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Chakraborty S, Nandi P, Mishra J, Niharika, Roy A, Manna S, Baral T, Mishra P, Mishra PK, Patra SK. Molecular mechanisms in regulation of autophagy and apoptosis in view of epigenetic regulation of genes and involvement of liquid-liquid phase separation. Cancer Lett 2024; 587:216779. [PMID: 38458592 DOI: 10.1016/j.canlet.2024.216779] [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: 01/13/2024] [Revised: 02/19/2024] [Accepted: 02/29/2024] [Indexed: 03/10/2024]
Abstract
Cellular physiology is critically regulated by multiple signaling nexuses, among which cell death mechanisms play crucial roles in controlling the homeostatic landscape at the tissue level within an organism. Apoptosis, also known as programmed cell death, can be induced by external and internal stimuli directing the cells to commit suicide in unfavourable conditions. In contrast, stress conditions like nutrient deprivation, infection and hypoxia trigger autophagy, which is lysosome-mediated processing of damaged cellular organelle for recycling of the degraded products, including amino acids. Apparently, apoptosis and autophagy both are catabolic and tumor-suppressive pathways; apoptosis is essential during development and cancer cell death, while autophagy promotes cell survival under stress. Moreover, autophagy plays dual role during cancer development and progression by facilitating the survival of cancer cells under stressed conditions and inducing death in extreme adversity. Despite having two different molecular mechanisms, both apoptosis and autophagy are interconnected by several crosslinking intermediates. Epigenetic modifications, such as DNA methylation, post-translational modification of histone tails, and miRNA play a pivotal role in regulating genes involved in both autophagy and apoptosis. Both autophagic and apoptotic genes can undergo various epigenetic modifications and promote or inhibit these processes under normal and cancerous conditions. Epigenetic modifiers are uniquely important in controlling the signaling pathways regulating autophagy and apoptosis. Therefore, these epigenetic modifiers of both autophagic and apoptotic genes can act as novel therapeutic targets against cancers. Additionally, liquid-liquid phase separation (LLPS) also modulates the aggregation of misfolded proteins and provokes autophagy in the cytosolic environment. This review deals with the molecular mechanisms of both autophagy and apoptosis including crosstalk between them; emphasizing epigenetic regulation, involvement of LLPS therein, and possible therapeutic approaches against cancers.
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Affiliation(s)
- Subhajit Chakraborty
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Piyasa Nandi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Jagdish Mishra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Soumen Manna
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Tirthankar Baral
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Prahallad Mishra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Pradyumna Kumar Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bypass Road, Bhauri, Bhopal, 462 030, MP, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India.
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Sultan S, AlMalki S. Analysis of global DNA methylation and epigenetic modifiers (DNMTs and HDACs) in human foetal endothelium exposed to gestational and type 2 diabetes. Epigenetics 2023; 18:2201714. [PMID: 37066707 PMCID: PMC10114969 DOI: 10.1080/15592294.2023.2201714] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/16/2023] [Accepted: 04/07/2023] [Indexed: 04/18/2023] Open
Abstract
Foetuses exposed to maternal gestational diabetes (GDM) and type 2 diabetes (T2D) have an increased risk of adverse perinatal outcomes. Epigenetic mechanisms, including DNA methylation and histone modifications, may act as mediators of persistent metabolic memory in endothelial cells (ECs) exposed to hyperglycaemia, even after glucose normalization. Therefore, we investigated alterations in global DNA methylation and epigenetic modifier expression (DNMT1, DNMT3a, DNMT3b, HDAC1, and HDAC2) in human umbilical vein ECs (HUVECs) from the umbilical cords of mothers with GDM (n = 8) and T2D (n = 3) compared to that of healthy mothers (n = 6). Global DNA alteration was measured using a 5-methylation cytosine colorimetric assay, followed by quantitative real-time polymerase chain reaction to measure DNA methyltransferase and histone acetylase transcript expression. We revealed that DNA hypermethylation occurs in both GDM- and T2D-HUVECs compared to that in Control-HUVECs. Furthermore, there was a significant increase in HDAC2 mRNA levels in GDM-HUVECs and increase in DNMT3b mRNA levels in T2D-HUVECs. Overall, our results suggest that GDM and T2D are associated with global DNA hypermethylation in foetal endothelial cells under normoglycemic conditions and the aberrant mRNA expression of HDAC2 and DNMT3b could play a role in this dysregulation.
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Affiliation(s)
- Samar Sultan
- Medical Laboratory Sciences Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sultanh AlMalki
- Medical Laboratory Sciences Department, King Abdulaziz University, Jeddah, Saudi Arabia
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Yaskolka Meir A, Keller M, Hoffmann A, Rinott E, Tsaban G, Kaplan A, Zelicha H, Hagemann T, Ceglarek U, Isermann B, Shelef I, Blüher M, Stumvoll M, Li J, Haange SB, Engelmann B, Rolle-Kampczyk U, von Bergen M, Hu FB, Stampfer MJ, Kovacs P, Liang L, Shai I. The effect of polyphenols on DNA methylation-assessed biological age attenuation: the DIRECT PLUS randomized controlled trial. BMC Med 2023; 21:364. [PMID: 37743489 PMCID: PMC10519069 DOI: 10.1186/s12916-023-03067-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/31/2023] [Indexed: 09/26/2023] Open
Abstract
BACKGROUND Epigenetic age is an estimator of biological age based on DNA methylation; its discrepancy from chronologic age warrants further investigation. We recently reported that greater polyphenol intake benefitted ectopic fats, brain function, and gut microbiota profile, corresponding with elevated urine polyphenols. The effect of polyphenol-rich dietary interventions on biological aging is yet to be determined. METHODS We calculated different biological aging epigenetic clocks of different generations (Horvath2013, Hannum2013, Li2018, Horvath skin and blood2018, PhenoAge2018, PCGrimAge2022), their corresponding age and intrinsic age accelerations, and DunedinPACE, all based on DNA methylation (Illumina EPIC array; pre-specified secondary outcome) for 256 participants with abdominal obesity or dyslipidemia, before and after the 18-month DIRECT PLUS randomized controlled trial. Three interventions were assigned: healthy dietary guidelines, a Mediterranean (MED) diet, and a polyphenol-rich, low-red/processed meat Green-MED diet. Both MED groups consumed 28 g walnuts/day (+ 440 mg/day polyphenols). The Green-MED group consumed green tea (3-4 cups/day) and Mankai (Wolffia globosa strain) 500-ml green shake (+ 800 mg/day polyphenols). Adherence to the Green-MED diet was assessed by questionnaire and urine polyphenols metabolomics (high-performance liquid chromatography quadrupole time of flight). RESULTS Baseline chronological age (51.3 ± 10.6 years) was significantly correlated with all methylation age (mAge) clocks with correlations ranging from 0.83 to 0.95; p < 2.2e - 16 for all. While all interventions did not differ in terms of changes between mAge clocks, greater Green-Med diet adherence was associated with a lower 18-month relative change (i.e., greater mAge attenuation) in Li and Hannum mAge (beta = - 0.41, p = 0.004 and beta = - 0.38, p = 0.03, respectively; multivariate models). Greater Li mAge attenuation (multivariate models adjusted for age, sex, baseline mAge, and weight loss) was mostly affected by higher intake of Mankai (beta = - 1.8; p = 0.061) and green tea (beta = - 1.57; p = 0.0016) and corresponded with elevated urine polyphenols: hydroxytyrosol, tyrosol, and urolithin C (p < 0.05 for all) and urolithin A (p = 0.08), highly common in green plants. Overall, participants undergoing either MED-style diet had ~ 8.9 months favorable difference between the observed and expected Li mAge at the end of the intervention (p = 0.02). CONCLUSIONS This study showed that MED and green-MED diets with increased polyphenols intake, such as green tea and Mankai, are inversely associated with biological aging. To the best of our knowledge, this is the first clinical trial to indicate a potential link between polyphenol intake, urine polyphenols, and biological aging. TRIAL REGISTRATION ClinicalTrials.gov, NCT03020186.
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Affiliation(s)
- Anat Yaskolka Meir
- The Health & Nutrition Innovative International Research Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 8410501, Be'er Sheva, Israel
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA, 02115, USA
| | - Maria Keller
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, University of Leipzig, Liebigstrasse 21, 04103, Leipzig, Germany
| | - Anne Hoffmann
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany
| | - Ehud Rinott
- The Health & Nutrition Innovative International Research Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 8410501, Be'er Sheva, Israel
| | - Gal Tsaban
- The Health & Nutrition Innovative International Research Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 8410501, Be'er Sheva, Israel
- Soroka University Medical Center, 84101, Be'er Sheva, Israel
| | - Alon Kaplan
- The Health & Nutrition Innovative International Research Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 8410501, Be'er Sheva, Israel
| | - Hila Zelicha
- The Health & Nutrition Innovative International Research Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 8410501, Be'er Sheva, Israel
| | - Tobias Hagemann
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany
| | - Uta Ceglarek
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Berend Isermann
- Institute of Laboratory Medicine, Clinical Chemistry, and Molecular Diagnostics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Ilan Shelef
- Soroka University Medical Center, 84101, Be'er Sheva, Israel
| | - Matthias Blüher
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, University of Leipzig, Liebigstrasse 21, 04103, Leipzig, Germany
| | - Michael Stumvoll
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, University of Leipzig, Liebigstrasse 21, 04103, Leipzig, Germany
| | - Jun Li
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and, Harvard Medical School, Boston, MA, 02115, USA
| | - Sven-Bastian Haange
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH, 04318, Leipzig, Germany
| | - Beatrice Engelmann
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH, 04318, Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH, 04318, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH, 04318, Leipzig, Germany
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, 04103, Leipzig, Germany
| | - Frank B Hu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA, 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Meir J Stampfer
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, University of Leipzig, Liebigstrasse 21, 04103, Leipzig, Germany.
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA, 02115, USA.
| | - Iris Shai
- The Health & Nutrition Innovative International Research Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 8410501, Be'er Sheva, Israel.
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany.
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
- Faculty of Medicine, Leipzig University, Leipzig, 04103, Germany.
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Wang J, Xie SA, Li N, Zhang T, Yao W, Zhao H, Pang W, Han L, Liu J, Zhou J. Matrix stiffness exacerbates the proinflammatory responses of vascular smooth muscle cell through the DDR1-DNMT1 mechanotransduction axis. Bioact Mater 2022; 17:406-424. [PMID: 35386458 PMCID: PMC8964982 DOI: 10.1016/j.bioactmat.2022.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/16/2021] [Accepted: 01/06/2022] [Indexed: 11/16/2022] Open
Abstract
Vascular smooth muscle cell (vSMC) is highly plastic as its phenotype can change in response to mechanical cues inherent to the extracellular matrix (ECM). VSMC may be activated from its quiescent contractile phenotype to a proinflammatory phenotype, whereby the cell secretes chemotactic and inflammatory cytokines, e.g. MCP1 and IL6, to functionally regulate monocyte and macrophage infiltration during the development of various vascular diseases including arteriosclerosis. Here, by culturing vSMCs on polyacrylamide (PA) substrates with variable elastic moduli, we discovered a role of discoidin domain receptor 1 (DDR1), a receptor tyrosine kinase that binds collagens, in mediating the mechanical regulation of vSMC gene expression, phenotype, and proinflammatory responses. We found that ECM stiffness induced DDR1 phosphorylation, oligomerization, and endocytosis to repress the expression of DNA methyltransferase 1 (DNMT1), very likely in a collagen-independent manner. The DDR1-to-DNMT1 signaling was sequentially mediated by the extracellular signal-regulated kinases (ERKs) and p53 pathways. ECM stiffness primed vSMC to a proinflammatory phenotype and this regulation was diminished by DDR1 inhibition. In agreement with the in vitro findings, increased DDR1 phosphorylation was observed in human arterial stiffening. DDR1 inhibition in mouse attenuated the acute injury or adenine diet-induced vascular stiffening and inflammation. Furthermore, mouse vasculature with SMC-specific deletion of Dnmt1 exhibited proinflammatory and stiffening phenotypes. Our study demonstrates a role of SMC DDR1 in perceiving the mechanical microenvironments and down-regulating expression of DNMT1 to result in vascular pathologies and has potential implications for optimization of engineering artificial vascular grafts and vascular networks. DDR1 is a mechanosensor in vSMC to perceive ECM stiffness in a collagen binding-independent way. Activation of DDR1 leads to repression of DNMT1 expression via the ERK-p53 pathway. The DDR1-DNMT1 axis mediates ECM stiffening-induced vascular inflammation.
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Affiliation(s)
- Jin Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Hemorheology Center, School of Basic Medical Sciences, Peking University, Beijing, PR China
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, PR China
- National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides; Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, PR China
| | - Si-an Xie
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Hemorheology Center, School of Basic Medical Sciences, Peking University, Beijing, PR China
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, PR China
- National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides; Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, PR China
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, PR China
| | - Ning Li
- Center for Biomechanics and Bioengineering, Key Laboratory of Microgravity (National Microgravity Laboratory), And Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, PR China
- School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, PR China
| | - Tao Zhang
- Department of Vascular Surgery, Peking University People's Hospital, Beijing, PR China
| | - Weijuan Yao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Hemorheology Center, School of Basic Medical Sciences, Peking University, Beijing, PR China
| | - Hucheng Zhao
- Institute of Biomechanics and Medical Engineering, School of Aerospace Engineering, Tsinghua University, Beijing, PR China
| | - Wei Pang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Hemorheology Center, School of Basic Medical Sciences, Peking University, Beijing, PR China
| | - Lili Han
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Hemorheology Center, School of Basic Medical Sciences, Peking University, Beijing, PR China
| | - Jiayu Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Hemorheology Center, School of Basic Medical Sciences, Peking University, Beijing, PR China
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, PR China
- National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides; Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, PR China
| | - Jing Zhou
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Hemorheology Center, School of Basic Medical Sciences, Peking University, Beijing, PR China
- Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, PR China
- National Health Commission Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides; Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, PR China
- Corresponding author. Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Hemorheology Center, School of Basic Medical Sciences, Peking University, Beijing, PR China.
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Martín MG, Dotti CG. Plasma membrane and brain dysfunction of the old: Do we age from our membranes? Front Cell Dev Biol 2022; 10:1031007. [PMID: 36274849 PMCID: PMC9582647 DOI: 10.3389/fcell.2022.1031007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022] Open
Abstract
One of the characteristics of aging is a gradual hypo-responsiveness of cells to extrinsic stimuli, mainly evident in the pathways that are under hormone control, both in the brain and in peripheral tissues. Age-related resistance, i.e., reduced response of receptors to their ligands, has been shown to Insulin and also to leptin, thyroid hormones and glucocorticoids. In addition, lower activity has been reported in aging for ß-adrenergic receptors, adenosine A2B receptor, and several other G-protein-coupled receptors. One of the mechanisms proposed to explain the loss of sensitivity to hormones and neurotransmitters with age is the loss of receptors, which has been observed in several tissues. Another mechanism that is finding more and more experimental support is related to the changes that occur with age in the lipid composition of the neuronal plasma membrane, which are responsible for changes in the receptors’ coupling efficiency to ligands, signal attenuation and pathway desensitization. In fact, recent works have shown that altered membrane composition—as occurs during neuronal aging—underlies reduced response to glutamate, to the neurotrophin BDNF, and to insulin, all these leading to cognition decay and epigenetic alterations in the old. In this review we present evidence that altered functions of membrane receptors due to altered plasma membrane properties may be a triggering factor in physiological decline, decreased brain function, and increased vulnerability to neuropathology in aging.
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Affiliation(s)
- Mauricio G. Martín
- Cellular and Molecular Neurobiology Department, Instituto Ferreyra (INIMEC)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba (UNC), Córdoba, Argentina
- *Correspondence: Mauricio G. Martín, ; Carlos G. Dotti,
| | - Carlos G. Dotti
- Molecular Neuropathology Unit, Physiological and Pathological Processes Program, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- *Correspondence: Mauricio G. Martín, ; Carlos G. Dotti,
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Patra SK, Szyf M. Epigenetic perspectives of COVID-19: Virus infection to disease progression and therapeutic control. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166527. [PMID: 36002132 PMCID: PMC9393109 DOI: 10.1016/j.bbadis.2022.166527] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/05/2022] [Accepted: 08/18/2022] [Indexed: 11/20/2022]
Abstract
COVID-19 has caused numerous deaths as well as imposed social isolation and upheaval world-wide. Although, the genome and the composition of the virus, the entry process and replication mechanisms are well investigated from by several laboratories across the world, there are many unknown remaining questions. For example, what are the functions of membrane lipids during entry, packaging and exit of virus particles? Also, the metabolic aspects of the infected tissue cells are poorly understood. In the course of virus replication and formation of virus particles within the host cell, the enhanced metabolic activities of the host is directly proportional to viral loads. The epigenetic landscape of the host cells is also altered, particularly the expression/repression of genes associated with cellular metabolism as well as cellular processes that are antagonistic to the virus. Metabolic pathways are enzyme driven processes and the expression profile and mechanism of regulations of the respective genes encoding those enzymes during the course of pathogen invasion might be highly informative on the course of the disease. Recently, the metabolic profile of the patients' sera have been analysed from few patients. In view of this, and to gain further insights into the roles that epigenetic mechanisms might play in this scenario in regulation of metabolic pathways during the progression of COVID-19 are discussed and summarised in this contribution for ensuring best therapy.
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Affiliation(s)
- Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
| | - Moshe Szyf
- Department of Pharmacology & Therapeutics, McIntyre Medical Sciences Building, McGill University, Montreal, QC H3G 1Y6, Canada
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Zhao X, Hao Y, Wang Q, Shen Y, Cheng Y, Li B, Gao Y, Wang T, Qiu Y. Novel deoxyribonucleic acid methylation perturbations in workers exposed to vinyl chloride. Toxicol Ind Health 2022; 38:377-388. [PMID: 35548910 DOI: 10.1177/07482337221098600] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To explore the epigenetic mechanism of deoxyribonucleic acid (DNA) damage induced by vinyl chloride (VC), we studied the micronuclei of peripheral blood lymphocytes in 193 subjects (92 in a VC exposure group employed in a chlorine-alkali plant; 101 in a control group employed in a power plant) and selected three pairs from the subjects (exposed and control) for whole-genome bisulfite sequencing (WGBS). The results showed that the rate of micronucleus formation in the VC exposure group was higher than that of control group (6.05 ± 3.28‰ vs. 2.01 ± 1.79‰). A total of 9534 differentially methylated regions (DMRs) were identified by WGBS, of which 4816 were hypomethylated and 4718 were hypermethylated. The Kyoto encyclopedia of genes and genomes (KEGG) pathway and gene ontology (GO) analyses showed the top three KEGG pathways were cancer , neuroactive ligand-receptor interaction, and axon guidance, and the top three GO-BP pathways enriched were multicellular organismal process, developmental process, and anatomical structure development. In the most enriched DMR pathway (pathways in cancer), we found that BCL2, TJP2, TAOK1, PFKFB3, LIPI, and LIPH were hypermethylated, and the methylation levels of BNIP1 and GRPEL2 were decreased. The methylation of differentially methylated genes (DMGs) mentioned above were verified by methylation-specific PCR (MSP) and agarose gel electrophoresis (AGE) in 50 pairs of subjects, where the coincidence rate was 60-100%. In conclusion, the epigenetic perturbations of specific DMGs (BCL2, TJP2, TAOK1, PFKFB3, LIPI, LIPH, BNIP1, and GRPEL2) may be associated with DNA damage from vinyl chloride exposure.
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Affiliation(s)
- Xiaotian Zhao
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Yan Hao
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Qian Wang
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Yongmei Shen
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Ying Cheng
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Ben Li
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Yi Gao
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Tong Wang
- Department of Statistics, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
| | - Yulan Qiu
- Department of Toxicology, School of Public Health, 74648Shanxi Medical University, Taiyuan, China
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Lin W, Huang Z, Ping S, Zhang S, Wen X, He Y, Ren Y. Toxicological effects of atenolol and venlafaxine on zebrafish tissues: Bioaccumulation, DNA hypomethylation, and molecular mechanism. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 299:118898. [PMID: 35081461 DOI: 10.1016/j.envpol.2022.118898] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 01/02/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
The beta-blocker atenolol (ATE), and the selective serotonin and norepinephrine reuptake inhibitor, venlafaxine (VEN) are frequently detected in municipal wastewater effluents, but little is known about their ecotoxicological effect on aquatic animals. Herein, ATE and VEN were selected to explore their accumulation and global DNA methylation (GDM) in zebrafish tissues after a 30-day exposure. Molecular dynamics (MD) stimulation was used to investigate the toxic mechanism of ATE and VEN exposure. The results demonstrated that ATE and VEN could reduce the condition factor of zebrafish. The bioaccumulation capacity for ATE and VEN was in the order of liver > gut > gill > brain and liver > gut > brain > gill, respectively. After a 30-day recovery, ATE and VEN could still be detected in zebrafish tissues when exposure concentrations were ≥10 μg/L. Moreover, ATE and VEN induced global DNA hypomethylation in different tissues with a dose-dependent manner and their main target tissues were liver and brain. When the exposure concentrations of ATE and VEN were increased to 100 μg/L, the global DNA hypomethylation of liver and brain were reduced to 27% and 18%, respectively. In the same tissue exposed to the same concentration, DNA hypomethylation induced by VEN was more serious than that of ATE. After a 30-day recovery, the global DNA hypomethylations caused by the two drugs were still persistent, and the recovery of VEN was slower than that of ATE. The MD simulation results showed that both ATE and VEN could reduce the catalytic activity of DNA Methyltransferase 1 (DNMT1), while the effect of VEN on the 3D conformational changes of the DNMT1 domain was more significant, resulting in a lower DNA methylation rate. The current study shed new light on the toxic mechanism and potential adverse impacts of ATE and VEN on zebrafish, providing essential information to the further ecotoxicological risk assessment of these drugs in the aquatic environment.
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Affiliation(s)
- Wenting Lin
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Zhishan Huang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Senwen Ping
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Shuan Zhang
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, PR China
| | - Xiufang Wen
- School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, PR China
| | - Yuhe He
- School of Energy and Environment, City University of Hong Kong, Hong Kong, China
| | - Yuan Ren
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, China; The Key Laboratory of Environmental Protection and Eco-Remediation of Guangdong Regular Higher Education Institutions, China.
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9
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Liu Y, Cheng H, Cheng C, Zheng F, Zhao Z, Chen Q, Zeng W, Zhang P, Huang C, Jiang W, Liu X, Liu G. ZNF191 alters DNA methylation and activates the PI3K‐AKT pathway in hepatoma cells via transcriptional regulation of
DNMT1. Cancer Med 2022; 11:1269-1280. [PMID: 35092191 PMCID: PMC8894703 DOI: 10.1002/cam4.4535] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/04/2021] [Indexed: 12/12/2022] Open
Abstract
Background Alteration of DNA methylation is an important event in pathogenesis and progression of hepatocellular carcinoma (HCC). DNA methyltransferase (DNMT) 1, the foremost contributor in DNA methylation machinery, was revealed elevated in HCC and significantly correlates with poor prognosis. However, the transcriptional regulation of DNMT1 in HCC remains unknown. Methods Real‐time PCR and immunohistochemistry were performed to detect DNMT1 and zinc finger transcription factor 191 (ZNF191) expressions in HCCs. Transcription activity of DNMT1promoter was analyzed with Luciferase reporter activity assay. The binding capacity of ZNF191 protein to DNMT1 promoter was examined with chromatin immunoprecipitation‐qPCR (ChIP‐qPCR) and electrophoretic mobility shift assay (EMSA). DNA methylation level of hepatoma cells was detected with Methylation array. Results ZNF191 can regulate DNMT1 mRNA and protein expression positively, and increase the transcription activity of the DNMT1 promoter. ChIP‐qPCR and EMSA revealed that ZNF191 protein directly binds to the DNMT1 promoter at nt‐240 AT(TCAT)3TC. Moreover, DNMT1 and ZNF191 expression correlate positively in human HCCs. With methylation array, DNA methylation alteration was observed in hepatoma cells with ZNF191 knockdown, and the differential methylation sites are enriched in the PI3K‐AKT pathway. Furthermore, we proved DNMT1 contributes the effect of ZNF191 on hepatoma cell growth via the PI3K‐AKT pathway. Conclusion ZNF191 is a novel transcription regulator for DNMT1, and the pro‐proliferation effect of ZNF191/DNMT1/p‐AKT axis in hepatoma cells implies that ZNF191 status in HCCs may affect the therapeutic effect of DNMTs inhibitors and PI3K inhibitors for precise treatment of the disease.
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Affiliation(s)
- Yufeng Liu
- Department of Pathology School of Basic Medical Sciences Fudan University Shanghai China
| | - Hanghang Cheng
- Department of Pathology School of Basic Medical Sciences Fudan University Shanghai China
| | - Chenchen Cheng
- Department of Pathology School of Basic Medical Sciences Fudan University Shanghai China
| | - Fengyun Zheng
- Institutes of Biomedical Sciences Fudan University Shanghai China
| | - Zhonghua Zhao
- Department of Pathology School of Basic Medical Sciences Fudan University Shanghai China
| | - Qi Chen
- Department of Pathology School of Basic Medical Sciences Fudan University Shanghai China
| | - Wenjiao Zeng
- Department of Pathology School of Basic Medical Sciences Fudan University Shanghai China
| | - Pingzhao Zhang
- Department of Pathology School of Basic Medical Sciences Fudan University Shanghai China
| | - Cheng Huang
- Department of Liver Surgery & Transplantation Liver Cancer Institute Zhongshan Hospital Fudan University Shanghai China
| | - Wei Jiang
- Key Laboratory of Metabolism and Molecular Medicine The Ministry of Education Department of Biochemistry and Molecular Biology School of Basic Medical Sciences Fudan University Shanghai China
| | - Xiuping Liu
- Department of Pathology Shanghai Fifth People’s Hospital School of Basic Medical Sciences Fudan University Shanghai China
| | - Guoyuan Liu
- Department of Pathology School of Basic Medical Sciences Fudan University Shanghai China
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10
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Mensah IK, Norvil AB, AlAbdi L, McGovern S, Petell CJ, He M, Gowher H. Misregulation of the expression and activity of DNA methyltransferases in cancer. NAR Cancer 2021; 3:zcab045. [PMID: 34870206 PMCID: PMC8634572 DOI: 10.1093/narcan/zcab045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/29/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022] Open
Abstract
In mammals, DNA methyltransferases DNMT1 and DNMT3's (A, B and L) deposit and maintain DNA methylation in dividing and nondividing cells. Although these enzymes have an unremarkable DNA sequence specificity (CpG), their regional specificity is regulated by interactions with various protein factors, chromatin modifiers, and post-translational modifications of histones. Changes in the DNMT expression or interacting partners affect DNA methylation patterns. Consequently, the acquired gene expression may increase the proliferative potential of cells, often concomitant with loss of cell identity as found in cancer. Aberrant DNA methylation, including hypermethylation and hypomethylation at various genomic regions, therefore, is a hallmark of most cancers. Additionally, somatic mutations in DNMTs that affect catalytic activity were mapped in Acute Myeloid Leukemia cancer cells. Despite being very effective in some cancers, the clinically approved DNMT inhibitors lack specificity, which could result in a wide range of deleterious effects. Elucidating distinct molecular mechanisms of DNMTs will facilitate the discovery of alternative cancer therapeutic targets. This review is focused on: (i) the structure and characteristics of DNMTs, (ii) the prevalence of mutations and abnormal expression of DNMTs in cancer, (iii) factors that mediate their abnormal expression and (iv) the effect of anomalous DNMT-complexes in cancer.
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Affiliation(s)
- Isaiah K Mensah
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Lama AlAbdi
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sarah McGovern
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Ming He
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
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11
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Zhu Y, Ye F, Zhou Z, Liu W, Liang Z, Hu G. Insights into Conformational Dynamics and Allostery in DNMT1-H3Ub/USP7 Interactions. Molecules 2021; 26:molecules26175153. [PMID: 34500587 PMCID: PMC8434485 DOI: 10.3390/molecules26175153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/23/2021] [Accepted: 08/23/2021] [Indexed: 01/03/2023] Open
Abstract
DNA methyltransferases (DNMTs) including DNMT1 are a conserved family of cytosine methylases that play crucial roles in epigenetic regulation. The versatile functions of DNMT1 rely on allosteric networks between its different interacting partners, emerging as novel therapeutic targets. In this work, based on the modeling structures of DNMT1-ubiquitylated H3 (H3Ub)/ubiquitin specific peptidase 7 (USP7) complexes, we have used a combination of elastic network models, molecular dynamics simulations, structural residue perturbation, network modeling, and pocket pathway analysis to examine their molecular mechanisms of allosteric regulation. The comparative intrinsic and conformational dynamics analysis of three DNMT1 systems has highlighted the pivotal role of the RFTS domain as the dynamics hub in both intra- and inter-molecular interactions. The site perturbation and network modeling approaches have revealed the different and more complex allosteric interaction landscape in both DNMT1 complexes, involving the events caused by mutational hotspots and post-translation modification sites through protein-protein interactions (PPIs). Furthermore, communication pathway analysis and pocket detection have provided new mechanistic insights into molecular mechanisms underlying quaternary structures of DNMT1 complexes, suggesting potential targeting pockets for PPI-based allosteric drug design.
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Affiliation(s)
- Yu Zhu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China; (Y.Z.); (Z.Z.); (W.L.)
| | - Fei Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China;
| | - Ziyun Zhou
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China; (Y.Z.); (Z.Z.); (W.L.)
| | - Wanlin Liu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China; (Y.Z.); (Z.Z.); (W.L.)
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China; (Y.Z.); (Z.Z.); (W.L.)
- Correspondence: (Z.L.); (G.H.)
| | - Guang Hu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China; (Y.Z.); (Z.Z.); (W.L.)
- Correspondence: (Z.L.); (G.H.)
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12
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Recalde M, Gárate-Rascón M, Elizalde M, Azkona M, Latasa MU, Bárcena-Varela M, Sangro B, Fernández-Barrena MG, Ávila MA, Arechederra M, Berasain C. The splicing regulator SLU7 is required to preserve DNMT1 protein stability and DNA methylation. Nucleic Acids Res 2021; 49:8592-8609. [PMID: 34331453 PMCID: PMC8421144 DOI: 10.1093/nar/gkab649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/01/2021] [Accepted: 07/21/2021] [Indexed: 01/13/2023] Open
Abstract
Gene expression is finely and dynamically controlled through the tightly coordinated and interconnected activity of epigenetic modulators, transcription and splicing factors and post-translational modifiers. We have recently identified the splicing factor SLU7 as essential for maintaining liver cell identity and genome integrity and for securing cell division both trough transcriptional and splicing mechanisms. Now we uncover a new function of SLU7 controlling gene expression at the epigenetic level. We show that SLU7 is required to secure DNMT1 protein stability and a correct DNA methylation. We demonstrate that SLU7 is part in the chromatome of the protein complex implicated in DNA methylation maintenance interacting with and controlling the integrity of DNMT1, its adaptor protein UHRF1 and the histone methyl-transferase G9a at the chromatin level. Mechanistically, we found that SLU7 assures DNMT1 stability preventing its acetylation and degradation by facilitating its interaction with HDAC1 and the desubiquitinase USP7. Importantly, we demonstrate that this DNMT1 dependency on SLU7 occurs in a large panel of proliferating cell lines of different origins and in in vivo models of liver proliferation. Overall, our results uncover a novel and non-redundant role of SLU7 in DNA methylation and present SLU7 as a holistic regulator of gene expression.
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Affiliation(s)
- Miriam Recalde
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain
| | - María Gárate-Rascón
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain
| | - María Elizalde
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain
| | - María Azkona
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain
| | - M Ujue Latasa
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona 31008, Spain
| | - Marina Bárcena-Varela
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain
| | - Bruno Sangro
- IdiSNA, Navarra Institute for Health Research, Pamplona 31008, Spain.,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid 28029, Spain.,Hepatology Unit, Navarra University Clinic, Pamplona 31008, Spain
| | - Maite G Fernández-Barrena
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona 31008, Spain.,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid 28029, Spain
| | - Matías A Ávila
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona 31008, Spain.,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid 28029, Spain
| | - María Arechederra
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona 31008, Spain
| | - Carmen Berasain
- Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona 31008, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona 31008, Spain.,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), Madrid 28029, Spain
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13
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Sahm A, Koch P, Horvath S, Hoffmann S. An analysis of methylome evolution in primates. Mol Biol Evol 2021; 38:4700-4714. [PMID: 34175932 PMCID: PMC8557466 DOI: 10.1093/molbev/msab189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Although the investigation of the epigenome becomes increasingly important, still little is known about the long-term evolution of epigenetic marks and systematic investigation strategies are still lacking. Here, we systematically demonstrate the transfer of classic phylogenetic methods such as maximum likelihood based on substitution models, parsimony, and distance-based to interval-scaled epigenetic data. Using a great apes blood data set, we demonstrate that DNA methylation is evolutionarily conserved at the level of individual CpGs in promotors, enhancers, and genic regions. Our analysis also reveals that this epigenomic conservation is significantly correlated with its transcription factor binding density. Binding sites for transcription factors involved in neuron differentiation and components of AP-1 evolve at a significantly higher rate at methylation than at the nucleotide level. Moreover, our models suggest an accelerated epigenomic evolution at binding sites of BRCA1, chromobox homolog protein 2, and factors of the polycomb repressor 2 complex in humans. For most genomic regions, the methylation-based reconstruction of phylogenetic trees is at par with sequence-based reconstruction. Most strikingly, phylogenetic reconstruction using methylation rates in enhancer regions was ineffective independently of the chosen model. We identify a set of phylogenetically uninformative CpG sites enriched in enhancers controlling immune-related genes.
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Affiliation(s)
- Arne Sahm
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Philipp Koch
- Core Facility Life Science Computing, Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
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14
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Singh P, Kairuz D, Arbuthnot P, Bloom K. Silencing hepatitis B virus covalently closed circular DNA: The potential of an epigenetic therapy approach. World J Gastroenterol 2021; 27:3182-3207. [PMID: 34163105 PMCID: PMC8218364 DOI: 10.3748/wjg.v27.i23.3182] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/23/2021] [Accepted: 05/07/2021] [Indexed: 02/06/2023] Open
Abstract
Global prophylactic vaccination programmes have helped to curb new hepatitis B virus (HBV) infections. However, it is estimated that nearly 300 million people are chronically infected and have a high risk of developing hepatocellular carcinoma. As such, HBV remains a serious health priority and the development of novel curative therapeutics is urgently needed. Chronic HBV infection has been attributed to the persistence of the covalently closed circular DNA (cccDNA) which establishes itself as a minichromosome in the nucleus of hepatocytes. As the viral transcription intermediate, the cccDNA is responsible for producing new virions and perpetuating infection. HBV is dependent on various host factors for cccDNA formation and the minichromosome is amenable to epigenetic modifications. Two HBV proteins, X (HBx) and core (HBc) promote viral replication by modulating the cccDNA epigenome and regulating host cell responses. This includes viral and host gene expression, chromatin remodeling, DNA methylation, the antiviral immune response, apoptosis, and ubiquitination. Elimination of the cccDNA minichromosome would result in a sterilizing cure; however, this may be difficult to achieve. Epigenetic therapies could permanently silence the cccDNA minichromosome and promote a functional cure. This review explores the cccDNA epigenome, how host and viral factors influence transcription, and the recent epigenetic therapies and epigenome engineering approaches that have been described.
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Affiliation(s)
- Prashika Singh
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2050, Gauteng, South Africa
| | - Dylan Kairuz
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2050, Gauteng, South Africa
| | - Patrick Arbuthnot
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2050, Gauteng, South Africa
| | - Kristie Bloom
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2050, Gauteng, South Africa
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15
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Hegde M, Joshi MB. Comprehensive analysis of regulation of DNA methyltransferase isoforms in human breast tumors. J Cancer Res Clin Oncol 2021; 147:937-971. [PMID: 33604794 PMCID: PMC7954751 DOI: 10.1007/s00432-021-03519-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/10/2021] [Indexed: 12/14/2022]
Abstract
Significant reprogramming of epigenome is widely described during pathogenesis of breast cancer. Transformation of normal cell to hyperplastic cell and to neoplastic phenotype is associated with aberrant DNA (de)methylation, which, through promoter and enhancer methylation changes, activates oncogenes and silence tumor suppressor genes in variety of tumors including breast. DNA methylation, one of the major epigenetic mechanisms is catalyzed by evolutionarily conserved isoforms namely, DNMT1, DNMT3A and DNMT3B in humans. Over the years, studies have demonstrated intricate and complex regulation of DNMT isoforms at transcriptional, translational and post-translational levels. The recent findings of allosteric regulation of DNMT isoforms and regulation by other interacting chromatin modifying proteins emphasizes functional integrity and their contribution for the development of breast cancer and progression. DNMT isoforms are regulated by several intrinsic and extrinsic parameters. In the present review, we have extensively performed bioinformatics analysis of expression of DNMT isoforms along with their transcriptional and post-transcriptional regulators such as transcription factors, interacting proteins, hormones, cytokines and dietary elements along with their significance during pathogenesis of breast tumors. Our review manuscript provides a comprehensive understanding of key factors regulating DNMT isoforms in breast tumor pathology and documents unsolved issues.
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Affiliation(s)
- Mangala Hegde
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Planetarium Complex, Manipal, 576104, India
| | - Manjunath B Joshi
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Planetarium Complex, Manipal, 576104, India.
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16
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Martella A, Fisher DI. Regulation of Gene Expression and the Elucidative Role of CRISPR-Based Epigenetic Modifiers and CRISPR-Induced Chromosome Conformational Changes. CRISPR J 2021; 4:43-57. [PMID: 33616442 DOI: 10.1089/crispr.2020.0108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In complex multicellular systems, gene expression is regulated at multiple stages through interconnected complex molecular pathways and regulatory networks. Transcription is the first step in gene expression and is subject to multiple layers of regulation in which epigenetic mechanisms such as DNA methylation, histone tail modifications, and chromosomal conformation play an essential role. In recent years, CRISPR-Cas9 systems have been employed to unearth this complexity and provide new insights on the contribution of chromatin dysregulation in the development of genetic diseases, as well as new tools to prevent or reverse this dysregulation. In this review, we outline the recent development of a variety of CRISPR-based epigenetic editors for targeted DNA methylation/demethylation, histone modification, and three-dimensional DNA conformational change, highlighting their relative performance and impact on gene regulation. Finally, we provide insights on the future developments aimed to accelerate our understanding of the causal relationship between epigenetic marks, genome organization, and gene regulation.
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Affiliation(s)
- Andrea Martella
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - David I Fisher
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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17
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Lin W, Yan Y, Ping S, Li P, Li D, Hu J, Liu W, Wen X, Ren Y. Metformin-Induced Epigenetic Toxicity in Zebrafish: Experimental and Molecular Dynamics Simulation Studies. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:1672-1681. [PMID: 33332093 DOI: 10.1021/acs.est.0c06052] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The increased detection of many prescription drugs in aquatic environments has heightened concerns of their potential ecotoxicological effects. In this study, the effects of metformin (MEF) exposure on tissue accumulation, gene expression, and global DNA methylation (GDM) in zebrafish were investigated. The toxic mechanism of MEF exposure was simulated by molecular dynamics (MD) to reveal any conformational changes to DNA methyltransferase 1 (DNMT1). The results showed MEF accumulation in the gills, gut, and liver of zebrafish after 30 days of exposure, and the bioaccumulation capacity was in the order of gut > liver > gills. After a 30 day recovery period, MEF could still be detected in zebrafish tissues in groups exposed to MEF concentrations ≥ 10 μg/L. Moreover, the liver was the main site of GDM, and the restoration of GDM in the liver was slower than that in the gut and gills during the recovery period. Furthermore, MEF could induce the abnormal expression of CYP3A65, GSTM1, p53, and DNMT1 genes in the liver due to the formation of hydrogen bonds between MEF and the protein residues of those genes. The MD simulation allowed for the mechanistic determination of MEF-induced three-dimensional (3D) conformational changes and changes to the catalytic activity of DNMT1.
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Affiliation(s)
- Wenting Lin
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yuanyang Yan
- School of Chemical and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Senwen Ping
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, P. R. China
| | - Ping Li
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, P. R. China
| | - Diandi Li
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, P. R. China
| | - Junjie Hu
- School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan 523808, P. R. China
| | - Wei Liu
- School of Medicine, South China University of Technology, Guangzhou 510006, P. R. China
| | - Xiufang Wen
- School of Chemical and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - Yuan Ren
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, P. R. China
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, China
- The Key Laboratory of Environmental Protection and Eco-Remediation of Guangdong Regular Higher Education Institutions, Guangzhou 510006, China
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18
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Redl E, Sheibani-Tezerji R, Cardona CDJ, Hamminger P, Timelthaler G, Hassler MR, Zrimšek M, Lagger S, Dillinger T, Hofbauer L, Draganić K, Tiefenbacher A, Kothmayer M, Dietz CH, Ramsahoye BH, Kenner L, Bock C, Seiser C, Ellmeier W, Schweikert G, Egger G. Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK-driven lymphomagenesis. Life Sci Alliance 2021; 4:e202000794. [PMID: 33310759 PMCID: PMC7768196 DOI: 10.26508/lsa.202000794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 11/28/2020] [Accepted: 12/01/2020] [Indexed: 12/31/2022] Open
Abstract
Malignant transformation depends on genetic and epigenetic events that result in a burst of deregulated gene expression and chromatin changes. To dissect the sequence of events in this process, we used a T-cell-specific lymphoma model based on the human oncogenic nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) translocation. We find that transformation of T cells shifts thymic cell populations to an undifferentiated immunophenotype, which occurs only after a period of latency, accompanied by induction of the MYC-NOTCH1 axis and deregulation of key epigenetic enzymes. We discover aberrant DNA methylation patterns, overlapping with regulatory regions, plus a high degree of epigenetic heterogeneity between individual tumors. In addition, ALK-positive tumors show a loss of associated methylation patterns of neighboring CpG sites. Notably, deletion of the maintenance DNA methyltransferase DNMT1 completely abrogates lymphomagenesis in this model, despite oncogenic signaling through NPM-ALK, suggesting that faithful maintenance of tumor-specific methylation through DNMT1 is essential for sustained proliferation and tumorigenesis.
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Affiliation(s)
- Elisa Redl
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | | | | | - Patricia Hamminger
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Gerald Timelthaler
- Institute of Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Melanie Rosalia Hassler
- Department of Pathology, Medical University of Vienna, Vienna, Austria
- Department of Urology, Medical University of Vienna, Vienna, Austria
| | - Maša Zrimšek
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Sabine Lagger
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Thomas Dillinger
- Department of Pathology, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute Applied Diagnostics (LBI AD), Vienna, Austria
| | - Lorena Hofbauer
- Department of Pathology, Medical University of Vienna, Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Kristina Draganić
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Andreas Tiefenbacher
- Department of Pathology, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute Applied Diagnostics (LBI AD), Vienna, Austria
| | - Michael Kothmayer
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Charles H Dietz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Bernard H Ramsahoye
- Centre for Genetic and Experimental Medicine, Institute of Genomic and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Lukas Kenner
- Department of Pathology, Medical University of Vienna, Vienna, Austria
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine Vienna, Vienna, Austria
- Christian Doppler Laboratory for Applied Metabolomics (CDL-AM), Medical University of Vienna, Vienna, Austria
- Center for Biomarker Research in Medicine (CBmed), CoreLab 2, Medical University of Vienna, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Christian Seiser
- Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Wilfried Ellmeier
- Division of Immunobiology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Gabriele Schweikert
- Max Planck Institute for Intelligent Systems, Tübingen, Germany
- Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Gerda Egger
- Department of Pathology, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute Applied Diagnostics (LBI AD), Vienna, Austria
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19
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Alves N, Neuparth T, Barros S, Santos MM. The anti-lipidemic drug simvastatin modifies epigenetic biomarkers in the amphipod Gammarus locusta. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 209:111849. [PMID: 33387775 DOI: 10.1016/j.ecoenv.2020.111849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
The adverse effects of certain environmental chemicals have been recently associated with the modulation of the epigenome. Although changes in the epigenetic signature have yet to be integrated into hazard and risk assessment, they are interesting candidates to link environmental exposures and altered phenotypes, since these changes may be passed across multiple non-exposed generations. Here, we addressed the effects of simvastatin (SIM), one of the most prescribed pharmaceuticals in the world, on epigenetic regulation using the amphipod Gammarus locusta as a proxy, to support its integration into hazard and environmental risk assessment. SIM is a known modulator of the epigenome in mammalian cell lines and has been reported to impact G. locusta ecological endpoints at environmentally relevant levels. G. locusta juveniles were exposed to three SIM environmentally relevant concentrations (0.32, 1.6 and 8 µg L-1) for 15 days. Gene transcription levels of selected epigenetic regulators, i.e., dnmt1, dmap1, usp7, kat5 and uhrf1 were assessed, along with the quantification of DNA methylation levels and evaluation of key ecological endpoints: survival and growth. Exposure to 0.32 and 8 µg L-1 SIM induced significant downregulation of DNA methyltransferase 1 (dnmt1), concomitant with global DNA hypomethylation and growth impacts. Overall, this work is the first to validate the basal expression of key epigenetic regulators in a keystone marine crustacean, supporting the integration of epigenetic biomarkers into hazard assessment frameworks.
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Affiliation(s)
- Nélson Alves
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Endocrine Disruptors and Emerging Contaminants Group, University of Porto, Avenida General Norton de Matos S/N, 4450-208 Matosinhos, Portugal; FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre nº 1021/1055, 4169-007 Porto, Portugal
| | - Teresa Neuparth
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Endocrine Disruptors and Emerging Contaminants Group, University of Porto, Avenida General Norton de Matos S/N, 4450-208 Matosinhos, Portugal.
| | - Susana Barros
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Endocrine Disruptors and Emerging Contaminants Group, University of Porto, Avenida General Norton de Matos S/N, 4450-208 Matosinhos, Portugal
| | - Miguel M Santos
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Endocrine Disruptors and Emerging Contaminants Group, University of Porto, Avenida General Norton de Matos S/N, 4450-208 Matosinhos, Portugal; FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre nº 1021/1055, 4169-007 Porto, Portugal.
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20
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Yang M, Barrios J, Yan J, Zhao W, Yuan S, Dong E, Ai X. Causal roles of stress kinase JNK2 in DNA methylation and binge alcohol withdrawal-evoked behavioral deficits. Pharmacol Res 2021; 164:105375. [PMID: 33316384 PMCID: PMC7867628 DOI: 10.1016/j.phrs.2020.105375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/20/2020] [Accepted: 12/06/2020] [Indexed: 11/27/2022]
Abstract
Excessive binge alcohol intake is a common drinking pattern in humans, especially during holidays. Cessation of the binge drinking often leads to aberrant withdrawal behaviors, as well as serious heart rhythm abnormalities (clinically diagnosed as Holiday Heart Syndrome (HHS)). In our HHS mouse model with well-characterized binge alcohol withdrawal (BAW)-induced heart phenotypes, BAW leads to anxiety-like behaviors and cognitive impairment. We have previously reported that stress-activated c-Jun NH(2)-terminal kinase (JNK) plays a causal role in BAW-induced heart phenotypes. In the HHS brain, we found that activation of JNK2 (but not JNK1 and JNK3) in the prefrontal cortex (PFC), but not hippocampus and amygdala, led to anxiety-like behaviors and impaired cognition. DNA methylation mediated by a crucial DNA methylation enzyme, DNA methyltransferase1 (DNMT1), is known to be critical in alcohol-associated behavioral deficits. In HHS mice, JNK2 in the PFC (but not hippocampus and amygdala) causally enhanced total genomic DNA methylation via increased DNMT1 expression, which was regulated by enhanced binding of JNK downstream transcriptional factor c-JUN to the DNMT1 promoter. JNK2-specific inhibition either by an inhibitor JNK2I or JNK2 knockout completely offset c-JUN-regulated DNMT1 upregulation and restored the level of DNA methylation in HHS PFC to the baseline levels seen in sham controls. Strikingly, either JNK2-specific inhibition or genetic JNK2 depletion or DNMT1 inhibition (by an inhibitor 5-Azacytidine) completely abolished BAW-evoked behavioral deficits. In conclusion, our studies revealed a novel mechanism by which JNK2 drives BAW-evoked behavioral deficits through a DNMT1-regulated DNA hypermethylation. JNK2 could be a novel therapeutic target for alcohol withdrawal treatment and/or prevention.
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Affiliation(s)
- Mei Yang
- Department of Physiology & Biophysics, Rush University Medical Center, Chicago, IL, 60607, USA
| | - Jasson Barrios
- Department of Physiology & Biophysics, Rush University Medical Center, Chicago, IL, 60607, USA
| | - Jiajie Yan
- Department of Physiology & Biophysics, Rush University Medical Center, Chicago, IL, 60607, USA
| | - Weiwei Zhao
- Department of Physiology & Biophysics, Rush University Medical Center, Chicago, IL, 60607, USA
| | - Shengtao Yuan
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing, 210009, China
| | - Erbo Dong
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, IL, 60612, USA.
| | - Xun Ai
- Department of Physiology & Biophysics, Rush University Medical Center, Chicago, IL, 60607, USA.
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21
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Nair J, Maheshwari A. Epigenetics in Necrotizing Enterocolitis. Curr Pediatr Rev 2021; 17:172-184. [PMID: 33882811 DOI: 10.2174/1573396317666210421110608] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/14/2021] [Accepted: 02/26/2021] [Indexed: 11/22/2022]
Abstract
Epigenetic alterations in our genetic material can lead to heritable changes in the risk, clinical manifestations, course, and outcomes of many diseases. Understanding these epigenetic mechanisms can help in identifying potential therapeutic targets. This is especially important in necrotizing enterocolitis (NEC), where prenatal as well as postnatal factors impact susceptibility to this devastating condition, but our therapeutic options are limited. Developmental factors affecting intestinal structure and function, our immune system, gut microbiome, and postnatal enteral nutrition are all thought to play a prominent role in this disease. In this manuscript, we have reviewed the epigenetic mechanisms involved in NEC. These include key developmental changes in DNA methylation in the immature intestine, the role of long non-coding RNA (lncRNA) in maintaining intestinal barrier function, epigenetic influences of prenatal inflammation on immunological pathways in NEC pathogenesis such as Toll-Like Receptor 4 (TLR4) and epigenetic changes associated with enteral feeding causing upregulation of pro-inflammatory genes. We have assimilated research findings from our own laboratory with an extensive review of the literature utilizing key terms in multiple databases, including PubMed, EMBASE, and Science Direct.
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Affiliation(s)
- Jayasree Nair
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| | - Akhil Maheshwari
- Department of Pediatrics, Johns Hopkins University, Baltimore, MA, United States
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22
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Lee KH, Hwang HJ, Cho JY. Long Non-Coding RNA Associated with Cholesterol Homeostasis and Its Involvement in Metabolic Diseases. Int J Mol Sci 2020; 21:E8337. [PMID: 33172104 PMCID: PMC7664438 DOI: 10.3390/ijms21218337] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
Cholesterol is an essential cell component that functions to create and maintain all kinds of cell membranes and lipoprotein particles. It is crucial to maintain the proper amount of cholesterol at both the cellular and systemic level. Recently, the importance of cholesterol has been reported not only in various cell development processes but also in the development of diseases. Furthermore, the involvement of long non-coding RNAs (lncRNAs), which are regarded as important epigenetic regulators in gene expression, has also been reported in cholesterol homeostasis. It is thus necessary to summarize the research on lncRNAs related to cholesterol with increased interest. This review organized the role of lncRNAs according to the major issues in cholesterol homeostasis: efflux, metabolism and synthesis, and disease process.
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Affiliation(s)
| | | | - Je-Yoel Cho
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul 08826, Korea; (K.-H.L.); (H.-J.H.)
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23
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Patra SK. Roles of OCT4 in pathways of embryonic development and cancer progression. Mech Ageing Dev 2020; 189:111286. [PMID: 32531293 DOI: 10.1016/j.mad.2020.111286] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/08/2020] [Accepted: 06/06/2020] [Indexed: 12/11/2022]
Abstract
Somatic cells may be reprogrammed to pluripotent state by ectopic expression of certain transcription factors; namely, OCT4, SOX2, KLF4 and c-MYC. However, the molecular and cellular mechanisms are not adequately understood, especially for human embryonic development. Studies during the last five years implicated importance of OCT4 in human zygotic genome activation (ZGA), patterns of OCT4 protein folding and role of specialized sequences in binding to DNA for modulation of gene expression during development. Epigenetic modulation of OCT4 gene and post translational modifications of OCT4 protein activity in the context of multiple cancers are important issues. A consensus is emerging that chromatin organization and epigenetic landscape play crucial roles for the interactions of transcription factors, including OCT4 with the promoters and/or regulatory sequences of genes associated with human embryonic development (ZGA through lineage specification) and that when the epigenome niche is deregulated OCT4 helps in cancer progression, and how OCT4 silencing in somatic cells of adult organisms may impact ageing.
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Affiliation(s)
- Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India.
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24
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Yang Q, Jiang W, Hou P. Emerging role of PI3K/AKT in tumor-related epigenetic regulation. Semin Cancer Biol 2019; 59:112-124. [DOI: 10.1016/j.semcancer.2019.04.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 03/14/2019] [Accepted: 04/01/2019] [Indexed: 01/23/2023]
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25
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Maric H, Supic G, Kandolf-Sekulovic L, Maric V, Mijuskovic Z, Radevic T, Rajovic M, Magic Z. DNMT1 and DNMT3B genetic polymorphisms affect the clinical course and outcome of melanoma patients. Melanoma Res 2019; 29:596-602. [PMID: 30950914 DOI: 10.1097/cmr.0000000000000612] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The aberrant DNA methylation plays a critical role in a number of different malignancies, including melanoma. DNA methylation is catalyzed by DNA methyltransferases (DNMTs), involved in methylation maintenance (DNMT1) and de novo DNA methylation (DNMT3A and DNMT3B). The current study investigated the association of genetic variants in the DNMT1 and DNMT3B with the clinicopathologic features and the clinical course of melanoma patients. In the present study, DNMT1 (rs2228612, rs2228611, and rs2114724) and DNMT3B (rs406193 and rs2424932) polymorphisms were examined in 123 melanoma patients. Single nucleotide polymorphisms were assessed using TaqMan SNPs Genotyping Assays according to the manufacturer's protocols. The carriers of the variant genotype of DNMT1 rs2228612 had poorer overall survival and recurrence-free survival, (P = 0.000 and 0.000, respectively), and an increased risk for adverse outcome [hazard ratio (HR) = 6.620, 95% confidence interval (CI): 2.214-19.791, P = 0.001]. DNMT1 rs2228612 was also associated with ulceration (P = 0.045), nodal status (P = 0.030), progression (P = 0. 007), and stage of disease (P = 0.003). Univariate analysis indicated that tumor-infiltrating lymphocytes could be a marker of good prognosis in melanoma patients (HR = 0.323, 95% CI: 0.127-0.855, P = 0.025), whereas the genotype distribution of the DNMT3B rs406193 polymorphism correlated significantly with the presence of tumor-infiltrating lymphocytes (P = 0.012). The multivariate analysis showed that the DNMT1 rs2228612 polymorphism (HR = 12.126, 95% CI: 2.345-62.715, P = 0.003) is an independent predictor of poor overall survival in melanoma patients. As expected, disease progression was also found to be an independent prognostic factor in melanoma patients (HR = 37.888, 95% CI: 3.615-397.062, P = 0.002). DNMT1 rs2228612 was found to be an independent predictor of poor overall survival in melanoma patients. DNMTs polymorphisms could serve as a potential target for novel therapeutic approaches.
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Affiliation(s)
- Helena Maric
- Second Surgery Clinic, University Hospital of Foca, Foca
| | | | | | - Veljko Maric
- Department of Surgery, Faculty of Medicine Foca, University of East Sarajevo, Lukavica, Serbia
| | | | | | - Milica Rajovic
- Clinic for Plastic and Reconstructive Surgery, Military Medical Academy, University of Defense, Belgrade
| | - Zvonko Magic
- Faculty of Medicine
- Institute for Medical Research
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26
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Yu J, Zayas J, Qin B, Wang L. Targeting DNA methylation for treating triple-negative breast cancer. Pharmacogenomics 2019; 20:1151-1157. [PMID: 31755366 PMCID: PMC7026764 DOI: 10.2217/pgs-2019-0078] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/23/2019] [Indexed: 12/31/2022] Open
Abstract
Triple-negative breast cancer (TNBC) accounts for 15-20% of all invasive breast cancers and tends to have aggressive histological features and poor clinical outcomes. Unlike, estrogen receptor- or HER2-positive diseases, TNBC patients currently lack the US FDA-approved targeted therapies. DNA methylation is a critical mechanism of epigenetic modification. It is well known that aberrant DNA methylation contributes to the malignant transformation of cells by silencing critical tumor suppressor genes. DNA methyltransferase inhibitors reactivate silenced tumor suppressor genes and result in tumor growth arrest, with therapeutic effects observed in patients with hematologic malignancies. The antitumor effect of these DNA methyltransferase inhibitors has also been explored in solid tumors, especially in TNBC that currently lacks targeted therapies.
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Affiliation(s)
- Jia Yu
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jacqueline Zayas
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic School of Medicine & The Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN 55905, USA
| | - Bo Qin
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Liewei Wang
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
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27
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Biological plasticity rescues target activity in CRISPR knock outs. Nat Methods 2019; 16:1087-1093. [PMID: 31659326 DOI: 10.1038/s41592-019-0614-5] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/11/2019] [Indexed: 12/26/2022]
Abstract
Gene knock outs (KOs) are efficiently engineered through CRISPR-Cas9-induced frameshift mutations. While the efficiency of DNA editing is readily verified by DNA sequencing, a systematic understanding of the efficiency of protein elimination has been lacking. Here we devised an experimental strategy combining RNA sequencing and triple-stage mass spectrometry to characterize 193 genetically verified deletions targeting 136 distinct genes generated by CRISPR-induced frameshifts in HAP1 cells. We observed residual protein expression for about one third of the quantified targets, at variable levels from low to original, and identified two causal mechanisms, translation reinitiation leading to N-terminally truncated target proteins or skipping of the edited exon leading to protein isoforms with internal sequence deletions. Detailed analysis of three truncated targets, BRD4, DNMT1 and NGLY1, revealed partial preservation of protein function. Our results imply that systematic characterization of residual protein expression or function in CRISPR-Cas9-generated KO lines is necessary for phenotype interpretation.
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28
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Yi Y, Xie H, Xiao X, Wang B, Du R, Liu Y, Li Z, Wang J, Sun L, Deng Z, Li J. Ultraviolet A irradiation induces senescence in human dermal fibroblasts by down-regulating DNMT1 via ZEB1. Aging (Albany NY) 2019; 10:212-228. [PMID: 29466247 PMCID: PMC5842848 DOI: 10.18632/aging.101383] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 02/09/2018] [Indexed: 12/20/2022]
Abstract
In this study, we report the role of DNA methyltransferase 1 (DNMT1) in ultraviolet A (UVA)-induced senescence in human dermal fibroblasts (HDFs). We show that DNMT1 expression was significantly reduced during UVA-induced senescence, and this senescence could be alleviated or aggravated by the up- or down-regulation of DNMT1, respectively. Expression of the transcription factor zinc finger E-box binding homeobox 1(ZEB1) also decreased after UVA irradiation, following a UVA-induced increase of intracellular reactive oxygen species (ROS). We show that ZEB1 binds to the DMNT1 promoter and regulates its transcription, which, in turn, affects cellular senescence. These changes in DMNT1 and ZEB1 expression following UVA exposure were confirmed in matched skin specimens that had or had not been sun-exposed. On analyzing the promoter methylation of 24 senescence associated genes in these matched skin specimens, we discovered that p53 promoter methylation was significantly reduced in sun-exposed skin. In vitro experiments confirmed that UVA irradiation reduced p53 promoter methylation, and DNMT1 up-regulation could reverse this effect. Collectively, down-regulation of ZEB1 caused by UVA induced ROS could transcriptionally inhibit DNMT1, leading to low methylation level of senescence related proteins p53 and increase its expression, eventually result in cellar senescence.
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Affiliation(s)
- Yuxin Yi
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongfu Xie
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiao Xiao
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Ben Wang
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Rui Du
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Yingzi Liu
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Zibo Li
- The State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha, China
| | - Jun Wang
- The State Key Laboratory of Medical Genetics & School of Life Sciences, Central South University, Changsha, China
| | - Lunquan Sun
- Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Zhili Deng
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, China.,Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Ji Li
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, China.,Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
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29
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Cao Y, Wang B, Wang D, Zhan D, Mai C, Wang P, Wei Q, Liu Y, Wang H, He W, Xu L. Expression of Sclerostin in Osteoporotic Fracture Patients Is Associated with DNA Methylation in the CpG Island of the SOST Gene. Int J Genomics 2019; 2019:7076513. [PMID: 30729116 PMCID: PMC6341240 DOI: 10.1155/2019/7076513] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 09/26/2018] [Accepted: 10/11/2018] [Indexed: 01/17/2023] Open
Abstract
PURPOSE SOST gene is one of the key factors in regulating bone absorption. Although there are reports showing diverse transcription factors, epigenetic modification could be responsible for regulating SOST gene expression. There is still little exploration on promoter methylation status of SOST gene in osteoporotic bone tissues. The aim of this study is to investigate the involvement of CpG methylation in regulation of SOST expression in patients with primary osteoporosis. METHODS The diagnosis of osteoporosis was established on the basis of dual energy X-ray absorptiometry to measure BMD. All femoral bone tissues were separated in surgeries. After extracting total RNA and protein, we checked the relative expression levels of SOST by quantitative real-time PCR and western blot. Also, immunohistochemical staining was performed to observe the expression of SOST protein in the bone samples. The genomic DNA of non-OPF (non-osteoporotic fracture bone tissues) and OPF (osteoporotic fracture bone tissues) were treated by bisulfite modification, and methylation status of CpG sites in the CpG island of SOST gene promoter was determined by DNA sequencing. RESULTS SOST gene expression in the non-OPF group was lower than that in OPF group. Bisulfite sequencing result showed that SOST gene promoter was slightly demethylated in the OPF group, as compared with non-OPF group. CONCLUSION Our study demonstrated that DNA methylation influenced the transcriptional expression of SOST gene, which probably may play an important role in the pathogenesis of primary osteoporosis.
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Affiliation(s)
- Yanming Cao
- Department of Orthopedics, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bin Wang
- Department of Orthopedics, People's Hospital of Sanshui, Foshan, China
| | - Ding Wang
- Key Laboratory of Orthopaedics & Traumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Dongxiang Zhan
- Key Laboratory of Orthopaedics & Traumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Caiyuan Mai
- Department of Obstetrics, Guangdong Women and Children's Hospital, Guangzhou 510010, China
| | - Peng Wang
- Key Laboratory of Orthopaedics & Traumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qiushi Wei
- Key Laboratory of Orthopaedics & Traumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yamei Liu
- Departments of Diagnostics of Traditional Chinese Medicine, Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Haibin Wang
- Key Laboratory of Orthopaedics & Traumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wei He
- Key Laboratory of Orthopaedics & Traumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Liangliang Xu
- Key Laboratory of Orthopaedics & Traumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Laboratory of Orthopaedics & Traumatology, Lingnan Medical Research Center, Guangzhou University of Chinese Medicine, Guangzhou, China
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30
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Zhou J, Wang Z, Zhang L, Gu Y, Ma Y, Li X. Association of five genetic variations in DNMT1 and DNMT3A with gastric cancer in a Chinese population. Future Oncol 2018; 14:1731-1739. [PMID: 29956566 DOI: 10.2217/fon-2017-0707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
AIM To determine whether genetic variations in DNMT1 and DNMT3A could be associated with gastric cancer risk. MATERIALS & METHODS A total of 466 patients and 452 healthy controls were enrolled in this study. Genotypes were examined by using the Sequenom MassARRAY platform. RESULTS No significant differences in the distribution frequencies were observed between the groups. However, subgroup analysis revealed that, in the group aged ≤60 years, DNMT3A rs13420827 was associated with reduced gastric cancer risk, and that carrier of GC/GG genotype was associated with reduced risk of gastric cancer with low differentiation or at the T3-T4 stage. CONCLUSION This study suggests that five genetic variations of interest in DNMT1 and DNMT3A are not associated with the presence of gastric cancer, but that rs13420827 may contribute to the gastric cancer risk for those younger individuals, the risk of which may be influenced by the characteristics of tumor.
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Affiliation(s)
- Jin Zhou
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, PR China
| | - Zhibing Wang
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing, PR China
| | - Lei Zhang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, PR China
| | - Yuanyuan Gu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, PR China
| | - Yong Ma
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, PR China
| | - Xiangcheng Li
- Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, PR China
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Grayson DR, Guidotti A. DNA Methylation in Animal Models of Psychosis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:105-132. [PMID: 29933947 DOI: 10.1016/bs.pmbts.2017.12.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Schizophrenia (SZ) is a debilitating disease that impacts 1% of the population worldwide. Association studies have shown that inherited genetic mutations account for a portion of disease risk. However, environmental factors play an important role in the pathophysiology of the disease by altering cellular epigenetic marks at the level of chromatin. Postmortem brain studies of SZ subjects suggest that the dynamic equilibrium between DNA methylation and demethylation network components is disrupted at the level of individual SZ target genes. Herein, we review the role of DNA methylation and demethylation in the context of what is currently known regarding SZ. Furthermore, we describe the deficits that accompany two mouse models of SZ. The chronic methionine mouse model of SZ is predicated on the administration of methionine to SZ patients and controls in the context of clinical studies that were carried out during the 1960s and 1970s. The prenatal restraint stress model of SZ is based on a prolonged stress paradigm administered to pregnant dams during gestation days 7-21. The adult offspring of these dams show various behavioral and biochemical deficits in adulthood. Both models are epigenetic in origin and mimic the positive and negative symptoms, as well as the cognitive endophenotypes commonly observed in SZ patients. We also discuss the utility of typical and atypical antipsychotic drugs in alleviating these symptoms in each model.
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Affiliation(s)
- Dennis R Grayson
- Center for Alcohol Research in Epigenetics, University of Illinois, Chicago, IL, United States.
| | - Alessandro Guidotti
- Center for Alcohol Research in Epigenetics, University of Illinois, Chicago, IL, United States
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Miller CN, Dye JA, Schladweiler MC, Richards JH, Ledbetter AD, Stewart E, Kodavanti UP. Acute inhalation of ozone induces DNA methylation of apelin in lungs of Long-Evans rats. Inhal Toxicol 2018; 30:178-186. [PMID: 29947284 PMCID: PMC6681647 DOI: 10.1080/08958378.2018.1483984] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/01/2018] [Accepted: 05/28/2018] [Indexed: 02/07/2023]
Abstract
Apelin has cardiopulmonary protective properties that promote vasodilation and maintenance of the endothelial barrier. While reductions in apelin have been identified as a contributor to various lung diseases, including pulmonary edema, its role in the effect of air pollutants has not been examined. Thus, in the current study, we sought to investigate if apelin is a downstream target of inhaled ozone and if such change in expression is related to altered DNA methylation in the lung. Male, Long-Evans rats were exposed to filtered air or 1.0 ppm ozone for 4 h. Ventilation changes were assessed using whole-body plethysmography immediately following exposure, and markers of pulmonary edema and inflammation were assessed in the bronchoaveolar lavage (BAL) fluid. The enzymatic regulators of DNA methylation were measured in the lung, along with methylation and hydroxymethylation of the apelin promoter. Data showed that ozone exposure was associated with increased enhanced pause and protein leakage in the BAL fluid. Ozone exposure reduced DNA cytosine-5-methyltransferase (DNMT) activity and Dnmt3a/b gene expression. Exposure-induced upregulation of proliferating cell nuclear antigen, indicative of DNA damage, repair, and maintenance methylation. Increased methylation and reduced hydroxymethylation were measured on the apelin promoter. These epigenetic modifications accompanied ozone-induced reduction of apelin expression and development of pulmonary edema. In conclusion, epigenetic regulation, specifically increased methylation of the apelin promoter downstream of DNA damage, may lead to reductions in protective signaling of the apelinergic system, contributing to the pulmonary edema observed following the exposure to oxidant air pollution.
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Affiliation(s)
- Colette N. Miller
- Environmental Public Health Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Janice A. Dye
- Environmental Public Health Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Mette C. Schladweiler
- Environmental Public Health Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Judy H. Richards
- Environmental Public Health Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Allen D. Ledbetter
- Environmental Public Health Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Erica Stewart
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Urmila P. Kodavanti
- Environmental Public Health Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
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Florean C, Schnekenburger M, Lee JY, Kim KR, Mazumder A, Song S, Kim JM, Grandjenette C, Kim JG, Yoon AY, Dicato M, Kim KW, Christov C, Han BW, Proksch P, Diederich M. Discovery and characterization of Isofistularin-3, a marine brominated alkaloid, as a new DNA demethylating agent inducing cell cycle arrest and sensitization to TRAIL in cancer cells. Oncotarget 2018; 7:24027-49. [PMID: 27006469 PMCID: PMC5029682 DOI: 10.18632/oncotarget.8210] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 03/02/2016] [Indexed: 12/20/2022] Open
Abstract
We characterized the brominated alkaloid Isofistularin-3 (Iso-3), from the marine sponge Aplysina aerophoba, as a new DNA methyltransferase (DNMT)1 inhibitor. Docking analysis confirmed our in vitro DNMT inhibition data and revealed binding of Iso-3 within the DNA binding site of DNMT1. Subsequent increased expression of tumor suppressor gene aryl hydrocarbon receptor (AHR) could be correlated to decreased methylation of CpG sites within the essential Sp1 regulatory region of its promoter. Iso-3 induced growth arrest of cancer cells in G0/G1 concomitant with increased p21 and p27 expression and reduced cyclin E1, PCNA and c-myc levels. Reduced proliferation was accompanied by morphological changes typical of autophagy revealed by fluorescent and transmission electron microscopy and validated by LC3I-II conversion. Furthermore, Iso-3 strongly synergized with tumor-necrosis-factor related apoptosis inducing ligand (TRAIL) in RAJI [combination index (CI) = 0.22] and U-937 cells (CI = 0.21) and increased TRAIL-induced apoptosis via a mechanism involving reduction of survivin expression but not of Bcl-2 family proteins nor X-linked inhibitor of apoptosis protein (XIAP). Iso-3 treatment decreased FLIPL expression and triggered activation of endoplasmatic reticulum (ER) stress with increased GRP78 expression, eventually inducing TRAIL receptor death receptor (DR)5 surface expression. Importantly, as a potential candidate for further anticancer drug development, Iso-3 reduced the viability, colony and in vivo tumor forming potential without affecting the viability of PBMCs from healthy donors or zebrafish development.
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Affiliation(s)
- Cristina Florean
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, Lëtzebuerg, Luxembourg
| | - Michael Schnekenburger
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, Lëtzebuerg, Luxembourg
| | - Jin-Young Lee
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Korea
| | - Kyung Rok Kim
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Korea
| | - Aloran Mazumder
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Korea
| | - Sungmi Song
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Korea
| | - Jae-Myun Kim
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Korea
| | - Cindy Grandjenette
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, Lëtzebuerg, Luxembourg
| | - Jeoung-Gyun Kim
- SNU-Harvard Neurovascular Protection Center, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Gwanak-gu, Korea
| | - Ah-Young Yoon
- SNU-Harvard Neurovascular Protection Center, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Gwanak-gu, Korea
| | - Mario Dicato
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, Lëtzebuerg, Luxembourg
| | - Kyu-Won Kim
- SNU-Harvard Neurovascular Protection Center, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Gwanak-gu, Korea
| | | | - Byung-Woo Han
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Korea
| | - Peter Proksch
- Institut für Pharmazeutische Biologie und Biotechnologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Marc Diederich
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Korea
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Yang L, Luo P, Song Q, Fei X. DNMT1/miR-200a/GOLM1 signaling pathway regulates lung adenocarcinoma cells proliferation. Biomed Pharmacother 2018; 99:839-847. [PMID: 29710483 DOI: 10.1016/j.biopha.2018.01.161] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 01/22/2018] [Accepted: 01/29/2018] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVES Lung adenocarcinoma (LAD) comprises about 80% of all diagnosed lung cancers. However, the underlying regulatory mechanism of LAD cell proliferation is largely unclear. The emergence of microRNAs and molecular-targeted therapies adds a new dimension in our efforts to combat this deadly disease. METHOD In this work, the A549 and H1650 human lung cancer cell lines were used in this study. The proliferation was evaluated by the MTT and BrdU assay. The expression level of related proteins was detected by western blot. RESULT We reported GOLM1 was highly expressed in LAD cells and associated with low survival ratio and higher grade malignancy. Knockdown of GOLM1 repressed the LAD cell proliferation. Overexpression of GOLM1 promoted the cell proliferation. Further we found that the level of microRNA-200a (miR-200a) expression was low in LAD cells. miR-200a repress GOLM1 expression by directly targeting its 3? UTR. Overexpression of miR-200a repressed the cell proliferation and blocked the increase of LAD cell proliferation caused by GOLM1 overexpression. Further, we found that miR-200 was downregulated by DNMT1.Overexpression of DNMT1 blocked the function of miR-200a on repressing proliferation. We then found that knockdown of DNMT1 repressed LAD cell proliferation, which could be rescued by GOLM1 overexpression. CONCLUSION This work revealed the critical function of GOLM1/miR-200a/DNMT1 signaling pathway on regulating LAD cell proliferation, and might lay the foundation for further clinical treatment of LAD.
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Affiliation(s)
- Longqiu Yang
- Department of Anesthesiology, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Edong Healthcare Group, Huangshi, 435000, China
| | - Pengcheng Luo
- Department of Urology Surgery, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic University, Edong Healthcare Group, Huangshi, 435000, China
| | - Qiong Song
- Department of Anesthesiology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, 195 Tongbai Road, Zhengzhou, Henan, 450007, China.
| | - Xuejie Fei
- Department of Intensive Care Unit, Shuguang Hospital Affiliated With Shanghai University of Traditional Chinese Medicine, Shanghai, 200021, China.
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Chen D, Jin C. Histone variants in environmental-stress-induced DNA damage repair. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 780:55-60. [PMID: 31395349 DOI: 10.1016/j.mrrev.2017.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 11/15/2017] [Accepted: 11/17/2017] [Indexed: 01/27/2023]
Abstract
Environmental stress such as genotoxic agents can cause DNA damage either indirectly through the generation of reactive oxygen species or directly by interactions with the DNA molecule. Damage to the genetic material may cause mutations and ultimately cancer. Genotoxic mutation can be prevented either by apoptosis or DNA repair. In response to DNA damage, cells have evolved DNA damage responses (DDR) to detect, signal, and repair DNA lesions. Epigenetic mechanisms play critically important roles in DDR, which requires changes in chromatin structure and dynamics to modulate DNA accessibility. Incorporation of histone variants into chromatin is considered as an epigenetic mechanism. Canonical histones can be replaced with variant histones that change chromatin structure, stability, and dynamics. Recent studies have demonstrated involvement of nearly all histone variants in environmental-stress-induced DNA damage repair through various mechanisms, including affecting nucleosome dynamics, carrying variant-specific modification, promoting transcriptional competence or silencing, mediating rearrangement of chromosomes, attracting specific repair proteins, among others. In this review, we will focus on the role of histone variants in DNA damage repair after exposure to environmental genotoxic agents. Understanding the mechanisms regulating environmental exposure-induced epigenetic changes, including replacement of canonical histones with histone variants, will promote the development of strategies to prevent or reverse these changes.
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Affiliation(s)
- Danqi Chen
- Department of Environmental Medicine & Biochemistry and Molecular Pharmacology, New York University School of Medicine, NY 10987, USA
| | - Chunyuan Jin
- Department of Environmental Medicine & Biochemistry and Molecular Pharmacology, New York University School of Medicine, NY 10987, USA.
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36
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Liu H, Wei Q, Huang C, Zhang Y, Guo Z. Potential Roles of Intrinsic Disorder in Maternal-Effect Proteins Involved in the Maintenance of DNA Methylation. Int J Mol Sci 2017; 18:E1898. [PMID: 28869544 PMCID: PMC5618547 DOI: 10.3390/ijms18091898] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 01/14/2023] Open
Abstract
DNA methylation is an important epigenetic modification that needs to be carefully controlled as a prerequisite for normal early embryogenesis. Compelling evidence now suggests that four maternal-effect proteins, primordial germ cell 7 (PGC7), zinc finger protein 57 (ZFP57), tripartite motif-containing 28 (TRIM28) and DNA methyltransferase (cytosine-5) 1 (DNMT1) are involved in the maintenance of DNA methylation. However, it is still not fully understood how these maternal-effect proteins maintain the DNA methylation imprint. We noticed that a feature common to these proteins is the presence of significant levels of intrinsic disorder so in this study we started from an intrinsic disorder perspective to try to understand these maternal-effect proteins. To do this, we firstly analysed the intrinsic disorder predispositions of PGC7, ZFP57, TRIM28 and DNMT1 by using a set of currently available computational tools and secondly conducted an intensive literature search to collect information on their interacting partners and structural characterization. Finally, we discuss the potential effect of intrinsic disorder on the function of these proteins in maintaining DNA methylation.
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Affiliation(s)
- Hongliang Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
| | - Qing Wei
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
- College of Eco-Environmental Engineering, Qinghai University, Xining 810016, China.
| | - Chenyang Huang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
| | - Yong Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
| | - Zekun Guo
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling 712100, China.
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Iridoy Zulet M, Pulido Fontes L, Ayuso Blanco T, Lacruz Bescos F, Mendioroz Iriarte M. Epigenetic changes in neurology: DNA methylation in multiple sclerosis. NEUROLOGÍA (ENGLISH EDITION) 2017. [DOI: 10.1016/j.nrleng.2015.03.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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TGF-β-mediated repression of MST1 by DNMT1 promotes glioma malignancy. Biomed Pharmacother 2017; 94:774-780. [PMID: 28802229 DOI: 10.1016/j.biopha.2017.07.081] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 07/14/2017] [Accepted: 07/19/2017] [Indexed: 12/28/2022] Open
Abstract
Human gliomas are related to high rates of morbidity and mortality. TGF-β promotes the growth of glioma cells, and correlate with the degree of malignancy of human gliomas. However, the molecular mechanisms involved in the malignant function of TGF-β are not fully elucidated. Here, we showed that TGF-β induced the downregulation of MST1 expression in U87 and U251 glioma cells. Treatment of glioma cells with the DNA methylation inhibitor 5-aza-2'-deoxycytidine (5-AzadC) prevented the loss of MST1 expression. Addition of 5-AzadC also reduced the TGF-β-stimulated proliferation, migration and invasiveness of glioma cells. Furthermore, Knockdown of DNMT1 upregulated MST1 expression in gliomas cells. In addition, the inhibition of DNMT1 blocked TGF-β-induced proliferation, migration and invasiveness in glioma cells. These results suggest that TGF-β promotes glioma malignancy through DNMT1-mediated loss of MST1 expression.
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Repression of DOK7 mediated by DNMT3A promotes the proliferation and invasion of KYSE410 and TE-12 ESCC cells. Biomed Pharmacother 2017; 90:93-99. [DOI: 10.1016/j.biopha.2017.02.111] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 02/23/2017] [Accepted: 02/24/2017] [Indexed: 12/13/2022] Open
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40
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Madeddu G, Ortu S, Garrucciu G, Maida I, Melis M, Muredda AA, Mura MS, Babudieri S. DNMT1 modulation in chronic hepatitis B patients and hypothetic influence on mitochondrial DNA methylation status during long-term nucleo(t)side analogs therapy. J Med Virol 2017; 89:1208-1214. [PMID: 27922198 DOI: 10.1002/jmv.24742] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 11/11/2016] [Indexed: 01/03/2023]
Abstract
Inhibition of viral replication is the most important goal in patients with Hepatitis B virus chronic infection (CHB). Currently, five oral nucleo(t)side analogs (NAs), including Lamivudine, Adefovir, Telbivudine, Entecavir, and Tenofovir, have been approved for treatment. The widespread use of NAs has also been linked with a progressive growth of unlikely anomaly attributable to mitochondrial dysfunctions, not previously recognized. Here, we explore the hypothesis that NAs may cause persistent epigenetic changes during prolonged NAs therapy in CHB patients. We obtained peripheral blood mononuclear cells (PBMC) from whole blood samples of consecutive patients with chronic HBV infection, 18 receiving NAs and 20 untreated patients. All patients were Caucasian and Italians. Epigenetic analysis was performed by Bisulphite sequencing PCR to search the existence of methylated cytosine residues in the Light (L)-strands of mitochondrial DNA control region (D-loop). Gene expression analysis of DNA methyltransferases 1 was performed by a quantitative relative Real-Time Polymerase Chain Reaction (PCR). DNMT1 expression was significantly (P < 000001) higher in NA treated patients (4.09, IQR 3.52-5.15) when compared with HBV naives (0.61, IQR 0.34-0.82). Besides, DNMT1 expression was significantly correlated with NA therapy duration (Spearman Rho = 0.67; P < 0.05). Furthermore, NA therapy duration was the only significant predictor of DNMT1 expression at multivariate analysis (Beta = 0.95, P < 0.0000001). Bisulphite PCR sequencing showed that methylation of cytosine residues occurred in a higher percentage in patients treated with NAs in comparison with untreated patients and healthy controls. Our data showed a DNMT1 overexpression significantly correlated to NA therapy duration and an higher regional mtDNA hypermethylation. This might suggest an epigenetic alteration that could be involved in one of the possible mechanisms of mitochondrial gene regulation during NAs therapy.
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Affiliation(s)
- Giordano Madeddu
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - Silvia Ortu
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - Giovanni Garrucciu
- Unit of Internal Medicine, Department of Clinical and Experimental Medicine, University Hospital, Sassari, Italy
| | - Ivana Maida
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - Michela Melis
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - Alberto Augusto Muredda
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - Maria Stella Mura
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - Sergio Babudieri
- Unit of Infectious Diseases, Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
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Wu Z, Mei X, Ying Z, Sun Y, Song J, Shi W. Ultraviolet B inhibition of DNMT1 activity via AhR activation dependent SIRT1 suppression in CD4+ T cells from systemic lupus erythematosus patients. J Dermatol Sci 2017; 86:230-237. [PMID: 28336124 DOI: 10.1016/j.jdermsci.2017.03.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/22/2017] [Accepted: 03/08/2017] [Indexed: 12/01/2022]
Abstract
BACKGROUND Previous studies have reported that ultraviolet B (UVB) inhibits DNA methyltransferase1 (DNMT1) activity in CD4+ T cells from systemic lupus erythematosus (SLE) patients. Silent mating type information regulation 2 homolog 1 (SIRT1) is a type of Class III histone deacetylases (HDACs), and has been reported to play roles in the pathogenesis of different autoimmune diseases and can modulate DNMT1 activity. Moreover, aryl hydrocarbon receptor (AhR) has been reported to link UVB with SLE. However, the exact mechanisms by which DNMT1 activity is inhibited by UVB in lupus CD4+ T cells remain largely unknown. OBJECTIVE To elucidate the exact mechanisms by which DNMT1 activity is inhibited by UVB in lupus CD4+ T cells. METHODS Twenty-two newly diagnosed active SLE patients and 30 healthy controls were enrolled in the study. CD4+ T cells were isolated, cultured and treated. DNMT1 activity assay, quantitative real-time PCR (qRT-PCR), Western blotting, RNA interference using small interfering RNA and Chromatin Immunoprecipitation (ChIP) assay were employed. RESULTS DNMT1 activity was inhibited in si-SIRT1-transfected CD4+ T cells, and increased by the established SIRT1 activator, SRT1720. Moreover, the mRNA and protein expression of SIRT1 were suppressed by UVB exposure in lupus CD4+ T cells. UVB-inhibited DNMT1 activity was reversed by SRT1720 in si-control-transfected lupus CD4+ T cells, but not in si-SIRT1-transfected lupus CD4 + T cells. Furthermore, AhR activation by VAF347 reduced the mRNA and protein expression of SIRT1. ChIP using an antibody against AhR in normal CD4+ T cells revealed a 16-fold stronger signal at the site about 1.6kb upstream from the translation start site of the SIRT1 promoter. Finally, UVB could activate AhR and inhibit the mRNA and protein expression of SIRT1. AhR knockdown abrogated the inhibition of UVB-mediated SIRT1 mRNA and protein expression and DNMT1 activity in lupus CD4+ T cells. CONCLUSION UVB suppressed SIRT1 expression via activating AhR, and subsequently inhibited DNMT1 activity in CD4+ T cells from SLE patients.
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Affiliation(s)
- Zhouwei Wu
- Department of Dermatology, Shanghai First People's Hospital, Shanghai Jiaotong University, Shanghai, China.
| | - Xingyu Mei
- Department of Dermatology, Shanghai First People's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Zuolin Ying
- Department of Dermatology, Shanghai First People's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Yue Sun
- Department of Dermatology, Shanghai First People's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Jun Song
- Department of Dermatology, Shanghai First People's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Weimin Shi
- Department of Dermatology, Shanghai First People's Hospital, Shanghai Jiaotong University, Shanghai, China.
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miR-377 induces senescence in human skin fibroblasts by targeting DNA methyltransferase 1. Cell Death Dis 2017; 8:e2663. [PMID: 28277545 PMCID: PMC5386568 DOI: 10.1038/cddis.2017.75] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 01/09/2017] [Indexed: 12/12/2022]
Abstract
Skin aging is a complicated physiological process and epigenetic feature, including microRNA-mediated regulation and DNA methylation, have been shown to contribute to this process. DNA methylation is regulated by DNA methyltransferase, of which DNA methyltransferase 1 (DNMT1) is the most abundantly known. But evidence supporting its role in skin aging remains scarce, and no report regards its specifical upstream-regulating molecules in the process of skin aging so far. Here, we found that DNMT1 expression was markedly higher in young human skin fibroblasts (HSFs) than that in passage-aged HSFs, and DNMT1 knockdown significantly induced the senescence phenotype in young HSFs. We predicted the upstream miRNAs which could regulate DNMT1 with miRNA databases and found miR-377 had high homology with a sequence in the 3′-UTR of human DNMT1 mRNA. We confirmed that miR-377 was a potential regulator of DNMT1 by luciferase reporter assays. miR-377 expression in passage-aged HSFs was markedly higher than that in the young HSFs. miR-377 overexpression promoted senescence in young HSFs, and inhibition of miR-377 reduced senescence in passage-aged HSFs. Moreover, these functions were mediated by targeting DNMT1. Microfluidic PCR and next-generation bisulfite sequencing of 24 senescent-associated genes' promoters revealed alterations of the promoter methylation levels of FoxD3,p53, and UTF1 in HSFs treated with miR-377 mimics or inhibitors. We also verified that the miR-377-mediated changes in p53 expression could be reversed by regulation of DNMT1 in HSFs. Similarly, there was a negative correlation between miR-377 and DNMT1 expression in young and photoaged HSFs, HSFs, or skin tissues from UV-unexposed areas of different aged donors. Our results highlight a novel role for miR-377-DNMT1-p53 axis in HSF senescence. These findings shed new light on the mechanisms of skin aging and identify future opportunities for its therapeutic prevention.
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Supic G, Kozomara R, Zeljic K, Jovic N, Magic Z. Prognostic value of the DNMTs mRNA expression and genetic polymorphisms on the clinical outcome in oral cancer patients. Clin Oral Investig 2017; 21:173-182. [PMID: 26966018 DOI: 10.1007/s00784-016-1772-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 02/29/2016] [Indexed: 01/07/2023]
Abstract
OBJECTIVES Although the importance of the epigenetic changes in tumors, including oral squamous cell carcinomas (OSCCs), is now becoming apparent, the mechanisms that trigger or cause aberrant DNA methylation in cancer are still unrevealed. DNA methylation is regulated by a family of enzymes, DNA methyltransferases (DNMTs). DNMT gene expression analysis, as well as genetic polymorphisms, has not been previously evaluated in OSCC. MATERIALS AND METHODS In 65 OSCC patients, SYBR Green real-time PCR method was assessed for relative quantification of DNMT1, DNMT3A, and DNMT3B mRNAs, normalized to TATA-binding protein (TBP) mRNA. The expression levels of all three genes were dichotomized as high or low, with a twofold change of normalized mRNA expression used as the cutoff value. Polymorphisms in DNMT1 (rs2228612) and DNMT3B (rs406193) were analyzed in 99 OSCCs by TaqMan SNPs genotyping assays. RESULTS DNMT1, DNMT3A, and DNMT3B were overexpressed in 36.9, 26, and 23 % of the OSCC patients, respectively. DNMT1 overexpression was significantly associated with the overall survival, p = 0.029, and relapse-free survival of OSCC patients, p = 0.003. Patients with DNMT1 overexpression, as an independent prognostic factor, had a 2.385 times higher risk to relapse than those with lower expression. The DNMT1 A201G gene polymorphism was associated with a reduced overall survival in OSCC patients, p = 0.036. CONCLUSIONS Our results suggest that DNMT1 could play an important role in modulating OSCC patient survival. CLINICAL RELEVANCE DNMT gene expression could be a potential prognostic marker that might lead to an improvement in diagnosis, prognosis, and prospective use of epigenetic-targeted therapy of OSCC.
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Affiliation(s)
- Gordana Supic
- Faculty of Medicine, Military Medical Academy, University of Defense, Belgrade, Serbia.
- Institute for Medical Research, Military Medical Academy, Crnotravska 17, Belgrade, 11002, Serbia.
| | - Ruzica Kozomara
- Faculty of Medicine, Military Medical Academy, University of Defense, Belgrade, Serbia
- Clinic for Maxillofacial Surgery, Military Medical Academy, Belgrade, Serbia
| | - Katarina Zeljic
- Institute for Medical Research, Military Medical Academy, Crnotravska 17, Belgrade, 11002, Serbia
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Nebojsa Jovic
- Faculty of Medicine, Military Medical Academy, University of Defense, Belgrade, Serbia
- Clinic for Maxillofacial Surgery, Military Medical Academy, Belgrade, Serbia
| | - Zvonko Magic
- Faculty of Medicine, Military Medical Academy, University of Defense, Belgrade, Serbia
- Institute for Medical Research, Military Medical Academy, Crnotravska 17, Belgrade, 11002, Serbia
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Abstract
Osteoarthritis (OA) was once defined as a non-inflammatory arthropathy, but it is now well-recognized that there is a major inflammatory component to this disease. In addition to synovial cells, articular chondrocytes and other cells of diarthrodial joints are also known to express inflammatory mediators. It has been proposed that targeting inflammation pathways could be a promising strategy to treat OA. There have been many reports of cross-talk between inflammation and epigenetic factors in cartilage. Specifically, inflammatory mediators have been shown to regulate levels of enzymes that catalyze changes in DNA methylation and histone structure, as well as alter levels of non-coding RNAs. In addition, expression levels of a number of these epigenetic factors have been shown to be altered in OA, thereby suggesting potential interplay between inflammation and epigenetics in this disease. This review provides information on inflammatory pathways in arthritis and summarizes published research on how epigenetic regulators are affected by inflammation in chondrocytes. Furthermore, we discuss data showing how altered expression of some of these epigenetic factors can induce either catabolic or anti-catabolic effects in response to inflammatory signals. A better understanding of how inflammation affects epigenetic factors in OA may provide us with novel therapeutic strategies to treat this condition.
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Affiliation(s)
- Jie Shen
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Yousef Abu-Amer
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO, USA,Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Regis J. O'Keefe
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Audrey McAlinden
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO, USA,Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO, USA
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Hussain S, Dutta A, Sarkar A, Singh A, Gupta ML, Biswas S. Proteomic analysis of irradiated lung tissue of mice using gel-based proteomic approach. Int J Radiat Biol 2016; 93:373-380. [PMID: 28000521 DOI: 10.1080/09553002.2016.1266058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PURPOSE Exposure to radiation causes severe alterations of protein expression level inside the cell, thus it may influence the biological events and stress response. In the present investigation, we have demonstrated the effect of radiation on mice lung tissues. MATERIALS AND METHODS Two-dimensional gel electrophoresis (2-DE) coupled with MALDI-TOF/TOF was used to check the expression changes in lung proteome profile of strain 'A' female mice after exposure to lethal doses of gamma irradiation at different time periods (24 and 48 h). Identified proteins were analysed for their altered expression and were further validated by Western blotting and enzyme-linked immunosorbent assay (ELISA). RESULTS Nine significant differentially expressed proteins were identified from irradiated lungs tissues. The expression level of zinc finger protein was found to be up regulated at 24 h irradiation in comparison to 48 h irradiation. CONCLUSIONS Zinc finger protein may be considered as a radiation responsive protein. Alteration in its expression pattern may primarily affect binding specificity of the protein that can further result in the interference in transcriptional control of multiple stress responsive genes.
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Affiliation(s)
- Shabir Hussain
- a Department of Genomics & Molecular Medicine , CSIR - Institute of Genomics & Integrative Biology (IGIB), Delhi University Campus , Delhi , India
| | - Ajaswrata Dutta
- b Division of Radioprotective Drug Development Research , Institute of Nuclear Medicine and Allied Sciences , Delhi , India
| | - Ashish Sarkar
- a Department of Genomics & Molecular Medicine , CSIR - Institute of Genomics & Integrative Biology (IGIB), Delhi University Campus , Delhi , India
| | - Abhinav Singh
- b Division of Radioprotective Drug Development Research , Institute of Nuclear Medicine and Allied Sciences , Delhi , India
| | - Manju Lata Gupta
- b Division of Radioprotective Drug Development Research , Institute of Nuclear Medicine and Allied Sciences , Delhi , India
| | - Sagarika Biswas
- a Department of Genomics & Molecular Medicine , CSIR - Institute of Genomics & Integrative Biology (IGIB), Delhi University Campus , Delhi , India
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Benetatos L, Vartholomatos G. On the potential role of DNMT1 in acute myeloid leukemia and myelodysplastic syndromes: not another mutated epigenetic driver. Ann Hematol 2016; 95:1571-82. [PMID: 26983918 DOI: 10.1007/s00277-016-2636-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/04/2016] [Indexed: 12/19/2022]
Abstract
DNA methylation is the most common epigenetic modification in the mammalian genome. DNA methylation is governed by the DNA methyltransferases mainly DNMT1, DNMT3A, and DNMT3B. DNMT1 methylates hemimethylated DNA ensuring accurate DNA methylation maintenance. DNMT1 is involved in the proper differentiation of hematopoietic stem cells (HSCs) through the interaction with effector molecules. DNMT1 is deregulated in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) as early as the leukemic stem cell stage. Through the interaction with fundamental transcription factors, non-coding RNAs, fusion oncogenes and by modulating core members of signaling pathways, it can affect leukemic cells biology. DNMT1 action might be also catalytic-independent highlighting a methylation-independent mode of action. In this review, we have gathered some current facts of DNMT1 role in AML and MDS and we also propose some perspectives for future studies.
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47
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Neuhof M, Levin M, Rechavi O. Vertically- and horizontally-transmitted memories - the fading boundaries between regeneration and inheritance in planaria. Biol Open 2016; 5:1177-88. [PMID: 27565761 PMCID: PMC5051648 DOI: 10.1242/bio.020149] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The Weismann barrier postulates that genetic information passes only from the germline to the soma and not in reverse, thus providing an obstacle to the inheritance of acquired traits. Certain organisms such as planaria – flatworms that can reproduce through asymmetric fission – avoid the limitations of this barrier, thus blurring the distinction between the processes of inheritance and development. In this paper, we re-evaluate canonical ideas about the interaction between developmental, genetic and evolutionary processes through the lens of planaria. Biased distribution of epigenetic effects in asymmetrically produced parts of a regenerating organism could increase variation and therefore affect the species' evolution. The maintenance and fixing of somatic experiences, encoded via stable biochemical or physiological states, may contribute to evolutionary processes in the absence of classically defined generations. We discuss different mechanisms that could induce asymmetry between the two organisms that eventually develop from the regenerating parts, including one particularly fascinating source – the potential capacity of the brain to produce long-lasting epigenetic changes. Summary: In this hypothesis paper we re-evaluate canonical ideas about the interaction between developmental, genetic and evolutionary processes through the lens of planaria, an invertebrate model organism which challenges fundamental assumptions regarding reproduction.
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Affiliation(s)
- Moran Neuhof
- Department of Neurobiology, Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Michael Levin
- Allen Discovery Center, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel Allen Discovery Center, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
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48
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Zhang C, Suo J, Katayama H, Wei Y, Garcia-Manero G, Hanash S. Quantitative proteomic analysis of histone modifications in decitabine sensitive and resistant leukemia cell lines. Clin Proteomics 2016; 13:14. [PMID: 27382363 PMCID: PMC4932764 DOI: 10.1186/s12014-016-9115-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/04/2016] [Indexed: 12/12/2022] Open
Abstract
Background The refractory nature of many cancers remains the main health challenge over the past century. The epigenetic drug, decitabine (DAC), represents one of the most promising therapeutic agents in cancers particularly in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). However, its ambiguous anti-tumor mechanism and the unpredictable drug-resistant nature in some population compromise its application in cancer therapy. In crosstalk with DNA methylation, histone post-translational modifications (PTMs) are the key players in modulating the downstream epigenetic status of tumor suppressor genes. This study targets the role of decitabine in epigenetic regulation in leukemia therapy and searches responsive predictors and therapeutic targets for pretreatment evaluation and drug development. Results A simple, fast, and robust proteomic strategy identified 15 novel PTMs and 60 PTM combinations in two leukemia cell lines (MDS-L and TF-1). Histone modification profiles have been generated and compared between DAC sensitive and resistant groups (n = 3) in response to DAC treatment. Among these histone PTMs, five of which were found differentially upon DAC treatment in drug sensitive and resistant cells: H3.3K36me3, H4K8acK12acK16ac in MDS-L cells; and H3.1K27me1, H3.1K36me1, H3.1K27me1K36me1 in TF-1 cells. They may serve as biomarkers in predicting leukemia and drug responsiveness. In addition, we also explored PTM differences in two cell lines which were developed from early and advanced stages of AML. Three PTMs (H3.1K27me3, H3.1K27me2K36me2 and H3.3K27me2K36me2) are highly abundant in TF-1 cells (advanced AML cell line), suggesting their relevance to leukemogenesis. Our method allowed deep analysis of histone proteins and elucidation of a large number of histone PTMs with high precision and sensitivity. Conclusion DAC-induced DNA hypomethylation has wide impact on chromatin modifications. This study represents first effort to investigate the undefined epigenetic mechanism of decitabine in leukemia therapy. The identification of 15 novel PTMs and the discovery of several marks have relevance to epigenetic directed therapies. Electronic supplementary material The online version of this article (doi:10.1186/s12014-016-9115-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chunchao Zhang
- Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, 6767 Bertner Ave, Houston, TX 77030 USA
| | - Jinfeng Suo
- Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, 6767 Bertner Ave, Houston, TX 77030 USA
| | - Hiroyuki Katayama
- Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, 6767 Bertner Ave, Houston, TX 77030 USA
| | - Yue Wei
- Department of Leukemia, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 428, Houston, TX 77030 USA
| | - Guillermo Garcia-Manero
- Department of Leukemia, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 428, Houston, TX 77030 USA
| | - Samir Hanash
- Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, 6767 Bertner Ave, Houston, TX 77030 USA
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Ke X, Zhang S, Xu J, Liu G, Zhang L, Xie E, Gao L, Li D, Sun R, Wang F, Pan S. Non-small-cell lung cancer-induced immunosuppression by increased human regulatory T cells via Foxp3 promoter demethylation. Cancer Immunol Immunother 2016; 65:587-99. [PMID: 27000869 PMCID: PMC11028464 DOI: 10.1007/s00262-016-1825-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 03/07/2016] [Indexed: 12/27/2022]
Abstract
Patients with non-small-cell lung cancer (NSCLC) have immune defects that are poorly understood. Forkhead box protein P3 (Foxp3) is crucial for immunosuppression by CD4(+) regulatory T cells (Tregs). It is not well known how NSCLC induces Foxp3 expression and causes immunosuppression in tumor-bearing patients. Our study found a higher percentage of CD4(+) Tregs in the peripheral blood of NSCLC compared with healthy donors. NSCLC patients showed demethylation of eight CpG sites within the Foxp3 promoter with methylation ratios negatively correlated with CD4(+)CD25(+)Foxp3(+) T levels. Foxp3 expression in CD4(+) Tregs was directly regulated by Foxp3 promoter demethylation and was involved in immunosuppression by NSCLC. To verify the effect of tumor cells on the phenotype and function of CD4(+) Tregs, we established a coculture system using NSCLC cell line and healthy CD4(+) T cells and showed that SPC-A1 induced IL-10 and TGF-β1 secretion by affecting the function of CD4(+) Tregs. The activity of DNA methyltransferases from CD4(+) T was decreased during this process. Furthermore, eight CpG sites within the Foxp3 promoter also appeared to have undergone demethylation. Foxp3 is highly expressed in CD4(+) T cells, and this may be caused by gene promoter demethylation. These induced Tregs are highly immunosuppressive and dramatically inhibit the proliferative activity of naïve CD4(+) T cells. Our study provides one possible mechanism describing Foxp3 promoter demethylation changes by which NSCLC down-regulates immune responses and contributes to tumor progression. Foxp3 represents an important target for NSCLC anti-tumor immunotherapy.
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MESH Headings
- Adult
- Aged
- Blotting, Western
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/immunology
- Carcinoma, Non-Small-Cell Lung/pathology
- Cell Line, Tumor
- Cells, Cultured
- Coculture Techniques
- CpG Islands/genetics
- CpG Islands/immunology
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/immunology
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation/genetics
- DNA Methylation/immunology
- DNA Methyltransferase 3A
- Female
- Forkhead Transcription Factors/genetics
- Forkhead Transcription Factors/immunology
- Humans
- Immune Tolerance/genetics
- Immune Tolerance/immunology
- Interleukin-10/genetics
- Interleukin-10/immunology
- Interleukin-10/metabolism
- Lung Neoplasms/genetics
- Lung Neoplasms/immunology
- Lung Neoplasms/pathology
- Male
- Middle Aged
- Promoter Regions, Genetic/genetics
- Promoter Regions, Genetic/immunology
- Reverse Transcriptase Polymerase Chain Reaction
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- Transforming Growth Factor beta1/genetics
- Transforming Growth Factor beta1/immunology
- Transforming Growth Factor beta1/metabolism
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Affiliation(s)
- Xing Ke
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, No. 300 of Guangzhou Road, Nanjing, 210029, China
- National Key Clinical Department of Laboratory Medicine, No. 300 of Guangzhou Road, 210029, Nanjing, China
| | - Shuping Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, No. 300 of Guangzhou Road, Nanjing, 210029, China
- National Key Clinical Department of Laboratory Medicine, No. 300 of Guangzhou Road, 210029, Nanjing, China
| | - Jian Xu
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, No. 300 of Guangzhou Road, Nanjing, 210029, China
- National Key Clinical Department of Laboratory Medicine, No. 300 of Guangzhou Road, 210029, Nanjing, China
| | - Genyan Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, No. 300 of Guangzhou Road, Nanjing, 210029, China
- National Key Clinical Department of Laboratory Medicine, No. 300 of Guangzhou Road, 210029, Nanjing, China
| | - Lixia Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, No. 300 of Guangzhou Road, Nanjing, 210029, China
- National Key Clinical Department of Laboratory Medicine, No. 300 of Guangzhou Road, 210029, Nanjing, China
| | - Erfu Xie
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, No. 300 of Guangzhou Road, Nanjing, 210029, China
- National Key Clinical Department of Laboratory Medicine, No. 300 of Guangzhou Road, 210029, Nanjing, China
| | - Li Gao
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, No. 300 of Guangzhou Road, Nanjing, 210029, China
- National Key Clinical Department of Laboratory Medicine, No. 300 of Guangzhou Road, 210029, Nanjing, China
| | - Daqian Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, No. 300 of Guangzhou Road, Nanjing, 210029, China
- National Key Clinical Department of Laboratory Medicine, No. 300 of Guangzhou Road, 210029, Nanjing, China
| | - Ruihong Sun
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, No. 300 of Guangzhou Road, Nanjing, 210029, China
- National Key Clinical Department of Laboratory Medicine, No. 300 of Guangzhou Road, 210029, Nanjing, China
| | - Fang Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, No. 300 of Guangzhou Road, Nanjing, 210029, China.
- National Key Clinical Department of Laboratory Medicine, No. 300 of Guangzhou Road, 210029, Nanjing, China.
| | - Shiyang Pan
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, No. 300 of Guangzhou Road, Nanjing, 210029, China.
- National Key Clinical Department of Laboratory Medicine, No. 300 of Guangzhou Road, 210029, Nanjing, China.
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50
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Wang B, Cui Z, Zhong Z, Sun Y, Yang GY, Sun Q, Bian L. The role and regulatory mechanism of IL-1β on the methylation of the NF2 gene in benign meningiomas and leptomeninges. Mol Carcinog 2016; 55:2268-2277. [PMID: 26840621 DOI: 10.1002/mc.22467] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 11/01/2015] [Accepted: 01/08/2016] [Indexed: 12/12/2022]
Abstract
Methylation of the neurofibromatosis type 2 (NF2) gene in low-grade meningioma (WHO grade I) has crucial roles in tumorigenesis and development. Meningioma formation might also occur in the setting of an inflammatory microenvironment. However, the association between inflammation and the methylation of NF2 remains unclear. The present study investigates the role and regulatory mechanism of IL-1β, one of the most important pro-inflammatory cytokines, in the methylation of NF2 in benign meningioma. Three primary low-grade meningioma cells and leptomeningeal cells were cultured. CCK-8 and BrdU assays demonstrated that proliferation of meningioma/leptomeningeal cells treated with IL-1β occurred in a dose- and time-dependent manner. Methylation-specific PCR verified that IL-1β induced methylation of the NF2 promoter and decreased NF2/merlin expression in meningioma/leptomeningeal cells. Real-time PCR, western blotting, and immunofluorescence showed that IL-1β up-regulated DNMT1 in meningioma cells and DNMT1/3b in leptomeningeal cells but did not up-regulate DNMT3a. After co-treatment with the DNMT inhibitor 5-Aza-2'-deoxycytidine and DNMT siRNA, methylation of NF2 induced by IL-1β was attenuated and merlin expression was restored. Furthermore, we showed that DNMT1 in meningiomas and DNMT1/3b in leptomeninges were regulated via activation of the MAPK (p38, ERK, JNK) and NF-κB pathways. These results suggest that IL-1β induces methylation of NF2 by up-regulating DNMT1 in benign meningioma cells and DNMT1/3b in leptomeningeal cells via MAPK and NF-κB pathways. Therefore, NF2 methylation is a linker between IL-1β and tumor development, and DNMTs might be potential therapeutic targets in meningioma for regulating NF2 and inhibiting tumor development. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Baofeng Wang
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenwen Cui
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhihong Zhong
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuhao Sun
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guo-Yuan Yang
- Neuroscience and Neuroengineering Research Center, Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China.,Department of Neurology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingfang Sun
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Neurosurgery, Ruijin Hospital Luwan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liuguan Bian
- Department of Neurosurgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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