexed: 02/06/2023] Open
Abstract
The etiology of individual differences in human anxiousness is complex and includes contributions from genetic, epigenetic (i.e., DNA methylation) and environmental factors. Past genomic approaches have been limited in their ability to detect human anxiety-related differences in these factors. To overcome these limitations, we employed both a multi-dimensional characterization method, to select monozygotic twin pairs discordant for anxiety, and whole genome DNA methylation sequencing. This approach revealed 230 anxiety-related differentially methylated loci that were annotated to 183 genes, including several known stress-related genes such as NAV1, IGF2, GNAS, and CRTC1. As an initial validation of these findings, we tested the significance of an overlap of these data with anxiety-related differentially methylated loci that we previously reported from a key neural circuit of anxiety (i.e., the central nucleus of the amygdala) in young monkeys and found a significant overlap (P-value < 0.05) of anxiety-related differentially methylated genes, including GNAS, SYN3, and JAG2. Finally, sequence motif predictions of all the human differentially methylated regions indicated an enrichment of five transcription factor binding motifs, suggesting that DNA methylation may regulate gene expression by mediating transcription factor binding of these transcripts. Together, these data demonstrate environmentally sensitive factors that may underlie the development of human anxiety.
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Affiliation(s)
- Reid S Alisch
- Departments of Psychiatry, University of Wisconsin, Madison, WI, USA.
- Neuroscience Training Program, University of Wisconsin, Madison, WI, USA.
| | | | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Su-Chun Zhang
- Neuroscience Training Program, University of Wisconsin, Madison, WI, USA
- Waisman Center, University of Wisconsin, Madison, WI, USA
- Departments of Neuroscience, University of Wisconsin, Madison, WI, USA
- Departments of Neurology, University of Wisconsin, Madison, WI, USA
| | - Richard J Davidson
- Departments of Psychiatry, University of Wisconsin, Madison, WI, USA
- Neuroscience Training Program, University of Wisconsin, Madison, WI, USA
- Waisman Center, University of Wisconsin, Madison, WI, USA
- Departments of Psychology, University of Wisconsin, Madison, WI, USA
- Center for Healthy Minds, Madison, WI, USA
| | - Ned H Kalin
- Departments of Psychiatry, University of Wisconsin, Madison, WI, USA
- Neuroscience Training Program, University of Wisconsin, Madison, WI, USA
| | - H Hill Goldsmith
- Waisman Center, University of Wisconsin, Madison, WI, USA.
- Departments of Psychology, University of Wisconsin, Madison, WI, USA.
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16
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Huo X, Li Z, Zhang S, Li C, Guo M, Lu J, Lv J, Du X, Chen Z. Analysis of the expression level and methylation of tumor protein p53, phosphatase and tensin homolog and mutS homolog 2 in N-methyl-N-nitrosourea-induced thymic lymphoma in C57BL/6 mice. Oncol Lett 2017; 14:4339-4348. [PMID: 28943948 DOI: 10.3892/ol.2017.6721] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 05/23/2017] [Indexed: 12/29/2022] Open
Abstract
Tumorigenesis is often caused by somatic mutation or epigenetic changes in genes that regulate aspects of cell death, proliferation and survival. Although the functions of multiple tumor suppressor genes have been well studied in isolation, how these genes cooperate during the progression of a single tumor remains unclear in numerous cases. The present study used N-methyl-N-nitrosourea (MNU), one of the most potent mutagenic nitrosourea compounds, to induce thymic lymphoma in C57BL/6J mice. Subsequently, the protein expression levels of phosphatase and tensin homolog (PTEN), transformation protein 53 and mutS homolog 2 (MSH2) were evaluated concomitantly in the thymus, liver, kidney and spleen of MNU-treated mice by western blotting. To determine whether changes in expression level were due to aberrant epigenetic regulation, the present study further examined the methylation status of each gene by MassARRAY analysis. During the tumorigenesis process of an MNU-induced single thymic lymphoma, the expression level of PTEN was revealed to be reduced in thymic lymphoma samples but not in normal or non-tumor thymus tissue samples. Furthermore, a marked reduction of P53 expression levels were demonstrated in thymic lymphomas and spleens with a metastatic tumor. Conversely, MSH2 upregulation was identified only in liver, kidney, and spleen samples that were infiltrated by thymic lymphoma cells. Furthermore, the present study revealed that a number of 5'-C-phosphate-G-3' sites located in the promoter of aberrantly expressed genes had significantly altered methylation statuses. These results improve the understanding of the course of mutagen-induced cancer, and highlight that epigenetic regulation may serve an important function in cancer.
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Affiliation(s)
- Xueyun Huo
- Department of Medical Genetics, School of Basic Medical Science, Capital Medical University, Beijing 100069, P.R. China
| | - Zhenkun Li
- Department of Medical Genetics, School of Basic Medical Science, Capital Medical University, Beijing 100069, P.R. China
| | - Shuangyue Zhang
- Department of Medical Genetics, School of Basic Medical Science, Capital Medical University, Beijing 100069, P.R. China
| | - Changlong Li
- Department of Medical Genetics, School of Basic Medical Science, Capital Medical University, Beijing 100069, P.R. China
| | - Meng Guo
- Department of Medical Genetics, School of Basic Medical Science, Capital Medical University, Beijing 100069, P.R. China
| | - Jing Lu
- Department of Medical Genetics, School of Basic Medical Science, Capital Medical University, Beijing 100069, P.R. China
| | - Jianyi Lv
- Department of Medical Genetics, School of Basic Medical Science, Capital Medical University, Beijing 100069, P.R. China
| | - Xiaoyan Du
- Department of Medical Genetics, School of Basic Medical Science, Capital Medical University, Beijing 100069, P.R. China
| | - Zhenwen Chen
- Department of Medical Genetics, School of Basic Medical Science, Capital Medical University, Beijing 100069, P.R. China
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17
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Chuang JY, Lo WL, Ko CY, Chou SY, Chen RM, Chang KY, Hung JJ, Su WC, Chang WC, Hsu TI. Upregulation of CYP17A1 by Sp1-mediated DNA demethylation confers temozolomide resistance through DHEA-mediated protection in glioma. Oncogenesis 2017; 6:e339. [PMID: 28530704 PMCID: PMC5523064 DOI: 10.1038/oncsis.2017.31] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 02/15/2017] [Accepted: 03/27/2017] [Indexed: 12/13/2022] Open
Abstract
Steroidogenesis-mediated production of neurosteroids is important for brain homeostasis. Cytochrome P450 17A1 (CYP17A1), which converts pregnenolone to dehydroepiandrosterone (DHEA) in endocrine organs and the brain, is required for prostate cancer progression and acquired chemotherapeutic resistance. However, whether CYP17A1-mediated DHEA synthesis is involved in brain tumor malignancy, especially in glioma, the most prevalent brain tumor, is unknown. To investigate the role of CYP17A1 in glioma, we determined that CYP17A1 expression is significantly increased in gliomas, which secrete more DHEA than normal astrocytes. We found that as gliomas became more malignant, both CYP17A1 and DHEA were significantly upregulated in temozolomide (TMZ)-resistant cells and highly invasive cells. In particular, the increase of CYP17A1 was caused by Sp1-mediated DNA demethylation, whereby Sp1 competed with DNMT3a for binding to the CYP17A1 promoter in TMZ-resistant glioma cells. CYP17A1 was required for the development of glioma cell invasiveness and resistance to TMZ-induced cytotoxicity. In addition, DHEA markedly attenuated TMZ-induced DNA damage and apoptosis. Together, our results suggest that components of the Sp1-CYP17A1-DHEA axis, which promotes the development of TMZ resistance, may serve as potential biomarkers and therapeutic targets in recurrent glioma.
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Affiliation(s)
- J-Y Chuang
- The Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei, Taiwan.,Comprehensive Cancer Center, Taipei Medical University, Taipei, Taiwan
| | - W-L Lo
- The Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei, Taiwan.,Division of Neurosurgery, Taipei Medical University-Shuang-Ho Hospital, Taipei, Taiwan
| | - C-Y Ko
- The Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei, Taiwan.,Comprehensive Cancer Center, Taipei Medical University, Taipei, Taiwan
| | - S-Y Chou
- The Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei, Taiwan.,Comprehensive Cancer Center, Taipei Medical University, Taipei, Taiwan
| | - R-M Chen
- Comprehensive Cancer Center, Taipei Medical University, Taipei, Taiwan.,Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - K-Y Chang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - J-J Hung
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - W-C Su
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - W-C Chang
- The Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei, Taiwan.,Comprehensive Cancer Center, Taipei Medical University, Taipei, Taiwan.,Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - T-I Hsu
- The Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei, Taiwan.,Comprehensive Cancer Center, Taipei Medical University, Taipei, Taiwan.,Center for Neurotrauma and Neuroregeneration, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
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18
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Neri F, Rapelli S, Krepelova A, Incarnato D, Parlato C, Basile G, Maldotti M, Anselmi F, Oliviero S. Intragenic DNA methylation prevents spurious transcription initiation. Nature 2017; 543:72-77. [PMID: 28225755 DOI: 10.1038/nature21373] [Citation(s) in RCA: 455] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/05/2017] [Indexed: 12/12/2022]
Abstract
In mammals, DNA methylation occurs mainly at CpG dinucleotides. Methylation of the promoter suppresses gene expression, but the functional role of gene-body DNA methylation in highly expressed genes has yet to be clarified. Here we show that, in mouse embryonic stem cells, Dnmt3b-dependent intragenic DNA methylation protects the gene body from spurious RNA polymerase II entry and cryptic transcription initiation. Using different genome-wide approaches, we demonstrate that this Dnmt3b function is dependent on its enzymatic activity and recruitment to the gene body by H3K36me3. Furthermore, the spurious transcripts can either be degraded by the RNA exosome complex or capped, polyadenylated, and delivered to the ribosome to produce aberrant proteins. Elongating RNA polymerase II therefore triggers an epigenetic crosstalk mechanism that involves SetD2, H3K36me3, Dnmt3b and DNA methylation to ensure the fidelity of gene transcription initiation, with implications for intragenic hypomethylation in cancer.
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Affiliation(s)
- Francesco Neri
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Stefania Rapelli
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
| | - Anna Krepelova
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
| | - Danny Incarnato
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
| | - Caterina Parlato
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
| | - Giulia Basile
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
| | - Mara Maldotti
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
| | - Francesca Anselmi
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
| | - Salvatore Oliviero
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
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19
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Ebrahimi G, Asadikaram G, Akbari H, Nematollahi MH, Abolhassani M, Shahabinejad G, Khodadadnejad L, Hashemi M. Elevated levels of DNA methylation at the OPRM1 promoter region in men with opioid use disorder. THE AMERICAN JOURNAL OF DRUG AND ALCOHOL ABUSE 2017; 44:193-199. [DOI: 10.1080/00952990.2016.1275659] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Ghasem Ebrahimi
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
- Department of Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Gholamreza Asadikaram
- Endocrinology and Metabolism Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
- Department of Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hamed Akbari
- Endocrinology and Metabolism Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
- Department of Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | | | - Moslem Abolhassani
- Department of Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Gholamabbas Shahabinejad
- Department of Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Leyla Khodadadnejad
- Physiology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Hashemi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences. Zahedan, Iran
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20
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Sølvsten CAE, de Paoli F, Christensen JH, Nielsen AL. Voluntary Physical Exercise Induces Expression and Epigenetic Remodeling of VegfA in the Rat Hippocampus. Mol Neurobiol 2016; 55:567-582. [DOI: 10.1007/s12035-016-0344-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/02/2016] [Indexed: 12/22/2022]
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21
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Pomozi V, Brampton C, Szeri F, Dedinszki D, Kozák E, van de Wetering K, Hopkins H, Martin L, Váradi A, Le Saux O. Functional Rescue of ABCC6 Deficiency by 4-Phenylbutyrate Therapy Reduces Dystrophic Calcification in Abcc6 -/- Mice. J Invest Dermatol 2016; 137:595-602. [PMID: 27826008 DOI: 10.1016/j.jid.2016.10.035] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 10/04/2016] [Accepted: 10/13/2016] [Indexed: 12/16/2022]
Abstract
Soft-tissue calcification is associated with aging, common conditions such as diabetes or hypercholesterolemia, and with certain genetic disorders. ABCC6 is an efflux transporter primarily expressed in liver facilitating the release of adenosine triphosphate from hepatocytes. Within the liver vasculature, adenosine triphosphate is converted into pyrophosphate, a major inhibitor of ectopic calcification. ABCC6 mutations thus lead to reduced plasma pyrophosphate levels, resulting in the calcification disorder pseudoxanthoma elasticum and some cases of generalized arterial calcification of infancy. Most mutations in ABCC6 are missense, and many preserve transport activity but are retained intracellularly. We have previously shown that the chemical chaperone 4-phenylbutyrate (4-PBA) promotes the maturation of ABCC6 mutants to the plasma membrane. In a humanized mouse model of pseudoxanthoma elasticum, we investigated whether 4-PBA treatments could rescue the calcification inhibition potential of selected ABCC6 mutants. We used the dystrophic cardiac calcification phenotype of Abcc6-/- mice as an indicator of ABCC6 function to quantify the effect of 4-PBA on human ABCC6 mutants transiently expressed in the liver. We showed that 4-PBA administrations restored the physiological function of ABCC6 mutants, resulting in enhanced calcification inhibition. This study identifies 4-PBA treatment as a promising strategy for allele-specific therapy of ABCC6-associated calcification disorders.
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Affiliation(s)
- Viola Pomozi
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Christopher Brampton
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA
| | - Flóra Szeri
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Dóra Dedinszki
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Eszter Kozák
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Koen van de Wetering
- Division of Molecular Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hi'ilani Hopkins
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA
| | - Ludovic Martin
- University of Angers, Angers, France; CHU Angers, Centre de consultation PXE, Angers, France
| | - András Váradi
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary
| | - Olivier Le Saux
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii, USA.
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22
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Liu X, Zhou P, Fan F, Li D, Wu J, Lu Y, Luo Y. CpG site methylation in CRYAA promoter affect transcription factor Sp1 binding in human lens epithelial cells. BMC Ophthalmol 2016; 16:141. [PMID: 27507241 PMCID: PMC4979130 DOI: 10.1186/s12886-016-0309-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 07/28/2016] [Indexed: 10/26/2022] Open
Abstract
BACKGROUND Age-related cataract (ARC) is the leading cause of visual impairment worldwide, and α-crystallin (CRYAA) is the predominant structural protein involved in the maintenance of lens clarity and refractive properties. We previously demonstrated that CRYAA genes undergo epigenetic repression in the lens epithelia in ARC. We further analyze the underlying mechanism in the current study. METHODS The transcription factor binding sites of the CpG island of CRYAA promoter were predicted by TESS website. An electrophoretic mobility shift assay (EMSA) was used to analyze the impact of the methylation of CpG sites on transcription factors. Human lens epithelial B-3 (HLE B-3) Cells were treated with demethylation agent zebularine in the concentrations of 0 (PBS as control), 10 μM, 20 μM, 50 μM, 100 μM and 200 μM, respectively. After treatment in the above concentrations for 24 h, 48 h and 72 h, respectively, CRYAA mRNA expression levels were detected by Quantitative Real-Time RT-PCR. RESULTS The methylation of the CpG site of the CRYAA promoter decreased the DNA-binding capacity of transcription factor Sp1. Zebularine increased CRYAA expression in HLE B-3 Cells in a dose- dependent and time- dependent pattern. CONCLUSIONS The evidence presented suggests that the methylation of the CpG sites of the CRYAA promotor directly affect Sp1 binding, leading to down expression of CRYAA in human lens epithelial cells. Zebularine treatment could restore CRYAA expression in a dose- dependent and time- dependent pattern.
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Affiliation(s)
- Xin Liu
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China.,Key Laboratory of Myopia, Ministry of Health, 83 FenYang Road, Shanghai, 200031, People's Republic of China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China
| | - Peng Zhou
- Department of Ophthalmology, Parkway Health, Specialty and Inpatient Center (Luwan), 170 DanShui Road, Floor 3, Shanghai, 200020, People's Republic of China.,Hong Qiao Medical Center, 2258 HongQiao Road, Shanghai, 200033, People's Republic of China
| | - Fan Fan
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China.,Key Laboratory of Myopia, Ministry of Health, 83 FenYang Road, Shanghai, 200031, People's Republic of China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China
| | - Dan Li
- Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China
| | - Jihong Wu
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China
| | - Yi Lu
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China.,Key Laboratory of Myopia, Ministry of Health, 83 FenYang Road, Shanghai, 200031, People's Republic of China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China
| | - Yi Luo
- Department of Ophthalmology, Eye and ENT Hospital of Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China. .,Key Laboratory of Myopia, Ministry of Health, 83 FenYang Road, Shanghai, 200031, People's Republic of China. .,Shanghai Key Laboratory of Visual Impairment and Restoration, Fudan University, 83 FenYang Road, Shanghai, 200031, People's Republic of China.
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23
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Butcher LM, Ito M, Brimpari M, Morris TJ, Soares FAC, Ährlund-Richter L, Carey N, Vallier L, Ferguson-Smith AC, Beck S. Non-CG DNA methylation is a biomarker for assessing endodermal differentiation capacity in pluripotent stem cells. Nat Commun 2016; 7:10458. [PMID: 26822956 PMCID: PMC4740175 DOI: 10.1038/ncomms10458] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/11/2015] [Indexed: 01/07/2023] Open
Abstract
Non-CG methylation is an unexplored epigenetic hallmark of pluripotent stem cells. Here we report that a reduction in non-CG methylation is associated with impaired differentiation capacity into endodermal lineages. Genome-wide analysis of 2,670 non-CG sites in a discovery cohort of 25 phenotyped human induced pluripotent stem cell (hiPSC) lines revealed unidirectional loss (Δβ=13%, P<7.4 × 10(-4)) of non-CG methylation that correctly identifies endodermal differentiation capacity in 23 out of 25 (92%) hiPSC lines. Translation into a simplified assay of only nine non-CG sites maintains predictive power in the discovery cohort (Δβ=23%, P<9.1 × 10(-6)) and correctly identifies endodermal differentiation capacity in nine out of ten pluripotent stem cell lines in an independent replication cohort consisting of hiPSCs reprogrammed from different cell types and different delivery systems, as well as human embryonic stem cell (hESC) lines. This finding infers non-CG methylation at these sites as a biomarker when assessing endodermal differentiation capacity as a readout.
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Affiliation(s)
- Lee M Butcher
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Mitsuteru Ito
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Minodora Brimpari
- Anne McLaren Laboratory, Department of Surgery, Wellcome Trust and Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Tiffany J Morris
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
- Cambridge Epigenetix, Jonas Webb Building, Babraham Campus, Cambridge CB22 3AT, UK
| | - Filipa A C Soares
- Anne McLaren Laboratory, Department of Surgery, Wellcome Trust and Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Lars Ährlund-Richter
- Division of Paediatric Oncology, Department of Women's and Children's Health, Karolinska Institutet,171 76 Stockholm, Sweden
| | - Nessa Carey
- PraxisUnico, The Jeffreys Building, St John's Innovation Park, Cambridge CB4 0DE, UK
| | - Ludovic Vallier
- Anne McLaren Laboratory, Department of Surgery, Wellcome Trust and Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | | | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
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24
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Menschikowski M, Hagelgans A, Nacke B, Jandeck C, Mareninova OA, Asatryan L, Siegert G. Epigenetic control of group V phospholipase A2 expression in human malignant cells. Tumour Biol 2015; 37:8097-105. [PMID: 26715269 DOI: 10.1007/s13277-015-4670-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 12/16/2015] [Indexed: 12/27/2022] Open
Abstract
Secreted phospholipases A2 (sPLA2) are suggested to play an important role in inflammation and tumorigenesis. Different mechanisms of epigenetic regulation are involved in the control of group IIA, III and X sPLA2s expression in cancer cells, but group V sPLA2 (GV-PLA2) in this respect has not been studied. Here, we demonstrate the role of epigenetic mechanisms in regulation of GV-PLA2 expression in different cell lines originating from leukaemia and solid cancers. In blood leukocytes from leukaemic patients, levels of GV-PLA2 transcripts were significantly lower in comparison to those from healthy individuals. Similarly, in DU-145 and PC-3 prostate and CAL-51 and MCF-7 mammary cancer cell lines, levels of GV-PLA2 transcripts were significantly lower in relation to those found in normal epithelial cells of prostate or mammary. By sequencing and methylation-specific high-resolution melting (MS-HRM) analyses of bisulphite-modified DNA, distinct CpG sites in the GV-PLA2 promoter region were identified that were differentially methylated in cancer cells in comparison to normal epithelial and endothelial cells. Spearman rank order analysis revealed a significant negative correlation between the methylation degree and the cellular expression of GV-PLA2 (r = -0.697; p = 0.01). The effects of demethylating agent (5-aza-2'-deoxycytidine) and histone deacetylase inhibitor (trichostatin A) on GV-PLA2 transcription in the analysed cells confirmed the importance of DNA methylation and histone modification in the regulation of the GV-PLA2 gene expression in leukaemic, prostate and mammary cancer cell lines. The exposure of tumour cells to human recombinant GV-PLA2 resulted in a reduced colony forming activity of MCF-7, HepG2 and PC-3 cells, but not of DU-145 cells suggesting a cell-type-dependent effect of GV-PLA2 on cell growth. In conclusion, our results suggest that epigenetic mechanisms such as DNA methylation and histone modification play an important role in downregulation of GV-PLA2 expression in cancer cells.
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Affiliation(s)
- Mario Menschikowski
- Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Fetscherstr. 74, D-01307, Dresden, Germany.
| | - Albert Hagelgans
- Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Fetscherstr. 74, D-01307, Dresden, Germany
| | - Brit Nacke
- Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Fetscherstr. 74, D-01307, Dresden, Germany
| | - Carsten Jandeck
- Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Fetscherstr. 74, D-01307, Dresden, Germany
| | - Olga A Mareninova
- Veterans Affairs Greater Los Angeles Healthcare System and University of California at Los Angeles, Los Angeles, CA, USA
| | - Liana Asatryan
- Titus Family Department of Clinical Pharmacy, USC School of Pharmacy, Los Angeles, CA, USA
| | - Gabriele Siegert
- Institute of Clinical Chemistry and Laboratory Medicine, Carl Gustav Carus University Hospital, Technical University of Dresden, Fetscherstr. 74, D-01307, Dresden, Germany
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25
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Ramboer E, Rogiers V, Vanhaecke T, Vinken M. Effects of Trichostatin A on drug uptake transporters in primary rat hepatocyte cultures. EXCLI JOURNAL 2015; 14:567-76. [PMID: 26648816 PMCID: PMC4669911 DOI: 10.17179/excli2015-220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 03/30/2015] [Indexed: 11/10/2022]
Abstract
The present study was set up to investigate the effects of Trichostatin A (TSA), a prototypical epigenetic modifier, on the expression and activity of hepatic drug uptake transporters in primary cultured rat hepatocytes. To this end, the expression of the sinusoidal transporters sodium-dependent taurocholate cotransporting polypeptide (Ntcp) and organic anion transporting polypeptide 4 (Oatp4) was monitored by real-time quantitative reverse transcriptase polymerase chain reaction analysis and immunoblotting. The activity of the uptake transporters was analyzed using radiolabeled substrates and chemical inhibitors. Downregulation of the expression and activity of Oatp4 and Ntcp was observed as a function of the cultivation time and could not be counteracted by TSA. In conclusion, the epigenetic modifier TSA does not seem to exert a positive effect on the expression and activity of the investigated uptake transporters in primary rat hepatocyte cultures.
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Affiliation(s)
- Eva Ramboer
- In Vitro Toxicology and Dermato-cosmetology research group, Center for Pharmaceutical Research, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel
| | - Vera Rogiers
- In Vitro Toxicology and Dermato-cosmetology research group, Center for Pharmaceutical Research, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel
| | - Tamara Vanhaecke
- In Vitro Toxicology and Dermato-cosmetology research group, Center for Pharmaceutical Research, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel
| | - Mathieu Vinken
- In Vitro Toxicology and Dermato-cosmetology research group, Center for Pharmaceutical Research, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel
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26
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Wachman EM, Hayes MJ, Lester BM, Terrin N, Brown MS, Nielsen DA, Davis JM. Epigenetic variation in the mu-opioid receptor gene in infants with neonatal abstinence syndrome. J Pediatr 2014; 165:472-8. [PMID: 24996986 PMCID: PMC4145036 DOI: 10.1016/j.jpeds.2014.05.040] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 05/09/2014] [Accepted: 05/22/2014] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Neonatal abstinence syndrome (NAS) from in utero opioid exposure is highly variable with genetic factors appearing to play an important role. Epigenetic changes in cytosine:guanine (CpG) dinucleotide methylation can occur after drug exposure and may help to explain NAS variability. We correlated DNA methylation levels in the mu-opioid receptor (OPRM1) promoter in opioid-exposed infants with NAS outcomes. STUDY DESIGN DNA samples from cord blood or saliva were analyzed for 86 infants who were being treated for NAS according to institutional protocol. Methylation levels at 16 OPRM1 CpG sites were determined and correlated with NAS outcome measures, including need for treatment, treatment with ≥ 2 medications, and length of hospital stay. We adjusted for covariates and multiple genetic testing. RESULTS Sixty-five percent of infants required treatment for NAS, and 24% required ≥ 2 medications. Hypermethylation of the OPRM1 promoter was measured at the -10 CpG in treated vs nontreated infants (adjusted difference δ = 3.2% [95% CI, 0.3-6.0%], P = .03; nonsignificant after multiple testing correction). There was hypermethylation at the -14 (δ = 4.9% [95% CI, 1.8%-8.1%], P = .003), -10 (δ = 5.0% [95% CI, 2.3-7.7%], P = .0005), and +84 (δ = 3.5% [95% CI, 0.6-6.4], P = .02) CpG sites in infants requiring ≥ 2 medications, which remained significant for -14 and -10 after multiple testing correction. CONCLUSIONS Increased methylation within the OPRM1 promoter is associated with worse NAS outcomes, consistent with gene silencing.
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Affiliation(s)
| | - Marie J Hayes
- Psychology, Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME
| | - Barry M Lester
- Center for the Study of Children at Risk, Alpert Medical School of Brown University and Women and Infant's Hospital, Providence, RI
| | - Norma Terrin
- Tufts Clinical and Translational Science Institute, Tufts University, Boston, MA; Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA
| | - Mark S Brown
- Pediatrics, Eastern Maine Medical Center, Bangor, ME
| | - David A Nielsen
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX
| | - Jonathan M Davis
- Tufts Clinical and Translational Science Institute, Tufts University, Boston, MA; Pediatrics, The Floating Hospital for Children at Tufts Medical Center, Boston, MA
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27
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Song W, Liu Y, Liu Y, Zhang C, Yuan B, Zhang L, Sun S. Increased p16 DNA methylation in mouse thymic lymphoma induced by irradiation. PLoS One 2014; 9:e93850. [PMID: 24747802 PMCID: PMC3991568 DOI: 10.1371/journal.pone.0093850] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 03/07/2014] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is an important part of epigenetics. In this study, we examined the methylation state of two CpG islands in the promoter of the p16 gene in radiation-induced thymic lymphoma samples. The mRNA and protein levels of P16 were significantly reduced in radiation-induced thymic lymphoma tissue samples. Twenty-three CpG sites of the CpG islands in the p16 promoter region were detected, and the methylation percentages of −71, −63, −239, −29, −38, −40, −23, 46 CpG sites were significantly higher in radiation-induced thymic lymphoma tissue samples than those in matched non-irradiated thymus tissue samples. This study provides new evidence for the methylation state of p16 in the radiation-induced thymic lymphoma samples, which suggests that the methylation of these CpG sites in the p16 promoter may reduce its expression in the thymic lymphoma after irradiation.
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Affiliation(s)
| | - Yongzhe Liu
- Department of Toxicology, School of Public Health, Tianjin Medical University, Tianjin, China
| | - Ying Liu
- Department of Toxicology, School of Public Health, Jilin University, Changchun, China
| | - Cong Zhang
- Ministry of Health, Key Laboratory of Radiobiology, Jilin University, Changchun, China, National Laboratory of Medical Molecular Biology, Tsinghua University, Beijing, PR China
| | - Bao Yuan
- College of Animal Sciences, Jilin University, Changchun, China
| | - Lianbo Zhang
- Department of Plastic and Reconstructive Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
- * E-mail:
| | - Shilong Sun
- Ministry of Health, Key Laboratory of Radiobiology, Jilin University, Changchun, China, National Laboratory of Medical Molecular Biology, Tsinghua University, Beijing, PR China
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28
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Malik RE, Rhodes SJ. The role of DNA methylation in regulation of the murine Lhx3 gene. Gene 2013; 534:272-81. [PMID: 24183897 DOI: 10.1016/j.gene.2013.10.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 10/09/2013] [Accepted: 10/23/2013] [Indexed: 12/20/2022]
Abstract
LHX3 is a LIM-homeodomain transcription factor with critical roles in pituitary and nervous system development. Mutations in the LHX3 gene are associated with pediatric diseases featuring severe hormone deficiencies, hearing loss, developmental delay, and other symptoms. The mechanisms that govern LHX3/Lhx3 transcription are poorly understood. In this study, we examined the role of DNA methylation in the expression status of the mouse Lhx3 gene. Pituitary cells that do not normally express Lhx3 (Pit-1/0 cells) were treated with 5-aza-2'-deoxycytidine, a demethylating reagent. This treatment leads to activation of Lhx3 gene expression suggesting that methylation contributes to Lhx3 regulation. Treatment of Pit-1/0 pituitary cells with a combination of a demethylating reagent and a histone deacetylase inhibitor led to rapid activation of Lhx3 expression, suggesting possible crosstalk between DNA methylation and histone modification processes. To assess DNA methylation levels, treated and untreated Pit-1/0 genomic DNAs were subjected to bisulfite conversion and sequencing. Treated Pit-1/0 cells had decreased methylation at specific sites in the Lhx3 locus compared to untreated cells. Chromatin immunoprecipitation assays demonstrated interactions between the MeCp2 methyl binding protein and Lhx3 promoter regions in the Pit-1/0 cell line. Overall, this study demonstrates that DNA methylation patterns of the Lhx3 gene are associated with its expression status.
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Affiliation(s)
- Raleigh E Malik
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Simon J Rhodes
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Biology, Indiana University-Purdue University Indianapolis, IN, USA; Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN, USA.
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29
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Pfendner EG, Uitto J, Gerard GF, Terry SF. Pseudoxanthoma elasticum: genetic diagnostic markers. ACTA ACUST UNITED AC 2013; 2:63-79. [PMID: 23485117 DOI: 10.1517/17530059.2.1.63] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Pseudoxanthoma elasticum (PXE), an autosomal recessive disorder with considerable phenotypic variability, mainly affects the eyes, skin and cardiovascular system, and is characterized by ectopic mineralization of elastic fibers of connective tissues. Since the identification of the ABCC6 gene (ATP-binding cassette family C member 6), which encodes a putative transmembrane transporter (ABCC6), as the site of mutations responsible for PXE, a number of researchers have disclosed mutations spanning the entire gene. An important advance in the ability to identify mutations has been the identification of two closely related pseudogenes and identifying sequence differences between the coding gene and the pseudogenes allowing accurate sequencing. In this review, the mutation spectrum in PXE is summarized and a strategy to optimize mutation detection in this difficult disorder is outlined.
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30
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Arányi T, Bacquet C, de Boussac H, Ratajewski M, Pomozi V, Fülöp K, Brampton CN, Pulaski L, Le Saux O, Váradi A. Transcriptional regulation of the ABCC6 gene and the background of impaired function of missense disease-causing mutations. Front Genet 2013; 4:27. [PMID: 23483032 PMCID: PMC3593682 DOI: 10.3389/fgene.2013.00027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 02/20/2013] [Indexed: 12/11/2022] Open
Abstract
The human ATP-binding cassette family C member 6 (ABCC6) gene encodes an ABC transporter protein expressed primarily in the liver and to a lesser extent in the kidneys and the intestines. We review here the mechanisms of this restricted tissue-specific expression and the role of hepatocyte nuclear factor 4α which is responsible for the expression pattern. Detailed analyses uncovered further regulators of the expression of the gene pointing to an intronic primate-specific regulator region, an activator of the expression of the gene by binding CCAAT/enhancer-binding protein beta, which interacts with other proteins acting in the proximal promoter. This regulatory network is affected by various environmental stimuli including oxidative stress and the extracellular signal-regulated protein kinases 1 and 2 pathway. We also review here the structural and functional consequences of disease-causing missense mutations of ABCC6. A significant clustering of the missense disease-causing mutations was found at the domain–domain interfaces. This clustering means that the domain contacts are much less permissive to amino acid replacements than the rest of the protein. We summarize the experimental methods resulting in the identification of mutants with preserved transport activity but failure in intracellular targeting. These mutants are candidates for functional rescue by chemical chaperons. The results of such research can provide the basis of future allele-specific therapy of ABCC6-mediated disorders like pseudoxanthoma elasticum or the generalized arterial calcification in infancy.
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Affiliation(s)
- Tamás Arányi
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences Budapest, Hungary
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31
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Kosten TA, Huang W, Nielsen DA. Sex and litter effects on anxiety and DNA methylation levels of stress and neurotrophin genes in adolescent rats. Dev Psychobiol 2013; 56:392-406. [PMID: 23460384 DOI: 10.1002/dev.21106] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 02/04/2013] [Indexed: 12/12/2022]
Abstract
Maternal care variations associate with DNA methylation of the glucocorticoid receptor gene, Nr3c1, in hippocampus at a nerve-growth factor-inducible protein 1 binding site. Epigenetic regulation of brain-derived neurotrophin factor is affected by early stress. These systems contribute to anxiety and fear. Early stress has sex-dependent effects perhaps reflecting sex differences in maternal care. Altering litter gender composition affects maternal behavior and DNA methylation levels of another gene in hippocampus and nucleus accumbens (NAc). We now test if DNA methylation levels of Nr3c1, Egr1, and Bdnf differ by litter composition or sex. Rats from mixed- or single-sex litters were tested for anxiety and fear on postnatal day 35. Brain tissues were collected and analyzed using direct sequencing methods. Females showed hypermethylation of Nr3c1 of hippocampal DNA and litter composition modified sex effects on methylation of Egr1 in NAc. Few differences were seen for Bdnf. LGC modified some sex differences in behavior.
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Affiliation(s)
- Therese A Kosten
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX 77030; Michael E. DeBakey Veteran's Affairs Medical Center, 2002 Holcombe Blvd, Houston, TX 77030.
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32
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Mamrut S, Harony H, Sood R, Shahar-Gold H, Gainer H, Shi YJ, Barki-Harrington L, Wagner S. DNA methylation of specific CpG sites in the promoter region regulates the transcription of the mouse oxytocin receptor. PLoS One 2013; 8:e56869. [PMID: 23441222 PMCID: PMC3575498 DOI: 10.1371/journal.pone.0056869] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 01/15/2013] [Indexed: 01/15/2023] Open
Abstract
Oxytocin is a peptide hormone, well known for its role in labor and suckling, and most recently for its involvement in mammalian social behavior. All central and peripheral actions of oxytocin are mediated through the oxytocin receptor, which is the product of a single gene. Transcription of the oxytocin receptor is subject to regulation by gonadal steroid hormones, and is profoundly elevated in the uterus and mammary glands during parturition. DNA methylation is a major epigenetic mechanism that regulates gene transcription, and has been linked to reduced expression of the oxytocin receptor in individuals with autism. Here, we hypothesized that transcription of the mouse oxytocin receptor is regulated by DNA methylation of specific sites in its promoter, in a tissue-specific manner. Hypothalamus-derived GT1-7, and mammary-derived 4T1 murine cell lines displayed negative correlations between oxytocin receptor transcription and methylation of the gene promoter, and demethylation caused a significant enhancement of oxytocin receptor transcription in 4T1 cells. Using a reporter gene assay, we showed that methylation of specific sites in the gene promoter, including an estrogen response element, significantly inhibits transcription. Furthermore, methylation of the oxytocin receptor promoter was found to be differentially correlated with oxytocin receptor expression in mammary glands and the uterus of virgin and post-partum mice, suggesting that it plays a distinct role in oxytocin receptor transcription among tissues and under different physiological conditions. Together, these results support the hypothesis that the expression of the mouse oxytocin receptor gene is epigenetically regulated by DNA methylation of its promoter.
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Affiliation(s)
- Shimrat Mamrut
- Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Hala Harony
- Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Rapita Sood
- Department of Human Biology, University of Haifa, Haifa, Israel
| | | | - Harold Gainer
- Laboratory of Neurochemistry, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yi-Jun Shi
- Laboratory of Neurochemistry, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | | | - Shlomo Wagner
- Department of Neurobiology, University of Haifa, Haifa, Israel
- * E-mail:
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Le Saux O, Martin L, Aherrahrou Z, Leftheriotis G, Váradi A, Brampton CN. The molecular and physiological roles of ABCC6: more than meets the eye. Front Genet 2012; 3:289. [PMID: 23248644 PMCID: PMC3520154 DOI: 10.3389/fgene.2012.00289] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 11/23/2012] [Indexed: 12/30/2022] Open
Abstract
Abnormal mineralization occurs in the context of several common conditions, including advanced age, diabetes, hypercholesterolemia, chronic renal failure, and certain genetic conditions. Metabolic, mechanical, infectious, and inflammatory injuries promote ectopic mineralization through overlapping yet distinct molecular mechanisms of initiation and progression. The ABCC6 protein is an ATP-dependent transporter primarily found in the plasma membrane of hepatocytes. ABCC6 exports unknown substrates from the liver presumably for systemic circulation. ABCC6 deficiency is the primary cause for chronic and acute forms of ectopic mineralization described in diseases such as pseudoxanthoma elasticum (PXE), β-thalassemia, and generalized arterial calcification of infancy (GACI) in humans and dystrophic cardiac calcification (DCC) in mice. These pathologies are characterized by mineralization of cardiovascular, ocular, and dermal tissues. PXE and to an extent GACI are caused by inactivating ABCC6 mutations, whereas the mineralization associated with β-thalassemia patients derives from a liver-specific change in ABCC6 expression. DCC is an acquired phenotype resulting from cardiovascular insults (ischemic injury or hyperlipidemia) and secondary to ABCC6 insufficiency. Abcc6-deficient mice develop ectopic calcifications similar to both the human PXE and mouse DCC phenotypes. The precise molecular and cellular mechanism linking deficient hepatic ABCC6 function to distal ectopic mineral deposition is not understood and has captured the attention of many research groups. Our previously published work along with that of others show that ABCC6 influences other modulators of calcification and that it plays a much greater physiological role than originally thought.
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Affiliation(s)
- Olivier Le Saux
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii Honolulu, HI, USA
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Imai S, Kikuchi R, Kusuhara H, Sugiyama Y. DNA methylation and histone modification profiles of mouse organic anion transporting polypeptides. Drug Metab Dispos 2012; 41:72-8. [PMID: 23033256 DOI: 10.1124/dmd.112.047969] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Organic anion transporting polypeptides (rodents, Oatps; human, OATPs) are primarily involved in the transmembrane transportation of a wide range of endogenous and exogenous compounds. Multiple mouse Oatp1 isoforms are closely located on chromosome 6, where each isoform shows distinct tissue distribution; Oatp1b2, Oatp1a6, and Oatp1c1 are expressed exclusively in the liver, kidney, and cerebrum, respectively; Oatp1a1 in the liver and kidney; and Oatp1a4 in the liver and cerebrum. We have identified tissue-dependent differentially methylated region (T-DMR) around the transcriptional start site (TSS) of Oatp1b2, which correlates with its liver-specific expression. Bisulfite sequencing also demonstrated the presence of T-DMRs around the TSS in other Oatp1 genes: CpG dinucleotides at +149 relative to the TSS for Oatp1c1; -48, +101, and +356 for Oatp1a4; -572 and -550 for Oatp1a1; and -122 and +216 for Oatp1a6 were differentially methylated among the liver, kidney, and cerebrum. These methylation profiles were largely consistent with the tissue distribution of Oatp1 mRNAs. Chromatin immunoprecipitation assay revealed that the mRNA expression of Oatp1 genes was accompanied by acetylated histone H3. Human OATP1B1 and OATP1B3 are located on chromosome 12p12 in the OATP1 cluster; both show predominant expression in the liver. These genes also contained T-DMRs that were hypomethylated in the liver, compared with kidney cortex: -511, -411, and +92 relative to the TSS for OATP1B1 and -331, +70, and +73 for OATP1B3. These results suggest that the difference in epigenetic profiles comprising DNA methylation and histone acetylation determines the distinct tissue distribution of Oatp/OATP mRNAs.
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Affiliation(s)
- Satoki Imai
- Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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Clifford RL, John AE, Brightling CE, Knox AJ. Abnormal histone methylation is responsible for increased vascular endothelial growth factor 165a secretion from airway smooth muscle cells in asthma. THE JOURNAL OF IMMUNOLOGY 2012; 189:819-31. [PMID: 22689881 DOI: 10.4049/jimmunol.1103641] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Vascular endothelial growth factor (VEGF), a key angiogenic molecule, is aberrantly expressed in several diseases including asthma where it contributes to bronchial vascular remodeling and chronic inflammation. Asthmatic human airway smooth muscle cells hypersecrete VEGF, but the mechanism is unclear. In this study, we defined the mechanism in human airway smooth muscle cells from nonasthmatic and asthmatic patients. We found that asthmatic cells lacked a repression complex at the VEGF promoter, which was present in nonasthmatic cells. Recruitment of G9A, trimethylation of histone H3 at lysine 9 (H3K9me3), and a resultant decrease in RNA polymerase II at the VEGF promoter was critical to repression of VEGF secretion in nonasthmatic cells. At the asthmatic promoter, H3K9me3 was absent because of failed recruitment of G9a; RNA polymerase II binding, in association with TATA-binding protein-associated factor 1, was increased; H3K4me3 was present; and Sp1 binding was exaggerated and sustained. In contrast, DNA methylation and histone acetylation were similar in asthmatic and nonasthmatic cells. This is the first study, to our knowledge, to show that airway cells in asthma have altered epigenetic regulation of remodeling gene(s). Histone methylation at genes such as VEGF may be an important new therapeutic target.
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Nielsen DA, Kreek MJ. Common and specific liability to addiction: approaches to association studies of opioid addiction. Drug Alcohol Depend 2012; 123 Suppl 1:S33-41. [PMID: 22542464 PMCID: PMC3689423 DOI: 10.1016/j.drugalcdep.2012.03.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 03/23/2012] [Accepted: 03/31/2012] [Indexed: 11/18/2022]
Abstract
BACKGROUND Opioid addiction, whether to opiates such as heroin and morphine, and/or to non-medical use of opioids, is a major problem worldwide. Although drug-induced and environmental factors are essential for the liability to develop opioid addiction, the genetic background of an individual is now known also to play a substantial role. METHODS The overall goal of this article is to address the common and specific liabilities to addiction in the context of approaches to studies of one addiction, opioid addiction. Literature on identifying genetic variants that may play a role in the development of opioid addiction was reviewed. RESULTS A substantial number of genetic variants have been reported to be associated with opioid addiction. No single variant has been found in any of the reported GWAS studies with a substantial effect size on the liability to develop heroin addiction. It appears that there is a complex interaction of a large number of variants, some rare, some common, which interact with the environment and in response to specific drugs of abuse to increase the liability of developing opioid addiction. CONCLUSIONS In spite of the inherent difficulties in obtaining large well-phenotyped cohorts for genetic studies, new findings have been reported that are being used to develop testable hypotheses into the biological basis of opioid addiction.
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Affiliation(s)
- David A. Nielsen
- Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, NY 10065, USA
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, and Michael E. DeBakey V.A. Medical Center, Houston, TX, USA
| | - Mary Jeanne Kreek
- Laboratory of the Biology of Addictive Diseases, The Rockefeller University, New York, NY 10065, USA
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Martin L, Douet V, VanWart CM, Heller MB, Le Saux O. A mouse model of β-thalassemia shows a liver-specific down-regulation of Abcc6 expression. THE AMERICAN JOURNAL OF PATHOLOGY 2011; 178:774-83. [PMID: 21281810 DOI: 10.1016/j.ajpath.2010.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 09/25/2010] [Accepted: 10/05/2010] [Indexed: 01/14/2023]
Abstract
β-Thalassemia and pseudoxanthoma elasticum (PXE) are distinct genetic disorders. Yet, a dystrophic mineralization phenotype similar to PXE has frequently been associated with β-thalassemia or sickle cell anemia patients of Mediterranean descent. These calcifications are clinically and structurally identical to inherited PXE. As we previously excluded the presence of PXE-causing mutations in the ABCC6 gene of β-thalassemia patients with PXE manifestations, we hypothesized that a molecular mechanism independent of gene mutations either altered the ABCC6 gene expression or disrupted the biologic properties of its product in the liver or kidneys, which are the tissues with the highest levels of expression. To test this possibility, we investigated Abcc6 synthesis in the liver and kidneys of a β-thalassemia mouse model (Hbb(th3/+)). We found a progressive liver-specific down-regulation of the Abcc6 gene expression and protein levels by quantitative PCR, Western blotting, and immunofluorescence. The levels of Abcc6 protein decreased significantly at 6 months of age and stabilized at 10 months and older ages at ∼25% of the wild-type protein levels. We studied the transcriptional regulation of the Abcc6 gene in wild-type and Hbb(th3/+) mice, and we identified the erythroid transcription factor NF-E2 as the main cause of the transcriptional down-regulation using transcription factor arrays and chromatin immunoprecipitation. The Hbb(th3/+) mice did not develop spontaneous calcification as seen in the Abcc6(-/-) mice probably because the Abcc6 protein decrease occurred late in life and was probably insufficient to promote mineralization in the Hbb(th3/+) mouse C57BL/6J genetic background. Nevertheless, our result suggested that a similar decrease of ABCC6 expression occurs in the liver of β-thalassemia patients and may be responsible for their frequent PXE-like manifestations.
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Affiliation(s)
- Ludovic Martin
- Department of Dermatology, University Hospital of Angers, Angers, France
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Sun S, Chen Z, Yan PS, Huang YW, Huang THM, Lin S. Identifying hypermethylated CpG islands using a quantile regression model. BMC Bioinformatics 2011; 12:54. [PMID: 21324121 PMCID: PMC3051900 DOI: 10.1186/1471-2105-12-54] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 02/15/2011] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND DNA methylation has been shown to play an important role in the silencing of tumor suppressor genes in various tumor types. In order to have a system-wide understanding of the methylation changes that occur in tumors, we have developed a differential methylation hybridization (DMH) protocol that can simultaneously assay the methylation status of all known CpG islands (CGIs) using microarray technologies. A large percentage of signals obtained from microarrays can be attributed to various measurable and unmeasurable confounding factors unrelated to the biological question at hand. In order to correct the bias due to noise, we first implemented a quantile regression model, with a quantile level equal to 75%, to identify hypermethylated CGIs in an earlier work. As a proof of concept, we applied this model to methylation microarray data generated from breast cancer cell lines. However, we were unsure whether 75% was the best quantile level for identifying hypermethylated CGIs. In this paper, we attempt to determine which quantile level should be used to identify hypermethylated CGIs and their associated genes. RESULTS We introduce three statistical measurements to compare the performance of the proposed quantile regression model at different quantile levels (95%, 90%, 85%, 80%, 75%, 70%, 65%, 60%), using known methylated genes and unmethylated housekeeping genes reported in breast cancer cell lines and ovarian cancer patients. Our results show that the quantile levels ranging from 80% to 90% are better at identifying known methylated and unmethylated genes. CONCLUSIONS In this paper, we propose to use a quantile regression model to identify hypermethylated CGIs by incorporating probe effects to account for noise due to unmeasurable factors. Our model can efficiently identify hypermethylated CGIs in both breast and ovarian cancer data.
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Affiliation(s)
- Shuying Sun
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA.
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40
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Wu SF, Zhang H, Hammoud SS, Potok M, Nix DA, Jones DA, Cairns BR. DNA methylation profiling in zebrafish. Methods Cell Biol 2011; 104:327-39. [PMID: 21924171 DOI: 10.1016/b978-0-12-374814-0.00018-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA methylation on cytosine in vertebrates such as zebrafish serves to silence gene expression by interfering with the binding of certain transcription factors and through the recruitment of repressive chromatin machinery. Cytosine DNA methylation is chemically stable and heritable through the germline - but also reversible through many modes, making it a useful and dynamic epigenetic modification. Virtually all of the enzymes and factors involved in the deposition, binding, and removal of cytosine methylation are conserved in zebrafish, and therefore the organism an excellent model for understanding the use of DNA methylation in the control of gene regulation and other processes. Here, we discuss the main approaches to quantifying DNA methylation levels genome-wide in zebrafish: one is an established method for revealing regional methylation (methylated DNA immunoprecipitation (MeDIP)), and the other is an emerging method that reveals DNA methylation at base-pair resolution (shotgun bisulphite sequencing). We also introduce some of the analytical methods that are useful for identifying regions of hypo- or hyper-methylation, and ways to identify differentially methylated regions.
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Affiliation(s)
- Shan-Fu Wu
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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Fuso A, Ferraguti G, Grandoni F, Ruggeri R, Scarpa S, Strom R, Lucarelli M. Early demethylation of non-CpG, CpC-rich, elements in the myogenin 5'-flanking region: a priming effect on the spreading of active demethylation. Cell Cycle 2010; 9:3965-76. [PMID: 20935518 DOI: 10.4161/cc.9.19.13193] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The dynamic changes and structural patterns of DNA methylation of genes without CpG islands are poorly characterized. The relevance of CpG to the non-CpG methylation equilibrium in transcriptional repression is unknown. In this work, we analyzed the DNA methylation pattern of the 5'-flanking of the myogenin gene, a positive regulator of muscle differentiation with no CpG island and low CpG density, in both C2C12 muscle satellite cells and embryonic muscle. Embryonic brain was studied as a non-expressing tissue. High levels of both CpG and non-CpG methylation were observed in non-expressing experimental conditions. Both CpG and non-CpG methylation rapidly dropped during muscle differentiation and myogenin transcriptional activation, with an active demethylation dynamics. Non-CpG demethylation occurred more rapidly than CpG demethylation. Demethylation spread from initially highly methylated short CpC-rich elements to a virtually unmethylated status. These short elements have a high CpC content and density, share some motifs and largely coincide with putative recognition sequences of some differentiation-related transcription factors. Our findings point to a dynamically controlled equilibrium between CpG and non-CpG active demethylation in the transcriptional control of tissue-specific genes. The short CpC-rich elements are new structural features of the methylation machinery, whose functions may include priming the complete demethylation of a transcriptionally crucial DNA region.
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Affiliation(s)
- Andrea Fuso
- Department of Surgery P. Valdoni, Sapienza University of Rome, Italy
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Nakaya Y, Shojima T, Yasuda J, Imakawa K, Miyazawa T. Epigenetic regulation on the 5'-proximal CpG island of human porcine endogenous retrovirus subgroup A receptor 2/GPR172B. Microbes Infect 2010; 13:49-57. [PMID: 20951222 DOI: 10.1016/j.micinf.2010.09.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 09/27/2010] [Accepted: 09/30/2010] [Indexed: 11/19/2022]
Abstract
Porcine endogenous retroviruses (PERVs) have been considered one of the major risks of xenotransplantation from pigs to humans. PERV-A efficiently utilizes human PERV-A receptor 2 (HuPAR-2)/GPR172B to infect human cells; however, there has been no study on the regulation mechanisms of HuPAR-2/GPR172B expression. In this study, we examined the expression of HuPAR-2/GPR172B from the standpoint of epigenetic regulation and discussed the risks of PERV-A infection in xenotransplantation. Quantitative real-time RT-PCR revealed that HuPAR-2 mRNA was preferentially expressed in placental tissue, whereas it was highly suppressed in BeWo cells (a human choriocarcinoma cell line) and HEK293 cells. A CpG island containing the HuPAR-2 transcription starting site was identified by in silico analysis. The DNA methylation ratio (the relative quantity of methylcytosine to total cytosine) and histone modification (H3K9me3) levels in the CpG island measured by bisulfite genomic sequencing and ChIP assay, respectively, were inversely correlated with the mRNA levels. Both HuPAR-2 mRNA and HuPAR-2 protein were up-regulated in HEK293 cells by inhibiting DNA methylation and histone deacetylation. Additionally, promoter/enhancer activities within the CpG island were suppressed by in vitro DNA methylation. Our results demonstrated that epigenetic modification regulates HuPAR-2 expression.
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Affiliation(s)
- Yuki Nakaya
- Laboratory of Signal Transduction, Department of Cell Biology, Institute for Virus Research, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, Japan
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Gu X, Manautou JE. Regulation of hepatic ABCC transporters by xenobiotics and in disease states. Drug Metab Rev 2010; 42:482-538. [PMID: 20233023 DOI: 10.3109/03602531003654915] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The subfamily of ABCC transporters consists of 13 members in mammals, including the multidrug resistance-associated proteins (MRPs), sulfonylurea receptors (SURs), and the cystic fibrosis transmembrane conductance regulator (CFTR). These proteins play roles in chemical detoxification, disposition, and normal cell physiology. ABCC transporters are expressed differentially in the liver and are regulated at the transcription and translation level. Their expression and function are also controlled by post-translational modification and membrane-trafficking events. These processes are tightly regulated. Information about alterations in the expression of hepatobiliary ABCC transporters could provide important insights into the pathogenesis of diseases and disposition of xenobiotics. In this review, we describe the regulation of hepatic ABCC transporters in humans and rodents by a variety of xenobiotics, under disease states and in genetically modified animal models deficient in transcription factors, transporters, and cell-signaling molecules.
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Affiliation(s)
- Xinsheng Gu
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, 06269, USA
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Li L, Davie JR. The role of Sp1 and Sp3 in normal and cancer cell biology. Ann Anat 2010; 192:275-83. [PMID: 20810260 DOI: 10.1016/j.aanat.2010.07.010] [Citation(s) in RCA: 448] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 07/22/2010] [Indexed: 10/19/2022]
Abstract
Sp1 and Sp3 are transcription factors expressed in all mammalian cells. These factors are involved in regulating the transcriptional activity of genes implicated in most cellular processes. Dysregulation of Sp1 and Sp3 is observed in many cancers and diseases. Due to the amino acid sequence similarity of the DNA binding domains, Sp1 and Sp3 recognize and associate with the same DNA element with similar affinity. However, others and our laboratory demonstrated that these two factors possess different properties and exert different functional roles. Both Sp1 and Sp3 can interact with and recruit a large number of proteins including the transcription initiation complex, histone modifying enzymes and chromatin remodeling complexes, which strongly suggest that Sp1 and Sp3 are important transcription factors in the remodeling chromatin and the regulation of gene expression. In this review, the role of Sp1 and Sp3 in normal and cancer cell biology and the multiple mechanisms deciding the functional roles of Sp1 and Sp3 will be presented.
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Affiliation(s)
- Lin Li
- Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, Manitoba R3E 0V9, Canada
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Identification and analysis of the promoter region of the human DHCR24 gene: involvement of DNA methylation and histone acetylation. Mol Biol Rep 2010; 38:1091-101. [PMID: 20568014 DOI: 10.1007/s11033-010-0206-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Accepted: 06/11/2010] [Indexed: 10/19/2022]
Abstract
Mutations in the DHCR24 gene, which encodes the cholesterol biosynthesis enzyme 3ß-hydroxysterol-∆24 reductase, result in an autosomal recessive disease called desmosterolosis. Further, reduced expression of DHCR24 is found in the temporal cortex of Alzheimer's disease patients. This suggests that variability in the regulatory regions of DHCR24 may contribute to the development of this neurodegenerative disease. In this work, we functionally characterised the proximal fragment of the human DHCR24 gene, for the first time. We show that the transcription of DHCR24 is initiated from a single CpG-rich promoter that is regulated by DNA methylation in some cell types. An activator sequence was also uncovered in the -1203/-665 bp region by reporter gene assays. Furthermore, sodium butyrate (a well-known HDAC inhibitor) increased DHCR24 expression in SH-SY5Y cells by recruiting acetylated core histones H3 and H4 to the enhancer region, as demonstrated by transient transfection and chromatin immunoprecipitation assays. Understanding the regulation of the DHCR24 gene may lead to alternative therapeutic strategies in at least some Alzheimer's patients.
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Nielsen DA, Hamon S, Yuferov V, Jackson C, Ho A, Ott J, Kreek MJ. Ethnic diversity of DNA methylation in the OPRM1 promoter region in lymphocytes of heroin addicts. Hum Genet 2010; 127:639-49. [PMID: 20237803 PMCID: PMC3739429 DOI: 10.1007/s00439-010-0807-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Accepted: 02/19/2010] [Indexed: 12/21/2022]
Abstract
The mu-opioid receptor is the site of action of many endogenous opioids as well as opiates. We hypothesize that differences in DNA methylation of specific CpG dinucleotides between former severe heroin addicts in methadone maintenance treatment and control subjects will depend, in part, upon ethnicity. DNA methylation analysis of the mu-opioid receptor gene (OPRM1) promoter region was performed on African-Americans (118 cases, 80 controls) and Hispanics (142 cases, 61 controls) and these were compared with a similar Caucasian cohort from our earlier study. In controls, a higher methylation level was found in the African-Americans compared with the Hispanics or Caucasians. Significant experiment-wise differences in methylation levels were found at the -25 and +12 CpG sites in the controls among the three ethnicities. The overall methylation level of the CpG sites were significantly higher in the former heroin addicts when compared with the controls (point-wise P = 0.0457). However, in the African-Americans, the degree of methylation was significantly decreased experiment-wise in the former heroin addicts at the +12 CpG site (P = 0.0032, Bonferroni corrected general estimating equations). In Hispanics, the degree of methylation was increased in the former heroin addicts at the -25 (P < 0.001, experiment-wise), -14 (P = 0.001, experiment-wise), and +27 (P < 0.001, experiment-wise) CpG sites. These changes in methylation of the OPRM1 promoter region may lead to altered expression of the mu-opioid receptor gene in the lymphocytes of former heroin addicts who are stabilized in methadone maintenance treatment.
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Affiliation(s)
- David A. Nielsen
- Laboratory of the Biology of Addictive Diseases, The Rockefeller University, Box 171, 1230 York Avenue, New York 10065, USA; Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX, USA; Michael E. DeBakey V.A. Medical Center, Houston, TX, USA
| | - Sara Hamon
- Laboratory of the Biology of Addictive Diseases, The Rockefeller University, Box 171, 1230 York Avenue, New York 10065, USA
| | - Vadim Yuferov
- Laboratory of the Biology of Addictive Diseases, The Rockefeller University, Box 171, 1230 York Avenue, New York 10065, USA
| | - Colin Jackson
- Laboratory of the Biology of Addictive Diseases, The Rockefeller University, Box 171, 1230 York Avenue, New York 10065, USA
| | - Ann Ho
- Laboratory of the Biology of Addictive Diseases, The Rockefeller University, Box 171, 1230 York Avenue, New York 10065, USA
| | - Jurg Ott
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Mary Jeanne Kreek
- Laboratory of the Biology of Addictive Diseases, The Rockefeller University, Box 171, 1230 York Avenue, New York 10065, USA
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de Boussac H, Ratajewski M, Sachrajda I, Köblös G, Tordai A, Pulaski L, Buday L, Váradi A, Arányi T. The ERK1/2-hepatocyte nuclear factor 4alpha axis regulates human ABCC6 gene expression in hepatocytes. J Biol Chem 2010; 285:22800-8. [PMID: 20463007 DOI: 10.1074/jbc.m110.105593] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
ABCC6 mutations are responsible for the development of pseudoxanthoma elasticum, a rare recessive disease characterized by calcification of elastic fibers. Although ABCC6 is mainly expressed in the liver the disease has dermatologic, ocular, and cardiovascular symptoms. We investigated the transcriptional regulation of the gene and observed that hepatocyte growth factor (HGF) inhibits its expression in HepG2 cells via the activation of ERK1/2. Similarly, other factors activating the cascade also inhibited ABCC6 expression. We identified the ERK1/2 response element in the proximal promoter by luciferase reporter gene assays. This site overlapped with a region conferring the tissue-specific expression pattern to the gene and with a putative hepatocyte nuclear factor 4alpha (HNF4alpha) binding site. We demonstrated that HNF4alpha regulates the expression of ABCC6, acts through the putative binding site, and determines its cell type-specific expression. We also showed that HNF4alpha is inhibited by the activation of the ERK1/2 cascade. In conclusion we describe here the first regulatory pathway of ABCC6 expression showing that the ERK1/2-HNF4alpha axis has an important role in regulation of the gene.
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Affiliation(s)
- Hugues de Boussac
- Institute of Enzymology, Hungarian Academy of Sciences, Karolina ut 29, 1113 Budapest, Hungary
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Choudhuri S, Cui Y, Klaassen CD. Molecular targets of epigenetic regulation and effectors of environmental influences. Toxicol Appl Pharmacol 2010; 245:378-93. [PMID: 20381512 DOI: 10.1016/j.taap.2010.03.022] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Revised: 03/25/2010] [Accepted: 03/29/2010] [Indexed: 12/31/2022]
Abstract
The true understanding of what we currently define as epigenetics evolved over time as our knowledge on DNA methylation and chromatin modifications and their effects on gene expression increased. The current explosion of research on epigenetics and the increasing documentation of the effects of various environmental factors on DNA methylation, chromatin modification, as well as on the expression of small non-coding RNAs (ncRNAs) have expanded the scope of research on the etiology of various diseases including cancer. The current review briefly discusses the molecular mechanisms of epigenetic regulation and expands the discussion with examples on the role of environment, such as the immediate environment during development, in inducing epigenetic changes and modulating gene expression.
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Affiliation(s)
- Supratim Choudhuri
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Food Additive Safety, Division of Biotechnology and GRAS Notice Review, College Park, MD, USA.
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Yuferov V, Levran O, Proudnikov D, Nielsen DA, Kreek MJ. Search for genetic markers and functional variants involved in the development of opiate and cocaine addiction and treatment. Ann N Y Acad Sci 2010; 1187:184-207. [PMID: 20201854 DOI: 10.1111/j.1749-6632.2009.05275.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Addiction to opiates and illicit use of psychostimulants is a chronic, relapsing brain disease that, if left untreated, can cause major medical, social, and economic problems. This article reviews recent progress in studies of association of gene variants with vulnerability to develop opiate and cocaine addictions, focusing primarily on genes of the opioid and monoaminergic systems. In addition, we provide the first evidence of a cis-acting polymorphism and a functional haplotype in the PDYN gene, of significantly higher DNA methylation rate of the OPRM1 gene in the lymphocytes of heroin addicts, and significant differences in genotype frequencies of three single-nucleotide polymorphisms of the P-glycoprotein gene (ABCB1) between "higher" and "lower" methadone doses in methadone-maintained patients. In genomewide and multigene association studies, we found association of several new genes and new variants of known genes with heroin addiction. Finally, we describe the development and application of a novel technique: molecular haplotyping for studies in genetics of drug addiction.
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Affiliation(s)
- Vadim Yuferov
- Laboratory of the Biology of Addictive Diseases, Rockefeller University, New York, New York 10065, USA
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Mutai H, Nagashima R, Sugitani Y, Noda T, Fujii M, Matsunaga T. Expression of Pou3f3/Brn-1 and its genomic methylation in developing auditory epithelium. Dev Neurobiol 2010; 69:913-30. [PMID: 19743445 DOI: 10.1002/dneu.20746] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the mammalian cochlea, both the sensory cells-called hair cells (HCs)-and nonsensory cells such as supporting cells (SCs) and mesenchymal cells participate in proper auditory function through the expression of various functional molecules. During development, expression of certain genes is repressed through genomic methylation, one of the major epigenetic regulatory mechanisms. We explored the genomic regions that were differentially methylated in rat auditory epithelium at postnatal day 1 (P1) and P14 using amplification of intermethylated sites (AIMS). An AIMS fragment was mapped to the 3'-flanking region of Pou3f3/Brn-1. Bisulfite-converted PCR and quantitative methylation-specific PCR showed that the methylation frequency of the AIMS region and the adjacent CpG island was increased at P14, when the expression of Pou3f3 and the noncoding RNAs nearby decreased. Expression of de novo DNA methyltransferases 3a and 3b also suggests a role of epigenetic regulation during postnatal inner ear development. Immunohistochemical analysis showed that Pou3f3 was expressed specifically in the SCs and mesenchymal cells in the cochlea and established that Pou3f3 is a new cell-type marker for studying inner ear development. Mice deficient in Pou3f3 or Pou3f2 plus Pou3f3 did not exhibit any abnormality in the embryonic cochlea. Absence of Pou3f3 affected neither the proliferation nor the differentiation activities of HC progenitor cells. Pou3f3 may, however, be important for the maintenance or functional development of the postnatal cochlea. This is the first report to study involvement of an epigenetic regulatory mechanism in the developing mammalian auditory epithelium.
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Affiliation(s)
- Hideki Mutai
- Laboratory of Auditory Disorders, National Institute of Sensory Organs, National Tokyo Medical Center, Tokyo, Japan
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