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Zhu Y, Li R, Wang Y, Zhang Q, He Y, Shang J, Liu X, Wang F. A Methylation-Gated DNAzyme Circuit for Spatially Controlled Imaging of MicroRNA in Cells and Animals. Anal Chem 2024; 96:9666-9675. [PMID: 38815126 DOI: 10.1021/acs.analchem.4c01556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Epigenetic modification plays an indispensable role in regulating routine molecular signaling pathways, yet it is rarely used to modulate molecular self-assembly networks. Herein, we constructed a bioorthogonal demethylase-stimulated DNA circuitry (DSC) system for high-fidelity imaging of microRNA (miRNA) in live cells and mice by eliminating undesired off-site signal leakage. The simple and robust DSC system is composed of a primary cell-specific circuitry regulation (CR) module and an ultimate signal-transducing amplifier (SA) module. After the modularly designed DSC system was delivered into target live cells, the DNAzyme of the CR module was site-specifically activated by endogenous demethylase to produce fuel strands for the subsequent miRNA-targeting SA module. Through the on-site and multiply guaranteed molecular recognitions, the lucid yet efficient DSC system realized the reliably amplified in vivo miRNA sensing and enabled the in-depth exploration of the demethylase-involved signal pathway with miRNA in live cells. Our bioorthogonally on-site-activated DSC system represents a universal and versatile biomolecular sensing platform via various demethylase regulations and shows more prospects for more different personalized theragnostics.
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Affiliation(s)
- Yuxuan Zhu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen 518057, P. R. China
| | - Ruomeng Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen 518057, P. R. China
| | - Yifei Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen 518057, P. R. China
| | - Qingqing Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen 518057, P. R. China
| | - Yuqiu He
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen 518057, P. R. China
| | - Jinhua Shang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen 518057, P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen 518057, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan 430072, P. R. China
- Research Institute of Shenzhen, Wuhan University, Shenzhen 518057, P. R. China
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2
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Tando Y, Matsui Y. Inheritance of environment-induced phenotypic changes through epigenetic mechanisms. ENVIRONMENTAL EPIGENETICS 2023; 9:dvad008. [PMID: 38094661 PMCID: PMC10719065 DOI: 10.1093/eep/dvad008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/09/2023] [Accepted: 11/20/2023] [Indexed: 03/08/2024]
Abstract
Growing evidence suggests that epigenetic changes through various parental environmental factors alter the phenotypes of descendants in various organisms. Environmental factors, including exposure to chemicals, stress and abnormal nutrition, affect the epigenome in parental germ cells by different epigenetic mechanisms, such as DNA methylation, histone modification as well as small RNAs via metabolites. Some current remaining questions are the causal relationship between environment-induced epigenetic changes in germ cells and altered phenotypes of descendants, and the molecular basis of how the abnormal epigenetic changes escape reprogramming in germ cells. In this review, we introduce representative examples of intergenerational and transgenerational inheritance of phenotypic changes through parental environmental factors and the accompanied epigenetic and metabolic changes, with a focus on animal species. We also discuss the molecular mechanisms of epigenomic inheritance and their possible biological significance.
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Affiliation(s)
- Yukiko Tando
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi 980-8575, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Yasuhisa Matsui
- Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi 980-8575, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
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3
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Liu Y, Chen C, Wang X, Sun Y, Zhang J, Chen J, Shi Y. An Epigenetic Role of Mitochondria in Cancer. Cells 2022; 11:cells11162518. [PMID: 36010594 PMCID: PMC9406960 DOI: 10.3390/cells11162518] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are not only the main energy supplier but are also the cell metabolic center regulating multiple key metaborates that play pivotal roles in epigenetics regulation. These metabolites include acetyl-CoA, α-ketoglutarate (α-KG), S-adenosyl methionine (SAM), NAD+, and O-linked beta-N-acetylglucosamine (O-GlcNAc), which are the main substrates for DNA methylation and histone post-translation modifications, essential for gene transcriptional regulation and cell fate determination. Tumorigenesis is attributed to many factors, including gene mutations and tumor microenvironment. Mitochondria and epigenetics play essential roles in tumor initiation, evolution, metastasis, and recurrence. Targeting mitochondrial metabolism and epigenetics are promising therapeutic strategies for tumor treatment. In this review, we summarize the roles of mitochondria in key metabolites required for epigenetics modification and in cell fate regulation and discuss the current strategy in cancer therapies via targeting epigenetic modifiers and related enzymes in metabolic regulation. This review is an important contribution to the understanding of the current metabolic-epigenetic-tumorigenesis concept.
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Affiliation(s)
- Yu’e Liu
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
| | - Chao Chen
- Department of Neurosurgery, Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai 200433, China
| | - Xinye Wang
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yihong Sun
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
| | - Jin Zhang
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Juxiang Chen
- Department of Neurosurgery, Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai 200433, China
- Correspondence: (J.C.); (Y.S.)
| | - Yufeng Shi
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
- Clinical Center for Brain and Spinal Cord Research, Tongji University, Shanghai 200092, China
- Correspondence: (J.C.); (Y.S.)
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4
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Samanta S, Mahata R, Santra MK. The Cross-Talk between Epigenetic Gene Regulation and Signaling Pathways Regulates Cancer Pathogenesis. Subcell Biochem 2022; 100:427-472. [PMID: 36301502 DOI: 10.1007/978-3-031-07634-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Cancer begins due to uncontrolled cell division. Cancer cells are insensitive to the signals that control normal cell proliferation. This uncontrolled cell division is due to the accumulation of abnormalities in different factors associated with the cell division, including different cyclins, cell cycle checkpoint inhibitors, and cellular signaling. Cellular signaling pathways are aberrantly activated in cancer mainly due to epigenetic regulation and post-translational regulation. In this chapter, the role of epigenetic regulation in aberrant activation of PI3K/AKT, Ras, Wnt, Hedgehog, Notch, JAK/STAT, and mTOR signaling pathways in cancer progression is discussed. The role of epigenetic regulators in controlling the upstream regulatory proteins and downstream effector proteins responsible for abnormal cellular signaling-mediated cancer progression is covered in this chapter. Similarly, the role of signaling pathways in controlling epigenetic gene regulation-mediated cancer progression is also discussed. We have tried to ascertain the current status of potential epigenetic drugs targeting several epigenetic regulators to prevent different cancers.
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Affiliation(s)
- Snigdha Samanta
- Molecular Oncology Laboratory, National Centre for Cell Science, NCCS Complex, S. P. Pune University Campus, Ganeshkhind Road, Pune, Maharashtra, India
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Rumpa Mahata
- Molecular Oncology Laboratory, National Centre for Cell Science, NCCS Complex, S. P. Pune University Campus, Ganeshkhind Road, Pune, Maharashtra, India
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Manas Kumar Santra
- Molecular Oncology Laboratory, National Centre for Cell Science, NCCS Complex, S. P. Pune University Campus, Ganeshkhind Road, Pune, Maharashtra, India.
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5
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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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Chen T, Cai C, Wang L, Li S, Chen L. Farnesyl Transferase Inhibitor Lonafarnib Enhances α7nAChR Expression Through Inhibiting DNA Methylation of CHRNA7 and Increases α7nAChR Membrane Trafficking. Front Pharmacol 2021; 11:589780. [PMID: 33447242 PMCID: PMC7801264 DOI: 10.3389/fphar.2020.589780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/15/2020] [Indexed: 11/25/2022] Open
Abstract
Inhibition of Ras farnesylation in acute has been found to upregulate the α7 nicotinic acetylcholine receptor (α7nAChR) activity. This study was carried out to investigate the effect of chronic administration for 7 days of farnesyl transferase inhibitor lonafarnib (50 mg/kg, intraperitoneally injected) to male mice on the expression and activity of α7nAChR in hippocampal CA1 pyramidal cells. Herein, we show that lonafarnib dose dependently enhances the amplitude of ACh-evoked inward currents (IACh), owning to the increased α7nAChR expression and membrane trafficking. Lonafarnib inhibited phosphorylation of c-Jun and JNK, which was related to DNA methylation. In addition, reduced DNA methyltransferase 1 (DNMT1) expression was observed in lonafarnib-treated mice, which was reversed by JNK activator. Lonafarnib-upregulated expression of α7nAChR was mimicked by DNMT inhibitor, and repressed by JNK activator. However, only inhibited DNA methylation did not affect IACh, and the JNK activator partially decreased the lonafarnib-upregulated IACh. On the other hand, lonafarnib also increased the membrane expression of α7nAChR, which was partially inhibited by JNK activator or CaMKII inhibitor, without changes in the α7nAChR phosphorylation. CaMKII inhibitor had no effect on the expression of α7nAChR. Lonafarnib-enhanced spatial memory of mice was also partially blocked by JNK activator or CaMKII inhibitor. These results suggest that Ras inhibition increases α7nAChR expression through depressed DNA methylation of CHRNA7 via Ras-c-Jun-JNK pathway, increases the membrane expression of α7nAChR resulting in part from the enhanced CaMKII pathway and total expression of this receptor, and consequently enhances the spatial memory.
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Affiliation(s)
- Tingting Chen
- Department of Pharmacology, School of Pharmacy, Nantong University, Nantong, China.,Jiangsu Province Key Laboratory of Inflammation and Molecular Drug Target, Nantong, China
| | - Chengyun Cai
- School of Life Science, Nantong University, Nantong, China
| | - Lifeng Wang
- Department of Pharmacology, School of Pharmacy, Nantong University, Nantong, China.,Jiangsu Province Key Laboratory of Inflammation and Molecular Drug Target, Nantong, China
| | - Shixin Li
- Department of Pharmacology, School of Pharmacy, Nantong University, Nantong, China.,Jiangsu Province Key Laboratory of Inflammation and Molecular Drug Target, Nantong, China
| | - Ling Chen
- Department of Physiology, Nanjing Medical University, Nanjing, China
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7
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Schönung M, Meyer J, Nöllke P, Olshen AB, Hartmann M, Murakami N, Wakamatsu M, Okuno Y, Plass C, Loh ML, Niemeyer CM, Muramatsu H, Flotho C, Stieglitz E, Lipka DB. International Consensus Definition of DNA Methylation Subgroups in Juvenile Myelomonocytic Leukemia. Clin Cancer Res 2020; 27:158-168. [PMID: 33139265 DOI: 10.1158/1078-0432.ccr-20-3184] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/01/2020] [Accepted: 10/21/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Known clinical and genetic markers have limitations in predicting disease course and outcome in juvenile myelomonocytic leukemia (JMML). DNA methylation patterns in JMML have correlated with outcome across multiple studies, suggesting it as a biomarker to improve patient stratification. However, standardized approaches to classify JMML on the basis of DNA methylation patterns are lacking. We, therefore, sought to define an international consensus for DNA methylation subgroups in JMML and develop classification methods for clinical implementation. EXPERIMENTAL DESIGN Published DNA methylation data from 255 patients with JMML were used to develop and internally validate a classifier model. Accuracy across platforms (EPIC-arrays and MethylSeq) was tested using a technical validation cohort (32 patients). The suitability of both methods for single-patient classification was demonstrated using an independent cohort (47 patients). RESULTS Analysis of pooled, published data established three DNA methylation subgroups as a de facto standard. Unfavorable prognostic parameters (PTPN11 mutation, elevated fetal hemoglobin, and older age) were significantly enriched in the high methylation (HM) subgroup. A classifier was then developed that predicted subgroups with 98% accuracy across different technological platforms. Applying the classifier to an independent validation cohort confirmed an association of HM with secondary mutations, high relapse incidence, and inferior overall survival (OS), while the low methylation subgroup was associated with a favorable disease course. Multivariable analysis established DNA methylation subgroups as the only significant factor predicting OS. CONCLUSIONS This study provides an international consensus definition for DNA methylation subgroups in JMML. We developed and validated methods which will facilitate the design of risk-stratified clinical trials in JMML.
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Affiliation(s)
- Maximilian Schönung
- Section Translational Cancer Epigenomics, Division Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Julia Meyer
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, California
| | - Peter Nöllke
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Adam B Olshen
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Mark Hartmann
- Section Translational Cancer Epigenomics, Division Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Norihiro Murakami
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Manabu Wakamatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yusuke Okuno
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Aichi, Japan
| | - Christoph Plass
- Division Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Charlotte M Niemeyer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), partner site Freiburg, Germany
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Christian Flotho
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), partner site Freiburg, Germany
| | - Elliot Stieglitz
- Department of Pediatrics, Benioff Children's Hospital, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Daniel B Lipka
- Section Translational Cancer Epigenomics, Division Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT), Heidelberg, Germany. .,Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany
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8
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Thaulow J, Song Y, Lindeman LC, Kamstra JH, Lee Y, Xie L, Aleström P, Salbu B, Tollefsen KE. Epigenetic, transcriptional and phenotypic responses in Daphnia magna exposed to low-level ionizing radiation. ENVIRONMENTAL RESEARCH 2020; 190:109930. [PMID: 32738623 DOI: 10.1016/j.envres.2020.109930] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/18/2020] [Accepted: 07/10/2020] [Indexed: 06/11/2023]
Abstract
Ionizing radiation is known to induce oxidative stress and DNA damage as well as epigenetic effects in aquatic organisms. Epigenetic changes can be part of the adaptive responses to protect organisms from radiation-induced damage, or act as drivers of toxicity pathways leading to adverse effects. To investigate the potential roles of epigenetic mechanisms in low-dose ionizing radiation-induced stress responses, an ecologically relevant crustacean, adult Daphnia magna were chronically exposed to low and medium level external 60Co gamma radiation ranging from 0.4, 1, 4, 10, and 40 mGy/h for seven days. Biological effects at the molecular (global DNA methylation, histone modification, gene expression), cellular (reactive oxygen species formation), tissue/organ (ovary, gut and epidermal histology) and organismal (fecundity) levels were investigated using a suite of effect assessment tools. The results showed an increase in global DNA methylation associated with loci-specific alterations of histone H3K9 methylation and acetylation, and downregulation of genes involved in DNA methylation, one-carbon metabolism, antioxidant defense, DNA repair, apoptosis, calcium signaling and endocrine regulation of development and reproduction. Temporal changes of reactive oxygen species (ROS) formation were also observed with an apparent transition from ROS suppression to induction from 2 to 7 days after gamma exposure. The cumulative fecundity, however, was not significantly changed by the gamma exposure. On the basis of the new experimental evidence and existing knowledge, a hypothetical model was proposed to provide in-depth mechanistic understanding of the roles of epigenetic mechanisms in low dose ionizing radiation induced stress responses in D. magna.
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Affiliation(s)
- Jens Thaulow
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, N-0349, Oslo, Norway; Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - You Song
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, N-0349, Oslo, Norway; Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway.
| | - Leif C Lindeman
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - Jorke H Kamstra
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Faculty of Veterinary Medicine, Institute for Risk Assessment Sciences, Utrecht University, PO Box 80177, NL-3508 TD, Utrecht, the Netherlands
| | - YeonKyeong Lee
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Faculty of BioSciences, Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - Li Xie
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, N-0349, Oslo, Norway; Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management (MINA), P.O. Box 5003, N-1432 Ås, Norway
| | - Peter Aleström
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - Brit Salbu
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management (MINA), P.O. Box 5003, N-1432 Ås, Norway
| | - Knut Erik Tollefsen
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, N-0349, Oslo, Norway; Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management (MINA), P.O. Box 5003, N-1432 Ås, Norway
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9
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Moradi Sarabi M, Mohammadrezaei Khorramabadi R, Zare Z, Eftekhar E. Polyunsaturated fatty acids and DNA methylation in colorectal cancer. World J Clin Cases 2019; 7:4172-4185. [PMID: 31911898 PMCID: PMC6940323 DOI: 10.12998/wjcc.v7.i24.4172] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/27/2019] [Accepted: 12/13/2019] [Indexed: 02/05/2023] Open
Abstract
Colorectal cancer (CRC) has been designated a major global problem, especially due to its high prevalence in developed countries. CRC mostly occurs sporadically (75%-80%), and only 20%-25% of patients have a family history. Several processes are involved in the development of CRC such as a combination of genetic and epigenetic alterations. Epigenetic changes, including DNA methylation play a vital role in the progression of CRC. Complex interactions between susceptibility genes and environmental factors, such as a diet and sedentary lifestyle, lead to the development of CRC. Clinical and experimental studies have confirmed the beneficial effects of dietary polyunsaturated fatty acids (PUFAs) in preventing CRC. From a mechanistic viewpoint, it has been suggested that PUFAs are pleiotropic agents that alter chromatin remodeling, membrane structure and downstream cell signaling. Moreover, PUFAs can alter the epigenome via modulation of DNA methylation. In this review, we summarize recent investigations linking PUFAs and DNA methylation-associated CRC risk.
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Affiliation(s)
- Mostafa Moradi Sarabi
- Department of Biochemistry and Genetics, School of Medicine, Lorestan University of Medical Sciences, Khorramabad 381251698, Iran
| | - Reza Mohammadrezaei Khorramabadi
- Department of Biochemistry and Genetics, School of Medicine, Lorestan University of Medical Sciences, Khorramabad 381251698, Iran
| | - Zohre Zare
- Department of Pharmaceutics, School of Pharmacy, Lorestan University of Medical Sciences, Khorramabad 381251698, Iran
| | - Ebrahim Eftekhar
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas 7919915519, Iran
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10
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An immortalized cell line derived from renal erythropoietin-producing (REP) cells demonstrates their potential to transform into myofibroblasts. Sci Rep 2019; 9:11254. [PMID: 31375751 PMCID: PMC6677766 DOI: 10.1038/s41598-019-47766-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 07/23/2019] [Indexed: 12/22/2022] Open
Abstract
The erythroid growth factor erythropoietin (Epo) is produced by renal interstitial fibroblasts, called REP (renal Epo-producing) cells, in a hypoxia-inducible manner. In chronic kidney disease (CKD), REP cells lose their Epo-production ability, leading to renal anaemia. Concurrently, REP cells are suggested to be transformed into myofibroblasts, which are the major player of renal fibrosis. Although establishment of cultured cell lines derived from REP cells has been a long-term challenge, we here successfully established a REP-cell-derived immortalized and cultivable cell line (Replic cells) by using a genetically modified mouse line. Replic cells exhibited myofibroblastic phenotypes and lost their Epo-production ability, reflecting the situation in renal fibrosis. Additionally, we found that cell-autonomous TGFβ signalling contributes to maintenance of the myofibroblastic features of Replic cells. Furthermore, the promoters of genes for Epo and HIF2α, a major activator of Epo gene expression, were highly methylated in Replic cells. Thus, these results strongly support our contention that REP cells are the origin of myofibroblasts in fibrotic kidneys and demonstrate that cell-autonomous TGFβ signalling and epigenetic silencing are involved in renal fibrosis and renal anaemia, respectively, in CKD. The Replic cell line is a useful tool to further investigate the molecular mechanisms underlying renal fibrosis.
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11
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Mayorga L, Salassa BN, Marzese DM, Loos MA, Eiroa HD, Lubieniecki F, García Samartino C, Romano PS, Roqué M. Mitochondrial stress triggers a pro-survival response through epigenetic modifications of nuclear DNA. Cell Mol Life Sci 2019; 76:1397-1417. [PMID: 30673822 PMCID: PMC11105675 DOI: 10.1007/s00018-019-03008-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/19/2018] [Accepted: 01/08/2019] [Indexed: 12/20/2022]
Abstract
Mitochondrial dysfunction represents an important cellular stressor and when intense and persistent cells must unleash an adaptive response to prevent their extinction. Furthermore, mitochondria can induce nuclear transcriptional changes and DNA methylation can modulate cellular responses to stress. We hypothesized that mitochondrial dysfunction could trigger an epigenetically mediated adaptive response through a distinct DNA methylation patterning. We studied cellular stress responses (i.e., apoptosis and autophagy) in mitochondrial dysfunction models. In addition, we explored nuclear DNA methylation in response to this stressor and its relevance in cell survival. Experiments in cultured human myoblasts revealed that intense mitochondrial dysfunction triggered a methylation-dependent pro-survival response. Assays done on mitochondrial disease patient tissues showed increased autophagy and enhanced DNA methylation of tumor suppressor genes and pathways involved in cell survival regulation. In conclusion, mitochondrial dysfunction leads to a "pro-survival" adaptive state that seems to be triggered by the differential methylation of nuclear genes.
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Affiliation(s)
- Lía Mayorga
- Instituto de Histología y Embriología de Mendoza (IHEM, Universidad Nacional de Cuyo, CONICET)-Centro Universitario UNCuyo, 5500, Mendoza, Argentina.
| | - Betiana N Salassa
- Instituto de Histología y Embriología de Mendoza (IHEM, Universidad Nacional de Cuyo, CONICET)-Centro Universitario UNCuyo, 5500, Mendoza, Argentina
- Facultad de Odontología, Univeridad Nacional de Cuyo- Centro Universitario UNCuyo, 5500, Mendoza, Argentina
| | - Diego M Marzese
- John Wayne Cancer Institute, 2200 Santa Monica Boulevard, Santa Monica, CA, 90404, USA
| | - Mariana A Loos
- Hospital de Pediatría J.P. Garrahan, Combate de los Pozos 1881, 1245, Buenos Aires, Argentina
| | - Hernán D Eiroa
- Hospital de Pediatría J.P. Garrahan, Combate de los Pozos 1881, 1245, Buenos Aires, Argentina
| | - Fabiana Lubieniecki
- Hospital de Pediatría J.P. Garrahan, Combate de los Pozos 1881, 1245, Buenos Aires, Argentina
| | - Clara García Samartino
- Facultad de Ciencias Médicas, Universidad Nacional de Cuyo-Centro Universitario UNCuyo, 5500, Mendoza, Argentina
| | - Patricia S Romano
- Instituto de Histología y Embriología de Mendoza (IHEM, Universidad Nacional de Cuyo, CONICET)-Centro Universitario UNCuyo, 5500, Mendoza, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de Cuyo-Centro Universitario UNCuyo, 5500, Mendoza, Argentina
| | - María Roqué
- Instituto de Histología y Embriología de Mendoza (IHEM, Universidad Nacional de Cuyo, CONICET)-Centro Universitario UNCuyo, 5500, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo-Centro Universitario UNCuyo, 5500, Mendoza, Argentina
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12
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Flotho C. Gene mutations do not operate in a vacuum: the increasing importance of epigenetics in juvenile myelomonocytic leukemia. Epigenetics 2019; 14:236-244. [PMID: 30773984 PMCID: PMC6557547 DOI: 10.1080/15592294.2019.1583039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/04/2019] [Accepted: 02/08/2019] [Indexed: 01/02/2023] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) stands out among malignant neoplasms of childhood in several ways. First, JMML is a model condition to elucidate the relevance of deregulated Ras signal transduction in human cancer. Second, the identification of Ras pathway mutations in JMML has informed the field of germline cancer predisposition and advanced the understanding of molecular mechanisms underlying the progression from predisposition to neoplasia. Third and not least, genomic DNA methylation was discovered to play a salient role in the classification and prognostication of the disease. This article discusses the evolution of epigenetic research on JMML over the past years and reviews the relevance of aberrant DNA methylation in the diagnosis, concept, and clinical decision-making of JMML.
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Affiliation(s)
- Christian Flotho
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg, German Cancer Research Center (DKFZ), Freiburg, Heidelberg, Germany
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13
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Moradi Sarabi M, Zahedi SA, Pajouhi N, Khosravi P, Bagheri S, Ahmadvand H, Shahryarhesami S. The effects of dietary polyunsaturated fatty acids on miR-126 promoter DNA methylation status and VEGF protein expression in the colorectal cancer cells. GENES AND NUTRITION 2018; 13:32. [PMID: 30598703 PMCID: PMC6299631 DOI: 10.1186/s12263-018-0623-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 11/29/2018] [Indexed: 02/06/2023]
Abstract
Background There is increasing evidence indicating an aberrant expression of miRNAs in colorectal cancer (CRC) development. Growing evidence has suggested that polyunsaturated fatty acids (PUFAs) could modulate the remodeling of the epigenome. No study has yet been published to examine the direct effect of PUFA on the promoter methylation of miRNAs. This study aimed to examine the potential clinical application of PUFA on the promoter DNA methylation of miR-126 and its angiogenic target molecule (VEGF) in the CRC cells. Methods We investigated the direct effect of 100 μM EPA, DHA, and LA for 24 h on promoter methylation status of miR-126 in a panel of five CRC cell lines (HCT116, HT29/219, Caco2, SW742, and LS180) by methylation-specific PCR (MSP). We also quantified the miR-126 and VEGF transcript expression levels in five CRC cell lines affected by PUFA by real-time PCR. Moreover, we analyzed the protein expression level of VEGF, as a target of miR-126, by western blotting assay. Results MSP analysis showed extensive DNA methylation of the miR-126 promoter in all five CRC cell lines, and among all three PUFAs, only DHA completely demethylated the promoter of miR-126 in HCT116 and Caco2 cell lines. We found that only DHA significantly induces the expression level of miR-126 in HCT116 and Caco2 cell lines, respectively, by 20.1-fold and 1.68-fold (p < 0.05). Our finding indicates that the downregulation of VEGF protein level is also effectively observed only in DHA-treated HCT116 and Caco2 cells compared to control cells (p < 0.05). Conclusions Our results provide evidence that n-3 PUFAs are able to modulate cellular miR-126 DNA methylation and inhibit VEGF expression level in a cell-type specific manner in colorectal cancer cells. DHA always showed higher efficacy than EPA and LA in our experiment. Overall, our results suggest a potential clinical application of n-3 PUFAs as anti-angiogenic agents in CRC therapy.
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Affiliation(s)
- Mostafa Moradi Sarabi
- 1Department of Biochemistry and Genetics, Lorestan University of Medical Sciences, School of Medicine, Khorramabad, 381251698 Iran.,3Razi Herbal Medicines Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Seyed Abdollah Zahedi
- 1Department of Biochemistry and Genetics, Lorestan University of Medical Sciences, School of Medicine, Khorramabad, 381251698 Iran
| | - Naser Pajouhi
- 2Department of Physiology, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran.,3Razi Herbal Medicines Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Peyman Khosravi
- 1Department of Biochemistry and Genetics, Lorestan University of Medical Sciences, School of Medicine, Khorramabad, 381251698 Iran.,4Student Research Committee, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Shahrokh Bagheri
- 1Department of Biochemistry and Genetics, Lorestan University of Medical Sciences, School of Medicine, Khorramabad, 381251698 Iran
| | - Hassan Ahmadvand
- 1Department of Biochemistry and Genetics, Lorestan University of Medical Sciences, School of Medicine, Khorramabad, 381251698 Iran
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14
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Ashok D, Sood TJ, Sah S, Palta P, Mukesh M, Chauhan MS, Manik RS, Singla SK. Buffalo SCNT embryos exhibit abnormal gene expression of ERK/MAPK pathway and DNA methylation. Reprod Domest Anim 2018; 53:1247-1252. [PMID: 30051511 DOI: 10.1111/rda.13217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 04/12/2018] [Accepted: 05/01/2018] [Indexed: 12/30/2022]
Abstract
Inhibition of ERK/MAPK pathway has been shown to decrease DNA methylation via down-regulation of DNA methyltransferases (DNMTs) in several studies suggesting that this pathway plays an important role in regulation of DNA methylation. We examined the relative expression level of seven important genes related to ERK/MAPK pathway and DNMTs (DNMT1, DNMT3a and DNMT3b) by quantitative real-time PCR in buffalo blastocysts produced by Hand-made cloning and compared it with that in blastocyst-stage embryos produced by in vitro fertilization (IVF). The expression level of six of seven genes related to ERK/MAPK pathway examined i.e., p21RAS, RAF1, AKT1, ERK2, PIK3R2 and c-Myc was significantly higher (p < 0.05) in cloned than in IVF embryos. However, the expression level of FOS was lower (p < 0.005) in cloned than in IVF embryos. The relative expression level of DNMT3a and DNMT3b but not that of DNMT1 was significantly higher (p < 0.05) in cloned than in IVF embryos. These results indicate that the cloned embryos exhibit an abnormal expression of several important genes related to ERK/MAPK pathway and DNMTs. Although a direct link between ERK/MAPK pathway and DNMTs was not examined in the present study, it can be speculated that ERK/MAPK pathway may have a role in regulating the expression of DNMTs in embryos, as also observed in other tissues.
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Affiliation(s)
- Disha Ashok
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
| | - Tanushri Jerath Sood
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
| | - Shrutika Sah
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
| | - Prabhat Palta
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
| | - Manishi Mukesh
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
| | - Manmohan Singh Chauhan
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
| | - Radhey Sham Manik
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
| | - Suresh Kumar Singla
- Embryo Biotechnology Laboratory, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, India
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15
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Lipka DB, Witte T, Toth R, Yang J, Wiesenfarth M, Nöllke P, Fischer A, Brocks D, Gu Z, Park J, Strahm B, Wlodarski M, Yoshimi A, Claus R, Lübbert M, Busch H, Boerries M, Hartmann M, Schönung M, Kilik U, Langstein J, Wierzbinska JA, Pabst C, Garg S, Catalá A, De Moerloose B, Dworzak M, Hasle H, Locatelli F, Masetti R, Schmugge M, Smith O, Stary J, Ussowicz M, van den Heuvel-Eibrink MM, Assenov Y, Schlesner M, Niemeyer C, Flotho C, Plass C. RAS-pathway mutation patterns define epigenetic subclasses in juvenile myelomonocytic leukemia. Nat Commun 2017; 8:2126. [PMID: 29259247 PMCID: PMC5736667 DOI: 10.1038/s41467-017-02177-w] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 11/13/2017] [Indexed: 01/15/2023] Open
Abstract
Juvenile myelomonocytic leukemia (JMML) is an aggressive myeloproliferative disorder of early childhood characterized by mutations activating RAS signaling. Established clinical and genetic markers fail to fully recapitulate the clinical and biological heterogeneity of this disease. Here we report DNA methylome analysis and mutation profiling of 167 JMML samples. We identify three JMML subgroups with unique molecular and clinical characteristics. The high methylation group (HM) is characterized by somatic PTPN11 mutations and poor clinical outcome. The low methylation group is enriched for somatic NRAS and CBL mutations, as well as for Noonan patients, and has a good prognosis. The intermediate methylation group (IM) shows enrichment for monosomy 7 and somatic KRAS mutations. Hypermethylation is associated with repressed chromatin, genes regulated by RAS signaling, frequent co-occurrence of RAS pathway mutations and upregulation of DNMT1 and DNMT3B, suggesting a link between activation of the DNA methylation machinery and mutational patterns in JMML.
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MESH Headings
- Antineoplastic Agents/therapeutic use
- Biopsy
- Child
- Child, Preschool
- Chromatin/genetics
- Chromatin/metabolism
- DNA (Cytosine-5-)-Methyltransferase 1/metabolism
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation
- DNA Mutational Analysis
- Epigenomics
- Female
- Gene Expression Regulation, Leukemic
- Hematopoietic Stem Cell Transplantation
- Humans
- Infant
- Leukemia, Myelomonocytic, Juvenile/genetics
- Leukemia, Myelomonocytic, Juvenile/mortality
- Leukemia, Myelomonocytic, Juvenile/pathology
- Leukemia, Myelomonocytic, Juvenile/therapy
- Male
- Mutation
- Noonan Syndrome/genetics
- Noonan Syndrome/pathology
- Prognosis
- Prospective Studies
- Protein Tyrosine Phosphatase, Non-Receptor Type 11/genetics
- Protein Tyrosine Phosphatase, Non-Receptor Type 11/metabolism
- Proto-Oncogene Proteins c-cbl
- Proto-Oncogene Proteins p21(ras)/genetics
- Proto-Oncogene Proteins p21(ras)/metabolism
- Signal Transduction/genetics
- Up-Regulation
- DNA Methyltransferase 3B
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Affiliation(s)
- Daniel B Lipka
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany.
- Department of Hematology and Oncology, Medical Center, Otto-von-Guericke-University, Leipziger Strasse 44, 39120, Magdeburg, Germany.
- Health Campus Immunology, Infectiology and Inflammation, Otto-von-Guericke-University, Leipziger Strasse 44, 39120, Magdeburg, Germany.
| | - Tania Witte
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
- Cancer Epigenetics Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Reka Toth
- Computational Epigenomics Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Jing Yang
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Manuel Wiesenfarth
- Division of Biostatistics, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Peter Nöllke
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine Medical Center, Faculty of Medicine, University of Freiburg, Heiliggeiststrasse 1, 79106, Freiburg, Germany
| | - Alexandra Fischer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine Medical Center, Faculty of Medicine, University of Freiburg, Heiliggeiststrasse 1, 79106, Freiburg, Germany
| | - David Brocks
- Cancer Epigenetics Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Zuguang Gu
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Jeongbin Park
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Brigitte Strahm
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine Medical Center, Faculty of Medicine, University of Freiburg, Heiliggeiststrasse 1, 79106, Freiburg, Germany
| | - Marcin Wlodarski
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine Medical Center, Faculty of Medicine, University of Freiburg, Heiliggeiststrasse 1, 79106, Freiburg, Germany
- German Cancer Consortium (DKTK), 79106, Freiburg, Germany
| | - Ayami Yoshimi
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine Medical Center, Faculty of Medicine, University of Freiburg, Heiliggeiststrasse 1, 79106, Freiburg, Germany
| | - Rainer Claus
- Division of Hematology, Oncology and Stem Cell Transplantation, University Medical Center, Hugstetter Strasse 55, 79106, Freiburg, Germany
| | - Michael Lübbert
- Division of Hematology, Oncology and Stem Cell Transplantation, University Medical Center, Hugstetter Strasse 55, 79106, Freiburg, Germany
| | - Hauke Busch
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Stefan-Meier-Strasse 17, 79104, Freiburg, Germany
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Melanie Boerries
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Stefan-Meier-Strasse 17, 79104, Freiburg, Germany
- German Cancer Consortium (DKTK), 79106, Freiburg, Germany
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Mark Hartmann
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Maximilian Schönung
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Umut Kilik
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Jens Langstein
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Justyna A Wierzbinska
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
- Cancer Epigenetics Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Caroline Pabst
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, INF 410, 69120, Heidelberg, Germany
| | - Swati Garg
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, INF 410, 69120, Heidelberg, Germany
| | - Albert Catalá
- Department of Hematology and Oncology, Hospital Sant Joan de Déu, Passeig de Sant Joan de Déu, 2, 08950, Esplugues de Llobrega, Barcelona, Spain
| | - Barbara De Moerloose
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, De Pintelaan 185, 9000, Ghent, Belgium
| | - Michael Dworzak
- St. Anna Children's Hospital and Children's Cancer Research Institute, Medical University of Vienna, Zimmermannplatz 10, 1090, Vienna, Austria
| | - Henrik Hasle
- Department of Pediatrics, Aarhus University Hospital Skejby, Palle Juul-Jensens Boulevard 82, 8200, Aarhus, Denmark
| | - Franco Locatelli
- Department of Pediatric Hematology and Oncology, Bambino Gesú Children's Hospital, University of Pavia, Piazza S. Onofrio 4, Rome, 00165, Italy
| | - Riccardo Masetti
- Department of Pediatric Oncology and Hematology, University of Bologna, Via Massarenti 11, 40138, Bologna, Italy
| | - Markus Schmugge
- Department of Hematology and Oncology, University Children's Hospital, Steinwiesstrasse 75, 8032, Zurich, Switzerland
| | - Owen Smith
- Department of Paediatric Oncology and Haematology, Our Lady's Children's Hospital Crumlin, Dublin, 12, Ireland
| | - Jan Stary
- Department of Pediatric Hematology and Oncology, Charles University and University Hospital Motol, V Úvalu 84, 150 06, Prague 5, Czech Republic
| | - Marek Ussowicz
- Department of Pediatric Hematology, Oncology and BMT, Wroclaw Medical University, ul. Borowska 213, 50-556, Wroclaw, Poland
| | | | - Yassen Assenov
- Computational Epigenomics Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
| | - Matthias Schlesner
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany
- Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Charlotte Niemeyer
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine Medical Center, Faculty of Medicine, University of Freiburg, Heiliggeiststrasse 1, 79106, Freiburg, Germany
- German Cancer Consortium (DKTK), 79106, Freiburg, Germany
| | - Christian Flotho
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine Medical Center, Faculty of Medicine, University of Freiburg, Heiliggeiststrasse 1, 79106, Freiburg, Germany
- German Cancer Consortium (DKTK), 79106, Freiburg, Germany
| | - Christoph Plass
- Cancer Epigenetics Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), INF 280, 69120, Heidelberg, Germany.
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.
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16
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Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer. Nature 2017; 549:543-547. [PMID: 28959968 PMCID: PMC5789792 DOI: 10.1038/nature23891] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/03/2017] [Indexed: 12/18/2022]
Abstract
In mammals, the canonical somatic DNA methylation landscape is established upon specification of the embryo proper and subsequently disrupted within many cancer types. However, the underlying mechanisms that direct this genome-scale transformation remain elusive, with no clear model for its systematic acquisition or potential developmental utility. Here, we analysed global remethylation from the mouse preimplantation embryo into the early epiblast and extraembryonic ectoderm. We show that these two states acquire highly divergent genomic distributions with substantial disruption of bimodal, CpG density-dependent methylation in the placental progenitor. The extraembryonic epigenome includes specific de novo methylation at hundreds of embryonically protected CpG island promoters, particularly those that are associated with key developmental regulators and are orthologously methylated across most human cancer types. Our data suggest that the evolutionary innovation of extraembryonic tissues may have required co-option of DNA methylation-based suppression as an alternative to regulation by Polycomb-group proteins, which coordinate embryonic germ-layer formation in response to extraembryonic cues. Moreover, we establish that this decision is made deterministically, downstream of promiscuously used-and frequently oncogenic-signalling pathways, via a novel combination of epigenetic cofactors. Methylation of developmental gene promoters during tumorigenesis may therefore reflect the misappropriation of an innate trajectory and the spontaneous reacquisition of a latent, developmentally encoded epigenetic landscape.
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17
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Liu F, Wang L, Perna F, Nimer SD. Beyond transcription factors: how oncogenic signalling reshapes the epigenetic landscape. Nat Rev Cancer 2016; 16:359-72. [PMID: 27220480 PMCID: PMC5548460 DOI: 10.1038/nrc.2016.41] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cancer, once thought to be caused largely by genetic alterations, is now considered to be a mixed genetic and epigenetic disease. The epigenetic landscape, which is dictated by covalent DNA and histone modifications, is profoundly altered in transformed cells. These abnormalities may arise from mutations in, or altered expression of, chromatin modifiers. Recent reports on the interplay between cellular signalling pathways and chromatin modifications add another layer of complexity to the already complex regulation of the epigenome. In this Review, we discuss these new studies and how the insights they provide can contribute to a better understanding of the molecular pathogenesis of neoplasia.
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Affiliation(s)
- Fan Liu
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL 33136
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136
| | - Lan Wang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fabiana Perna
- Molecular Pharmacology and Chemistry Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Stephen D. Nimer
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL 33136
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136
- Department of Internal Medicine, University of Miami, Miller School of Miami, FL33136
- Corresponding Author:
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18
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Pathania R, Ramachandran S, Mariappan G, Thakur P, Shi H, Choi JH, Manicassamy S, Kolhe R, Prasad PD, Sharma S, Lokeshwar BL, Ganapathy V, Thangaraju M. Combined Inhibition of DNMT and HDAC Blocks the Tumorigenicity of Cancer Stem-like Cells and Attenuates Mammary Tumor Growth. Cancer Res 2016; 76:3224-35. [PMID: 27197203 DOI: 10.1158/0008-5472.can-15-2249] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 03/17/2016] [Indexed: 02/07/2023]
Abstract
Recently, impressive technical advancements have been made in the isolation and validation of mammary stem cells and cancer stem cells (CSC), but the signaling pathways that regulate stem cell self-renewal are largely unknown. Furthermore, CSCs are believed to contribute to chemo- and radioresistance. In this study, we used the MMTV-Neu-Tg mouse mammary tumor model to identify potential new strategies for eliminating CSCs. We found that both luminal progenitor and basal stem cells are susceptible to genetic and epigenetic modifications, which facilitate oncogenic transformation and tumorigenic potential. A combination of the DNMT inhibitor 5-azacytidine and the HDAC inhibitor butyrate markedly reduced CSC abundance and increased the overall survival in this mouse model. RNA-seq analysis of CSCs treated with 5-azacytidine plus butyrate provided evidence that inhibition of chromatin modifiers blocks growth-promoting signaling molecules such as RAD51AP1 and SPC25, which play key roles in DNA damage repair and kinetochore assembly. Moreover, RAD51AP1 and SPC25 were significantly overexpressed in human breast tumor tissues and were associated with reduced overall patient survival. In conclusion, our studies suggest that breast CSCs are intrinsically sensitive to genetic and epigenetic modifications and can therefore be significantly affected by epigenetic-based therapies, warranting further investigation of combined DNMT and HDAC inhibition in refractory or drug-resistant breast cancer. Cancer Res; 76(11); 3224-35. ©2016 AACR.
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Affiliation(s)
- Rajneesh Pathania
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Sabarish Ramachandran
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Gurusamy Mariappan
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Priyanka Thakur
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Huidong Shi
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia. CRU Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Jeong-Hyeon Choi
- CRU Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia. Department of Biostatistics, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Santhakumar Manicassamy
- CRU Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia. Immunotherapy Center, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Ravindra Kolhe
- CRU Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia. Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Puttur D Prasad
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia. CRU Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Suash Sharma
- CRU Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia. Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Bal L Lokeshwar
- CRU Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia. Charlie Norwood VA Medical Center and Department of Medicine and Surgery, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Vadivel Ganapathy
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Muthusamy Thangaraju
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia. CRU Cancer Center, Medical College of Georgia, Augusta University, Augusta, Georgia.
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da Silva RA, Sammartino Mariano F, Planello AC, Line SRP, de Souza AP. HaCaT anchorage blockade leads to oxidative stress, DNA damage and DNA methylation changes. Biochem Biophys Rep 2015; 2:94-102. [PMID: 29124149 PMCID: PMC5668640 DOI: 10.1016/j.bbrep.2015.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/14/2015] [Accepted: 05/19/2015] [Indexed: 11/24/2022] Open
Abstract
Cell adhesion plays an important role in neoplastic transformation. Thus, anchorage-independent growth and epithelial-mesenchymal transition, which are features associated to anoikis-resistance, are vital steps in cancer progression and metastatic colonization. Cell attachment loss may induce intracellular oxidative stress, which triggers DNA damage as methylation changes. HaCaT lineage cells were submitted to periods of 1, 3, 5 and 24 h of anchorage blockage with the purpose of study of oxidative stress effect on changes in the DNA methylation pattern, derived from attachment blockade. Through this study, HaCaT anchorage blockage-induced oxidative stress was reported to mediate alterations in global DNA methylation changes and into TP53 gene promoter pattern during anoikis-resistance acquisition. Furthermore, at the first experimental time-periods (1, 3 and 5 h), genome hypermethylation was found; however, genome hypomethylation was observed in later time-periods (24 h) of attachment impediment. The TP 53 methylation analyses were performed after 24 h of replated anoikis-resistance cells and same methylation pattern was observed, occurring an early (1 and 3 h) hypermethylation that was followed by late (5 and 24 h) hypomethylation. However, LINE-1, a marker of genomic instability, was perceived in time-dependent hypomethylation. The mRNA levels of the DNMTs enzymes were influenced by cell attachment blockage, but non-conclusive results were obtained in order to match DNMTs transcription to pattern methylation results. In conclusion, DNA damage was found, leaded by oxidative stress that has come up from HaCaT anchorage blockade, which rises a global genome hypomethylation tendency as consequence, which might denote genomic instability.
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Affiliation(s)
- Rodrigo A da Silva
- Department of Morphology, School of Dentistry of Piracicaba, University of Campinas - UNICAMP, Av. Limeira, 901, 13414-018 Piracicaba, SP, Brazil
| | - Flavia Sammartino Mariano
- Department of Morphology, School of Dentistry of Piracicaba, University of Campinas - UNICAMP, Av. Limeira, 901, 13414-018 Piracicaba, SP, Brazil
| | - Aline C Planello
- Department of Morphology, School of Dentistry of Piracicaba, University of Campinas - UNICAMP, Av. Limeira, 901, 13414-018 Piracicaba, SP, Brazil
| | - Sergio R P Line
- Department of Morphology, School of Dentistry of Piracicaba, University of Campinas - UNICAMP, Av. Limeira, 901, 13414-018 Piracicaba, SP, Brazil
| | - Ana Paula de Souza
- Department of Morphology, School of Dentistry of Piracicaba, University of Campinas - UNICAMP, Av. Limeira, 901, 13414-018 Piracicaba, SP, Brazil
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20
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Cheishvili D, Boureau L, Szyf M. DNA demethylation and invasive cancer: implications for therapeutics. Br J Pharmacol 2015; 172:2705-15. [PMID: 25134627 DOI: 10.1111/bph.12885] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 08/01/2014] [Accepted: 08/13/2014] [Indexed: 02/06/2023] Open
Abstract
One of the hallmarks of cancer is aberrant DNA methylation, which is associated with abnormal gene expression. Both hypermethylation and silencing of tumour suppressor genes as well as hypomethylation and activation of prometastatic genes are characteristic of cancer cells. As DNA methylation is reversible, DNA methylation inhibitors were tested as anticancer drugs with the idea that such agents would demethylate and reactivate tumour suppressor genes. Two cytosine analogues, 5-azacytidine (Vidaza) and 5-aza-2'-deoxycytidine, were approved by the Food and Drug Administration as antitumour agents in 2004 and 2006 respectively. However, these agents might cause activation of a panel of prometastatic genes in addition to activating tumour suppressor genes, which might lead to increased metastasis. This poses the challenge of how to target tumour suppressor genes and block cancer growth with DNA-demethylating drugs while avoiding the activation of prometastatic genes and precluding the morbidity of cancer metastasis. This paper reviews current progress in using DNA methylation inhibitors in cancer therapy and the potential promise and challenges ahead.
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Affiliation(s)
- David Cheishvili
- Department of Pharmacology and Therapeutics, McGill University Medical School, Montreal, QC, Canada
| | - Lisa Boureau
- Department of Pharmacology and Therapeutics, McGill University Medical School, Montreal, QC, Canada.,Department of Physiology Medical Sciences, University of Toronto 1 King's College Circle Toronto, ON, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, McGill University Medical School, Montreal, QC, Canada.,Sackler Program for Epigenetics and Developmental Psychobiology, McGill University Medical School, Montreal, QC, Canada.,Canadian Institute for Advanced Research, Faculty of Medicine, University of Toronto 1 King's College Circle Toronto, ON, Canada
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21
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Xiao Y, Word B, Lyn-Cook L, Lyn-Cook B, Hammons G. Cigarette smoke condensate and individual constituents modulate DNA methyltransferase expression in human liver cells. SAGE Open Med 2015; 3:2050312115578317. [PMID: 26770776 PMCID: PMC4679232 DOI: 10.1177/2050312115578317] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 02/03/2015] [Indexed: 01/02/2023] Open
Abstract
Objectives: Previous studies found higher expression levels of DNA methyltransferase 1 in liver samples from smokers compared to those from non-smokers. In contrast, expression levels of DNA methyltransferase 3a and DNA methyltransferase 3b were similar in smokers and non-smokers. This study extends these studies to establish a causal linkage to cigarette smoke exposure by examining whether DNA methyltransferase expression is modulated by cigarette smoke condensate. Methods: These experiments were conducted in an in vitro system using HepG2 human liver cells. The dose range of cigarette smoke condensate was 0.1–120 µg/mL. The duration of exposure was up to 72 h. Results: In a 24-h exposure, DNA methyltransferase 1 expression was found to increase significantly in a dose-dependent manner (greater than threefold at 100 µg/mL cigarette smoke condensate). Expression levels of DNA methyltransferase 3a and DNA methyltransferase 3b were, however, not affected under these conditions. The effect of two cigarette constituents, nicotine and cotinine, on DNA methyltransferase 1 expression was also examined. Nicotine exposure significantly increased DNA methyltransferase 1 expression in a dose-dependent manner (greater than twofold at 50 µM). However, under these conditions, cotinine did not increase DNA methyltransferase 1 expression. Conclusion: These results clearly provide additional support of the modulating effect of cigarette smoke on DNA methyltransferase 1 expression. Given the potential of alterations in DNA methyltransferase expression to affect cellular function, this pathway may play a critical role in cigarette smoke-induced toxicity.
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Affiliation(s)
- Yongmei Xiao
- National Center for Toxicological Research, Jefferson, AR, USA
| | - Beverly Word
- National Center for Toxicological Research, Jefferson, AR, USA
| | | | | | - George Hammons
- National Center for Toxicological Research, Jefferson, AR, USA
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22
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Cridge AG, Leask MP, Duncan EJ, Dearden PK. What do studies of insect polyphenisms tell us about nutritionally-triggered epigenomic changes and their consequences? Nutrients 2015; 7:1787-97. [PMID: 25768950 PMCID: PMC4377881 DOI: 10.3390/nu7031787] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/02/2015] [Accepted: 03/04/2015] [Indexed: 11/29/2022] Open
Abstract
Many insects are capable of remarkable changes in biology and form in response to their environment or diet. The most extreme example of these are polyphenisms, which are when two or more different phenotypes are produced from a single genotype in response to the environment. Polyphenisms provide a fascinating opportunity to study how the environment affects an animal’s genome, and how this produces changes in form. Here we review the current state of knowledge of the molecular basis of polyphenisms and what can be learnt from them to understand how nutrition may influence our own genomes.
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Affiliation(s)
- Andrew G Cridge
- Gravida and Genetics Otago, Biochemistry Department, University of Otago, P.O. Box 56, Dunedin 9016, New Zealand.
| | - Megan P Leask
- Gravida and Genetics Otago, Biochemistry Department, University of Otago, P.O. Box 56, Dunedin 9016, New Zealand.
| | - Elizabeth J Duncan
- Gravida and Genetics Otago, Biochemistry Department, University of Otago, P.O. Box 56, Dunedin 9016, New Zealand.
| | - Peter K Dearden
- Gravida and Genetics Otago, Biochemistry Department, University of Otago, P.O. Box 56, Dunedin 9016, New Zealand.
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23
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Herman D, Leakey TI, Behrens A, Yao-Borengasser A, Cooney CA, Jousheghany F, Phanavanh B, Siegel ER, Safar AM, Korourian S, Kieber-Emmons T, Monzavi-Karbassi B. CHST11 gene expression and DNA methylation in breast cancer. Int J Oncol 2015; 46:1243-51. [PMID: 25586191 PMCID: PMC4324579 DOI: 10.3892/ijo.2015.2828] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 12/03/2014] [Indexed: 01/09/2023] Open
Abstract
Our previously published data link P-selectin-reactive chondroitin sulfate structures on the surface of breast cancer cells to metastatic behavior of cells. We have shown that a particular sulfation pattern mediated by the expression of carbohydrate (chondroitin 4) sulfotransferase-11 (CHST11) correlates with P-selectin binding and aggressiveness of human breast cancer cell lines. The present study was performed to evaluate the prognostic value of CHST11 expression and determine whether aberrant DNA methylation controls CHST11 expression in breast cancer. Publicly available datasets were used to examine the association of CHST11 expression to aggressiveness and progression of breast cancer. Methylation status was analyzed using bisulfite genomic sequencing. 5-aza-2′-deoxycytidine (5AzadC) was used for DNA demethylation. Reduced representation bisulfite sequencing was performed in the CpG island of CHST11 with a minimum coverage of 10. Quantitative real-time RT-PCR was employed to confirm the expression profile of CHST11 in breast cancer cell lines. Flow cytometry was also used to confirm the expression of the CHST11 product, chondroitin sulfate A (CS-A). The expression of CHST11 was significantly higher in basal-like and Her2-amplified cell lines compared to luminal cell lines. CHST11 was also highly expressed in cancer tissues compared to normal tissues and the expression levels were significantly associated with tumor progression. We observed very low levels of DNA methylation in a CpG island of CHST11 in basal-like cells but very high levels in the same region in luminal cells. Treatment of MCF7 cells, a luminal cell line with very low expression of CHST11, with 5AzadC increased the expression of CHST11 and its immediate product, CS-A, in a dose-dependent manner. These results suggest that CHST11 may play a direct role in progression of breast cancer and that its expression is controlled by DNA methylation. Therefore, in addition to CHST11 mRNA levels, the methylation status of this gene also has potential as a prognostic biomarker.
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Affiliation(s)
- Damir Herman
- Division of Hematology/Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Tatiana I Leakey
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Alice Behrens
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Aiwei Yao-Borengasser
- Department of Medical Genetics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Craig A Cooney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Fariba Jousheghany
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Bounleut Phanavanh
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Eric R Siegel
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - A Mazin Safar
- Division of Hematology/Oncology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Soheila Korourian
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Thomas Kieber-Emmons
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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Kim KH, Ryu HM, Oh SH, Oh EJ, Ahn JS, Lee JH, Choi JY, Cho JH, Kim CD, Kim YL, Park SH. Effect of DNA demethylation in experimental encapsulating peritoneal sclerosis. Ther Apher Dial 2014; 18:628-36. [PMID: 25256793 DOI: 10.1111/1744-9987.12186] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Encapsulating peritoneal sclerosis (EPS) involves excessive peritoneal fibrosis in patients on peritoneal dialysis, eventually leading to visceral constriction and bowel obstruction. Few studies have investigated epigenetic mechanisms relating to EPS. Here we evaluated the therapeutic effects of DNA demethylation in experimental EPS. Experimental EPS was induced by intraperitoneal injection of 0.1% chlorhexidine gluconate (CG) and 15% ethanol in non-uremic male Sprague-Dawley (SD) rats. Rats were divided into three groups: group C (N=5) with saline injection only, group CG (N=7) with EPS induction for 4 weeks, and chlorhexidine gluconate and azacytidine (CGA) treated group (N=7) with EPS induction for 4 weeks and 5'-azacytidine injection for the last 2 weeks. Morphometric analysis of peritoneum and immunohistochemical staining for type 1 collagen and α-smooth muscle actin (α-SMA) were performed. Expressions of transforming growth factor-β (TGF-β), fibroblast-specific protein 1 (FSP1), and DNA methyltransferase 1 (DNMT1) were analyzed by Western blot. Methylation-specific polymerase chain reaction (PCR) for Ras GTPase activating-like protein 1 (RASAL1) was performed with measurement of RASAL1 protein expression. Parietal peritoneal thickness and the number of vessels in omental tissue were significantly decreased in group CGA compared to group CG, as were the expressions of type 1 collagen, α-SMA, TGF-β, and FSP1. DNMT1 was significantly increased in group CG, and reduced in group CGA. RASAL1 hypermethylation was associated with decreased RASAL1 protein expression in group CG, which was reversed in group CGA. DNA demethylation by 5'-azacytidine treatment improved pathologic changes of the peritoneum in experimental EPS, and was associated with reversal of increased DNMT1 expression and RASAL1 hypermethylation.
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Affiliation(s)
- Kyung-Hoon Kim
- Division of Nephrology and Department of Internal Medicine, Kyungpook National University Hospital, Daegu, Korea
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25
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Causes and Consequences of Age-Related Changes in DNA Methylation: A Role for ROS? BIOLOGY 2014; 3:403-25. [PMID: 24945102 PMCID: PMC4085615 DOI: 10.3390/biology3020403] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 05/28/2014] [Accepted: 05/31/2014] [Indexed: 01/15/2023]
Abstract
Recent genome-wide analysis of C-phosphate-G (CpG) sites has shown that the DNA methylome changes with increasing age, giving rise to genome-wide hypomethylation with site‑specific incidences of hypermethylation. This notion has received a lot of attention, as it potentially explains why aged organisms generally have a higher risk of age-related diseases. However, very little is known about the mechanisms that could cause the occurrence of these changes. Moreover, there does not appear to be a clear link between popular theories of aging and alterations in the methylome. Some of the most fruitful of these theories attribute an important role to reactive oxygen species, which seem to be responsible for an increase in oxidative damage to macromolecules, such as DNA, during the lifetime of an organism. In this review, the connection between changes in DNA methylation and these reactive oxygen species is discussed, as well as the effect of these changes on health. Deeper insights into the nature, causes and consequences of the aging methylome might provide a deeper understanding of the molecular mechanisms of aging and eventually contribute to the development of new diagnostic and therapeutic tools.
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26
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Sánchez-Molina S, Estarás C, Oliva JL, Akizu N, Asensio-Juan E, Rojas JM, Martínez-Balbás MA. Regulation of CBP and Tip60 coordinates histone acetylation at local and global levels during Ras-induced transformation. Carcinogenesis 2014; 35:2194-202. [DOI: 10.1093/carcin/bgu111] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Subramaniam D, Thombre R, Dhar A, Anant S. DNA methyltransferases: a novel target for prevention and therapy. Front Oncol 2014; 4:80. [PMID: 24822169 PMCID: PMC4013461 DOI: 10.3389/fonc.2014.00080] [Citation(s) in RCA: 320] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 03/31/2014] [Indexed: 12/14/2022] Open
Abstract
Cancer is the second leading cause of death in US. Despite the emergence of new, targeted agents, and the use of various therapeutic combinations, none of the available treatment options are curative in patients with advanced cancer. Epigenetic alterations are increasingly recognized as valuable targets for the development of cancer therapies. DNA methylation at the 5-position of cytosine, catalyzed by DNA methyltransferases (DNMTs), is the predominant epigenetic modification in mammals. DNMT1, the major enzyme responsible for maintenance of the DNA methylation pattern is located at the replication fork and methylates newly biosynthesized DNA. DNMT2 or TRDMT1, the smallest mammalian DNMT is believed to participate in the recognition of DNA damage, DNA recombination, and mutation repair. It is composed solely of the C-terminal domain, and does not possess the regulatory N-terminal region. The levels of DNMTs, especially those of DNMT3B, DNMT3A, and DNMT3L, are often increased in various cancer tissues and cell lines, which may partially account for the hypermethylation of promoter CpG-rich regions of tumor suppressor genes in a variety of malignancies. Moreover, it has been shown to function in self-renewal and maintenance of colon cancer stem cells and need to be studied in several cancers. Inhibition of DNMTs has demonstrated reduction in tumor formation in part through the increased expression of tumor suppressor genes. Hence, DNMTs can potentially be used as anti-cancer targets. Dietary phytochemicals also inhibit DNMTs and cancer stem cells; this represents a promising approach for the prevention and treatment of many cancers.
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Affiliation(s)
- Dharmalingam Subramaniam
- Department of Molecular and Integrative Physiology, The University of Kansas Medical Center , Kansas City, KS , USA ; The University of Kansas Cancer Center , Kansas City, KS , USA
| | - Ravi Thombre
- Department of Molecular and Integrative Physiology, The University of Kansas Medical Center , Kansas City, KS , USA
| | - Animesh Dhar
- The University of Kansas Cancer Center , Kansas City, KS , USA ; Department of Cancer Biology, The University of Kansas Medical Center , Kansas City, KS , USA
| | - Shrikant Anant
- Department of Molecular and Integrative Physiology, The University of Kansas Medical Center , Kansas City, KS , USA ; The University of Kansas Cancer Center , Kansas City, KS , USA ; Department of Cancer Biology, The University of Kansas Medical Center , Kansas City, KS , USA
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Fagan RL, Wu M, Chédin F, Brenner C. An ultrasensitive high throughput screen for DNA methyltransferase 1-targeted molecular probes. PLoS One 2013; 8:e78752. [PMID: 24236046 PMCID: PMC3827244 DOI: 10.1371/journal.pone.0078752] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/20/2013] [Indexed: 12/20/2022] Open
Abstract
DNA methyltransferase 1 (DNMT1) is the enzyme most responsible for epigenetic modification of human DNA and the intended target of approved cancer drugs such as 5-aza-cytidine and 5-aza-2'-deoxycytidine. 5-aza nucleosides have complex mechanisms of action that require incorporation into DNA, and covalent trapping and proteolysis of DNMT isozymes. Direct DNMT inhibitors are needed to refine understanding of the role of specific DNMT isozymes in cancer etiology and, potentially, to improve cancer prevention and treatment. Here, we developed a high throughput pipeline for identification of direct DNMT1 inhibitors. The components of this screen include an activated form of DNMT1, a restriction enzyme-coupled fluorigenic assay performed in 384 well plates with a z-factor of 0.66, a counter screen against the restriction enzyme, a screen to eliminate DNA intercalators, and a differential scanning fluorimetry assay to validate direct binders. Using the Microsource Spectrum collection of 2320 compounds, this screen identified nine compounds with dose responses ranging from 300 nM to 11 µM, representing at least two different pharmacophores with DNMT1 inhibitory activity. Seven of nine inhibitors identified exhibited two to four-fold selectivity for DNMT1 versus DNMT3A.
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Affiliation(s)
- Rebecca L. Fagan
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Meng Wu
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome Center, University of California Davis, Davis, California, United States of America
| | - Charles Brenner
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail:
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The interplay between epigenetic silencing, oncogenic KRas and HIF-1 regulatory pathways in control of BNIP3 expression in human colorectal cancer cells. Biochem Biophys Res Commun 2013; 441:707-12. [PMID: 24211581 DOI: 10.1016/j.bbrc.2013.10.098] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 10/18/2013] [Indexed: 01/22/2023]
Abstract
Bcl-2/adenovirus E1B-19kDa-interacting protein 3 (BNIP3) is an important mediator of cell survival and a member of the Bcl-2 family of proteins that regulate programmed cell death and autophagy. We have previously established a link between the expression of oncogenic HRas and up-regulation of BNIP3 and the control of autophagy in cancer cells. However, in view of varied expression of BNIP3 in different tumor types and emerging uncertainties as to the role of epigenetic silencing, oncogenic regulation and the role of BNIP3 in cancer are still poorly understood. In the present study we describe profound effect of KRas on the expression of methylated BNIP3 in colorectal cancer cells and explore the interplay between HIF-1, hypoxia pathway and oncogenic KRas in this context. We observed that BNIP3 mRNA remains undetectable in aggressive DLD-1 cells harboring G13D mutant KRAS and HT-29 colorectal cancer cells unless the cells are exposed to demethylating agents such as 5-aza-2'-deoxycytidine. Following this treatment BNIP3 expression remains uniquely dependent on the Ras activity. We found that hypoxia or pharmacological activation of HIF-1 alone contributes to, but is not sufficient for efficient induction of BNIP3 mRNA transcription in cells lacking mutant KRas activity. The up-regulation of BNIP3 by KRas in this setting is mediated by the MAPK pathway, and is attenuated by the respective inhibitors (PD98059, U0126). Thus, we demonstrate the novel mechanism where activity of Ras is essential for 5-aza-2'-deoxycytidine-mediated BNIP3 expression. Moreover, we found that 5-aza-2'-deoxycytidine-mediated or enforced up-regulation of BNIP3 in DLD-1 cells results in KRas-dependent resistance to 5-Fluorouracil.
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Abstract
SLC5A8 is a putative tumor suppressor that is inactivated in more than 10 different types of cancer, but neither the oncogenic signaling responsible for SLC5A8 inactivation nor the functional relevance of SLC5A8 loss to tumor growth has been elucidated. Here, we identify oncogenic HRAS (HRAS(G12V)) as a potent mediator of SLC5A8 silencing in human nontransformed normal mammary epithelial cell lines and in mouse mammary tumors through DNMT1. Further, we demonstrate that loss of Slc5a8 increases cancer-initiating stem cell formation and promotes mammary tumorigenesis and lung metastasis in an HRAS-driven murine model of mammary tumors. Mammary-gland-specific overexpression of Slc5a8 (mouse mammary tumor virus-Slc5a8 transgenic mice), as well as induction of endogenous Slc5a8 in mice with inhibitors of DNA methylation, protects against HRAS-driven mammary tumors. Collectively, our results provide the tumor-suppressive role of SLC5A8 and identify the oncogenic HRAS as a mediator of tumor-associated silencing of this tumor suppressor in mammary glands. These findings suggest that pharmacological approaches to reactivate SLC5A8 expression in tumor cells have potential as a novel therapeutic strategy for breast cancer treatment.
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31
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Fagan RL, Cryderman DE, Kopelovich L, Wallrath LL, Brenner C. Laccaic acid A is a direct, DNA-competitive inhibitor of DNA methyltransferase 1. J Biol Chem 2013; 288:23858-67. [PMID: 23839987 DOI: 10.1074/jbc.m113.480517] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Methylation of cytosines in CpG dinucleotides is the predominant epigenetic mark on vertebrate DNA. DNA methylation is associated with transcriptional repression. The pattern of DNA methylation changes during development and with disease. Human DNA methyltransferase 1 (Dnmt1), a 1616-amino acid multidomain enzyme, is essential for maintenance of DNA methylation in proliferating cells and is considered an important cancer drug target. Using a fluorogenic, endonuclease-coupled DNA methylation assay with an activated form of Dnmt1 engineered to lack the replication foci targeting sequence domain, we discovered that laccaic acid A (LCA), a highly substituted anthraquinone natural product, is a direct inhibitor with a 310 nm Ki. LCA is competitive with the DNA substrate in in vitro methylation assays and alters the expression of methylated genes in MCF-7 breast cancer cells synergistically with 5-aza-2'-deoxycytidine. LCA represents a novel class of Dnmt-targeted molecular probes, with biochemical properties that allow it to distinguish between non DNA-bound and DNA-bound Dnmt1.
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Affiliation(s)
- Rebecca L Fagan
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
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Abstract
AbstractRas genes are pre-eminent genes that are frequently linked with cancer biology. The functional loss of ras protein caused by various point mutations within the gene, is established as a prognostic factor for the genesis of a constitutively active Ras-MAPK pathway leading to cancer. Ras signaling circuit follows a complex pathway, which connects many signaling molecules and cells. Several strategies have come up for targeting mutant ras proteins for cancer therapy, however, the clinical benefits remain insignificant. Targeting the Ras-MAPK pathway is extremely complicated due its intricate networks involving several upstream and downstream regulators. Blocking oncogenic Ras is still in latent stage and requires alternative approaches to screen the genes involved in Ras transformation. Understanding the mechanism of Ras induced tumorigenesis in diverse cancers and signaling networks will open a path for drug development and other therapeutic approaches.
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Healy S, Khan P, Davie JR. Immediate early response genes and cell transformation. Pharmacol Ther 2013; 137:64-77. [DOI: 10.1016/j.pharmthera.2012.09.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 09/06/2012] [Indexed: 01/20/2023]
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Gorelik GJ, Yarlagadda S, Patel DR, Richardson BC. Protein kinase Cδ oxidation contributes to ERK inactivation in lupus T cells. ACTA ACUST UNITED AC 2012; 64:2964-74. [PMID: 22549474 DOI: 10.1002/art.34503] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
OBJECTIVE CD4+ T cells from patients with active lupus have impaired ERK pathway signaling that decreases DNA methyltransferase expression, resulting in DNA demethylation, overexpression of immune genes, and autoimmunity. The ERK pathway defect is due to impaired phosphorylation of T(505) in the protein kinase Cδ (PKCδ) activation loop. However, the mechanisms that prevent PKCδ T(505) phosphorylation in lupus T cells are unknown. Others have reported that oxidative modifications, and nitration in particular, of T cells as well as serum proteins correlate with lupus disease activity. We undertook this study to test our hypothesis that nitration inactivates PKCδ, contributing to impaired ERK pathway signaling in lupus T cells. METHODS CD4+ T cells were purified from lupus patients and controls and then stimulated with phorbol myristate acetate (PMA). Signaling protein levels, nitration, and phosphorylation were quantitated by immunoprecipitation and immunoblotting of T cell lysates. Transfections were performed by electroporation. RESULTS Treating CD4+ T cells with peroxynitrite nitrated PKCδ, preventing PKCδ T(505) phosphorylation and inhibiting ERK pathway signaling similar to that observed in lupus T cells. Patients with active lupus had higher nitrated T cell PKCδ levels than did controls, which correlated directly with disease activity, and antinitrotyrosine immunoprecipitations demonstrated that nitrated PKCδ, but not unmodified PKCδ, was refractory to PMA-stimulated T(505) phosphorylation, similar to PKCδ in peroxynitrite-treated cells. CONCLUSION Oxidative stress causes PKCδ nitration, which prevents its phosphorylation and contributes to the decreased ERK signaling in lupus T cells. These results identify PKCδ as a link between oxidative stress and the T cell epigenetic modifications in lupus.
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Hasanali Z, Stuart A, Yee N, Sharma K, Epner E. The Epigenetics of Gastrointestinal Malignancies. CURRENT COLORECTAL CANCER REPORTS 2012. [DOI: 10.1007/s11888-012-0147-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Kar S, Deb M, Sengupta D, Shilpi A, Parbin S, Torrisani J, Pradhan S, Patra S. An insight into the various regulatory mechanisms modulating human DNA methyltransferase 1 stability and function. Epigenetics 2012; 7:994-1007. [PMID: 22894906 DOI: 10.4161/epi.21568] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is one of the principal epigenetic signals that participate in cell specific gene expression in vertebrates. DNA methylation plays a quintessential role in the control of gene expression, cellular differentiation and development. It also plays a central role in the preservation of chromatin structure and chromosomal integrity, parental imprinting, X-chromosome inactivation, aging and carcinogenesis. The foremost contributor in the mammalian methylation scheme is DNMT1, a maintenance methyltransferase that faithfully copies the pre-existing methyl marks onto hemimethylated daughter strands during DNA replication to maintain the established methylation patterns across successive cell divisions. The ever-changing cellular physiology and the significant part that DNA methylation plays in genome regulation necessitate rigid management of this enzyme. In mammalian cells, a host of intrinsic and extrinsic mechanisms regulate the expression, activity and stability of DNMT1. Transcriptional regulation, post-transcriptional auto-inhibitory controls and post-translational modifications of the enzyme are responsible for the efficient inheritance of DNA methylation patterns. Also, a large number of intra- and intercellular signaling cascades and numerous interactions with other modulator molecules that affect the catalytic activity of the enzyme at multiple levels function as major checkpoints of the DNMT1 control system. An in-depth understanding of the DNMT1 enzyme, its targeting and function is crucial for comprehending how DNA methylation is coordinated with other critical developmental and physiological processes. This review aims to provide a comprehensive account of the various regulatory mechanisms and interactions of DNMT1 so as to elucidate its function at the molecular level and understand the dynamics of DNA methylation at the cellular level.
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Affiliation(s)
- Swayamsiddha Kar
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
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Samudio-Ruiz SL, Hudson LG. Increased DNA methyltransferase activity and DNA methylation following Epidermal Growth Factor stimulation in ovarian cancer cells. Epigenetics 2012; 7:216-24. [PMID: 22430797 DOI: 10.4161/epi.7.3.19273] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Ovarian cancer progression is correlated with accumulation of aberrant CpG island methylation. In ovarian cancer, ascites fluid contains numerous Epidermal-Growth-Factor-Receptor (EGFR) activators, which could result in a tumor microenvironment of constant EGFR activation. Signaling pathways downstream of EGFR, such as Ras, regulate DNA methylation. We hypothesized that chronic EGFR activation could alter DNA methylation. We found that EGFR activation increased DNA methyltransferase (DNMT) activity acutely, as well as after long-term EGF treatment or expression of a mutationally activated EGFR. Furthermore, this increase in DNMT activity was dependent on EGFR catalytic activity and resulted in increased global DNA methylation. Additionally, treatment with the DNMT inhibitor/hypomethylating agent 5-Aza-2'-deoxycytidine (AZA) inhibited the EGF induced increase of both DNMT activity and global methylation. These data support a role for EGFR in the process of accumulated DNA methylation during ovarian cancer progression and suggest that epigenetic therapy may be beneficial for the treatment of ovarian cancer.
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Affiliation(s)
- Sabrina L Samudio-Ruiz
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, NM, USA.
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Amato RJ, Stephenson J, Hotte S, Nemunaitis J, Bélanger K, Reid G, Martell RE. MG98, a second-generation DNMT1 inhibitor, in the treatment of advanced renal cell carcinoma. Cancer Invest 2012; 30:415-21. [PMID: 22571342 DOI: 10.3109/07357907.2012.675381] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND In carcinogenesis, methylation of DNA promoter regions results in inactivation of tumor-suppressing genes. MG98 was designed to inhibit DNA methyltransferases enzyme 1 production. METHODS This multicenter study explored two schedules of MG98 with Interferon-α-2β to identify schedule and dose for patients with metastatic RCC. RESULTS Doses of IFN 9 MIU/MG98 125 mg/m(2) for a continuous schedule and IFN 9 MIU/MG98 200 mg/m(2) for an intermittent schedule were considered the MTDs. Treatment resulted in one PR and eight SD. CONCLUSION MG98 combined with IFN was safe and resulted in clinical activity.
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Affiliation(s)
- Robert J Amato
- Department of Internal Medicine, The University of Texas Medical School/ Memorial Hermann Cancer Center, Houston, Texas 77030, USA.
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Duerr EM, Mizukami Y, Moriichi K, Gala M, Jo WS, Kikuchi H, Xavier RJ, Chung DC. Oncogenic KRAS regulates BMP4 expression in colon cancer cell lines. Am J Physiol Gastrointest Liver Physiol 2012; 302:G1223-30. [PMID: 22383492 PMCID: PMC3362092 DOI: 10.1152/ajpgi.00047.2011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Activating mutations in the KRAS oncogene are common in colorectal cancer. However, the complete spectrum of KRAS targets that mediate its tumorigenic effect has not yet been fully delineated. We identified bone morphogenetic protein 4 (Bmp4), a transforming growth factor-β family member that regulates development and tissue homeostasis, as a new target of KRAS. In SW480, Hela, and 293 cells, oncogenic KRAS(V12) downregulated BMP4 RNA levels, a BMP4 promoter luciferase construct, and Bmp4 protein levels. The MEK inhibitor PD98059 but not the phosphatidylinositol 3-kinase inhibitor LY294002 blocked this downregulation of BMP4. To identify the region of the BMP4 promoter that mediated this regulation by KRAS, serial 5'-deletions of the promoter were generated. An inhibitory region was identified between -3,285 and -3,258 bp in the Bmp4 promoter. In summary, oncogenic KRAS can downregulate Bmp4 through a transcriptional pathway that depends on ERK. These findings point to a unique link between two pathways that are frequently altered in colon cancer.
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Affiliation(s)
- Eva-Maria Duerr
- 1Gastrointestinal Unit, ,3Department of Gastroenterology, Klinikum Grosshadern, Ludwig-Maximilians-University of Munich, Munich, Germany; and
| | - Yusuke Mizukami
- 1Gastrointestinal Unit, ,4Center for Clinical and Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
| | | | | | | | | | - Ramnik J. Xavier
- 1Gastrointestinal Unit, ,2Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts;
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Hou P, Liu D, Dong J, Xing M. The BRAF(V600E) causes widespread alterations in gene methylation in the genome of melanoma cells. Cell Cycle 2012; 11:286-95. [PMID: 22189819 DOI: 10.4161/cc.11.2.18707] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Although BRAF(V600E) is well known to play an important role in the tumorigenesis of melanoma, its molecular mechanism, particularly the epigenetic aspect, has been incompletely understood. Here, we investigated the role of BRAF(V600E) signaling in altering gene methylation in the genome of melanoma cells using a methylated CpG island amplification/CpG island microarray system and searched for genes coupled to the BRAF(V600E) signaling through methylation aberrations. The results indicated that a wide range of genes with broad functions were linked to BRAF(V600E) signaling through their hyper- or hypomethylation. Expression of 59 genes hypermethylated upon BRAF knockdown was selectively tested and found to be largely correspondingly underexpressed, suggesting that these genes were naturally hypomethylated, and overexpressed with BRAF(V600E) in melanoma. This BRAF(V600E)-promoted hypomethylation was confirmed on genes selectively examined in primary melanoma tumors. Some of these genes were functionally tested and demonstrated to play a role in melanoma cell proliferation and invasion. As a mechanism of aberrant gene methylation driven by BRAF(V600E), expression of the DNA methyltransferase 1 and histone methyltransferase EZH2 was profoundly affected by BRAF(V600E). We have thus uncovered a previously unrecognized prominent epigenetic mechanism in the tumorigenesis of melanoma driven by BRAF(V600E). Many of the functionally important genes controlled by the BRAF(V600E) signaling through aberrant methylation may prove to be novel therapeutic targets for melanoma.
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Affiliation(s)
- Peng Hou
- Division of Endocrinology and Metabolism, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Yamakoshi K, Hara E. Visualizing the dynamics of senescence stress response in living animals. Inflamm Regen 2012. [DOI: 10.2492/inflammregen.32.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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Strickland FM, Hewagama A, Lu Q, Wu A, Hinderer R, Webb R, Johnson K, Sawalha AH, Delaney C, Yung R, Richardson BC. Environmental exposure, estrogen and two X chromosomes are required for disease development in an epigenetic model of lupus. J Autoimmun 2011; 38:J135-43. [PMID: 22142890 DOI: 10.1016/j.jaut.2011.11.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 11/03/2011] [Accepted: 11/08/2011] [Indexed: 10/14/2022]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease primarily afflicting women. The reason for the gender bias is unclear, but genetic susceptibility, estrogen and environmental agents appear to play significant roles in SLE pathogenesis. Environmental agents can contribute to lupus susceptibility through epigenetic mechanisms. We used (C57BL/6xSJL)F1 mice transgenic for a dominant-negative MEK (dnMEK) that was previously shown to be inducibly and selectively expressed in T cells. In this model, induction of the dnMEK by doxycycline treatment suppresses T cell ERK signaling, decreasing DNA-methyltransferase expression and resulting in DNA demethylation, overexpression of immune genes Itgal (CD11a) and Tnfsf7 (CD70), and anti-dsDNA antibody. To examine the role of gender and estrogen in this model, male and female transgenic mice were neutered and implanted with time-release pellets delivering placebo or estrogen. Doxycycline induced IgG anti-dsDNA antibodies in intact and neutered, placebo-treated control female but not male transgenic mice. Glomerular IgG deposits were also found in the kidneys of female but not male transgenic mice, and not in the absence of doxycycline. Estrogen enhanced anti-dsDNA IgG antibodies only in transgenic, ERK-impaired female mice. Decreased ERK activation also resulted in overexpression and demethylation of the X-linked methylation-sensitive gene CD40lg in female but not male mice, consistent with demethylation of the second X chromosome in the females. The results show that both estrogen and female gender contribute to the female predisposition in lupus susceptibility through hormonal and epigenetic X-chromosome effects and through suppression of ERK signaling by environmental agents.
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Affiliation(s)
- Faith M Strickland
- Department of Internal Medicine, Rheumatology Division, The University of Michigan, Ann Arbor, MI 48109-2200, USA.
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He S, Wang F, Yang L, Guo C, Wan R, Ke A, Xu L, Hu G, Xu X, Shen J, Wang X. Expression of DNMT1 and DNMT3a are regulated by GLI1 in human pancreatic cancer. PLoS One 2011; 6:e27684. [PMID: 22110720 PMCID: PMC3215738 DOI: 10.1371/journal.pone.0027684] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 10/21/2011] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND AND AIMS GLI1, as an indispensable transcriptional factor of Hedgehog signaling pathway, plays an important role in the development of pancreatic cancer (PC). DNA methyltransferases (DNMTs) mediate the methylation of quantity of tumor-related genes. Our study aimed to explore the relationship between GLI1 and DNMTs. METHODS Expressions of GLI1 and DNMTs were detected in tumor and adjacent normal tissues of PC patients by immunohistochemistry (IHC). PANC-1 cells were treated by cyclopamine and GLI1-siRNA, while BxPC-3 cells were transfected with overexpression-GLI1 lentiviral vector. Then GLI1 and DNMTs expression were analyzed by qRT-PCR and western blot (WB). Then we took chromatin immunoprecipitation (ChIP) to demonstrate GLI1 bind to DNMT1. Finally, nested MSP was taken to valuate the methylation levels of APC and hMLH1, when GLI1 expression altered. RESULTS IHC result suggested the expressions of GLI1, DNMT1 and DNMT3a in PC tissues were all higher than those in adjacent normal tissues (p<0.05). After GLI1 expression repressed by cyclopamine in mRNA and protein level (down-regulation 88.1±2.2%, 86.4±2.2%, respectively), DNMT1 and DNMT3a mRNA and protein level decreased by 91.6%±2.2% and 83.8±4.8%, 87.4±2.7% and 84.4±1.3%, respectively. When further knocked down the expression of GLI1 by siRNA (mRNA decreased by 88.6±2.1%, protein decreased by 63.5±4.5%), DNMT1 and DNMT3a mRNA decreased by 80.9±2.3% and 78.6±3.8% and protein decreased by 64.8±2.8% and 67.5±5.6%, respectively. Over-expression of GLI1 by GLI1 gene transfection (mRNA increased by 655.5±85.9%, and protein increased by 272.3±14.4%.), DNMT1 and DNMT3a mRNA and protein increased by 293.0±14.8% and 578.3±58.5%, 143.5±17.4% and 214.0±18.9%, respectively. ChIP assays showed GLI1 protein bound to DNMT1 but not to DNMT3a. Results of nested MSP demonstrated GLI1 expression affected the DNA methylation level of APC but not hMLH1 in PC. CONCLUSION DNMT1 and DNMT3a are regulated by GLI1 in PC, and DNMT1 is its direct target gene.
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Affiliation(s)
- ShanShan He
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University, Shanghai, People's Republic of China
| | - Feng Wang
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University, Shanghai, People's Republic of China
| | - LiJuan Yang
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University, Shanghai, People's Republic of China
- Department of Gastroenterology, The First People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - ChuanYong Guo
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University, Shanghai, People's Republic of China
| | - Rong Wan
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University, Shanghai, People's Republic of China
| | - AiWu Ke
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University, Shanghai, People's Republic of China
| | - Ling Xu
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University, Shanghai, People's Republic of China
| | - GuoYong Hu
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University, Shanghai, People's Republic of China
| | - XuanFu Xu
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University, Shanghai, People's Republic of China
| | - Jie Shen
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University, Shanghai, People's Republic of China
| | - XingPeng Wang
- Department of Gastroenterology, Shanghai 10th People's Hospital, Tongji University, Shanghai, People's Republic of China
- Department of Gastroenterology, The First People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
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Hughes T, Sawalha AH. The role of epigenetic variation in the pathogenesis of systemic lupus erythematosus. Arthritis Res Ther 2011; 13:245. [PMID: 22044622 PMCID: PMC3308098 DOI: 10.1186/ar3484] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The focus of the present review is on the extent to which epigenetic alterations influence the development of systemic lupus erythematosus. Lupus is a systemic autoimmune disease characterized by the production of autoantibodies directed at nuclear self-antigens. A DNA methylation defect in CD4+ T cells has long been observed in idiopathic and drug-induced lupus. Recent studies utilizing high-throughput technologies have further characterized the nature of the DNA methylation defect in lupus CD4+ T cells. Emerging evidence in the literature is revealing an increasingly interconnected network of epigenetic dysregulation in lupus. Recent reports describe variable expression of a number of regulatory microRNAs in lupus CD4+ T cells, some of which govern the expression of DNA methyltransferase 1. While studies to date have revealed a significant role for epigenetic defects in the pathogenesis of lupus, the causal nature of epigenetic variation in lupus remains elusive. Future longitudinal epigenetic studies in lupus are therefore needed.
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Affiliation(s)
- Travis Hughes
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Amr H Sawalha
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- US Department of Veterans Affairs Medical Center, Oklahoma City, OK 73104, USA
- 825 NE 13th Street, MS#24, Oklahoma City, OK 73104, USA
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Krawetz SA, Kruger A, Lalancette C, Tagett R, Anton E, Draghici S, Diamond MP. A survey of small RNAs in human sperm. Hum Reprod 2011; 26:3401-12. [PMID: 21989093 DOI: 10.1093/humrep/der329] [Citation(s) in RCA: 270] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND There has been substantial interest in assessing whether RNAs (mRNAs and sncRNAs, i.e. small non-coding) delivered from mammalian spermatozoa play a functional role in early embryo development. While the cadre of spermatozoal mRNAs has been characterized, comparatively little is known about the distribution or function of the estimated 24,000 sncRNAs within each normal human spermatozoon. METHODS RNAs of <200 bases in length were isolated from the ejaculates from three donors of proved fertility. RNAs of 18-30 nucleotides in length were then used to construct small RNA Digital Gene Expression libraries for Next Generation Sequencing. Known sncRNAs that uniquely mapped to a single location in the human genome were identified. RESULTS Bioinformatic analysis revealed the presence of multiple classes of small RNAs in human spermatozoa. The primary classes resolved included microRNA (miRNAs) (≈ 7%), Piwi-interacting piRNAs (≈ 17%), repeat-associated small RNAs (≈ 65%). A minor subset of short RNAs within the transcription start site/promoter fraction (≈ 11%) frames the histone promoter-associated regions enriched in genes of early embryonic development. These have been termed quiescent RNAs. CONCLUSIONS A complex population of male derived sncRNAs that are available for delivery upon fertilization was revealed. Sperm miRNA-targeted enrichment in the human oocyte is consistent with their role as modifiers of early post-fertilization. The relative abundance of piRNAs and repeat-associated RNAs suggests that they may assume a role in confrontation and consolidation. This may ensure the compatibility of the genomes at fertilization.
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Affiliation(s)
- Stephen A Krawetz
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA.
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Zhang Q, Chen L, Helfand BT, Jang TL, Sharma V, Kozlowski J, Kuzel TM, Zhu LJ, Yang XJ, Javonovic B, Guo Y, Lonning S, Harper J, Teicher BA, Brendler C, Yu N, Catalona WJ, Lee C. TGF-β regulates DNA methyltransferase expression in prostate cancer, correlates with aggressive capabilities, and predicts disease recurrence. PLoS One 2011; 6:e25168. [PMID: 21980391 PMCID: PMC3184137 DOI: 10.1371/journal.pone.0025168] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 08/26/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND DNA methyltransferase (DNMT) is one of the major factors mediating the methylation of cancer related genes such as TGF-β receptors (TβRs). This in turn may result in a loss of sensitivity to physiologic levels of TGF-β in aggressive prostate cancer (CaP). The specific mechanisms of DNMT's role in CaP remain undetermined. In this study, we describe the mechanism of TGF-β-mediated DNMT in CaP and its association with clinical outcomes following radical prostatectomy. METHODOLOGY/PRINCIPAL FINDINGS We used human CaP cell lines with varying degrees of invasive capability to describe how TGF-β mediates the expression of DNMT in CaP, and its effects on methylation status of TGF-β receptors and the invasive capability of CaP in vitro and in vivo. Furthermore, we determined the association between DNMT expression and clinical outcome after radical prostatectomy. We found that more aggressive CaP cells had significantly higher TGF-β levels, increased expression of DNMT, but reduced TβRs when compared to benign prostate cells and less aggressive prostate cancer cells. Blockade of TGF-β signaling or ERK activation (p-ERK) was associated with a dramatic decrease in the expression of DNMT, which results in a coincident increase in the expression of TβRs. Blockade of either TGF-β signaling or DNMT dramatically decreased the invasive capabilities of CaP. Inhibition of TGF-β in an TRAMP-C2 CaP model in C57BL/6 mice using 1D11 was associated with downregulation of DNMTs and p-ERK and impairment in tumor growth. Finally, independent of Gleason grade, increased DNMT1 expression was associated with biochemical recurrence following surgical treatment for prostate cancer. CONCLUSIONS AND SIGNIFICANCE Our findings demonstrate that CaP derived TGF-β may induce the expression of DNMTs in CaP which is associated with methylation of its receptors and the aggressive potential of CaP. In addition, DNMTs is an independent predictor for disease recurrence after prostatectomy, and may have clinical implications for CaP prognostication and therapy.
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Affiliation(s)
- Qiang Zhang
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America.
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Diaz-Moralli S, Tarrado-Castellarnau M, Alenda C, Castells A, Cascante M. Transketolase-like 1 expression is modulated during colorectal cancer progression and metastasis formation. PLoS One 2011; 6:e25323. [PMID: 21980427 PMCID: PMC3181277 DOI: 10.1371/journal.pone.0025323] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 09/01/2011] [Indexed: 12/19/2022] Open
Abstract
Background Transketolase-like 1 (TKTL1) induces glucose degradation through anaerobic pathways, even in presence of oxygen, favoring the malignant aerobic glycolytic phenotype characteristic of tumor cells. As TKTL1 appears to be a valid biomarker for cancer prognosis, the aim of the current study was to correlate its expression with tumor stage, probability of tumor recurrence and survival, in a series of colorectal cancer patients. Methodolody/Principal Findings Tumor tissues from 63 patients diagnosed with colorectal cancer at different stages of progression were analyzed for TKTL1 by immunohistochemistry. Staining was quantified by computational image analysis, and correlations between enzyme expression, local growth, lymph-node involvement and metastasis were assessed. The highest values for TKTL1 expression were detected in the group of stage III tumors, which showed significant differences from the other groups (Kruskal-Wallis test, P = 0.000008). Deeper analyses of T, N and M classifications revealed a weak correlation between local tumor growth and enzyme expression (Mann-Whitney test, P = 0.029), a significant association of the enzyme expression with lymph-node involvement (Mann-Whitney test, P = 0.0014) and a significant decrease in TKTL1 expression associated with metastasis (Mann-Whitney test, P = 0.0004). Conclusions/Significance To our knowledge, few studies have explored the association between variations in TKTL1 expression in the primary tumor and metastasis formation. Here we report downregulation of enzyme expression when metastasis appears, and a correlation between enzyme expression and regional lymph-node involvement in colon cancer. This finding may improve our understanding of metastasis and lead to new and more efficient therapies against cancer.
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Affiliation(s)
- Santiago Diaz-Moralli
- Departament de Bioquimica i Biologia Molecular, Facultat de Biologia, Institut de Biomedicina at Universitat de Barcelona IBUB and IDIBAPS-Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Miriam Tarrado-Castellarnau
- Departament de Bioquimica i Biologia Molecular, Facultat de Biologia, Institut de Biomedicina at Universitat de Barcelona IBUB and IDIBAPS-Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Cristina Alenda
- Pathology Department, Hospital General Universitario de Alicante, Alicante, Spain
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, IDIBAPS, CIBEREHD, University of Barcelona, Barcelona, Spain
| | - Marta Cascante
- Departament de Bioquimica i Biologia Molecular, Facultat de Biologia, Institut de Biomedicina at Universitat de Barcelona IBUB and IDIBAPS-Hospital Clinic, University of Barcelona, Barcelona, Spain
- * E-mail:
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Ji M, Guan H, Gao C, Shi B, Hou P. Highly frequent promoter methylation and PIK3CA amplification in non-small cell lung cancer (NSCLC). BMC Cancer 2011; 11:147. [PMID: 21507233 PMCID: PMC3098185 DOI: 10.1186/1471-2407-11-147] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Accepted: 04/20/2011] [Indexed: 12/26/2022] Open
Abstract
Background Lung cancer is the leading cause of cancer-related death worldwide. Genetic and epigenetic alterations have been identified frequently in lung cancer, such as promoter methylation, gene mutations and genomic amplification. However, the interaction between genetic and epigenetic events and their significance in lung tumorigenesis remains poorly understood. Methods We determined the promoter methylation of 6 genes and PIK3CA amplification using quantitative methylation-specific PCR (Q-MSP) and real-time quantitative PCR, respectively, and explore the association of promoter methylation with PIK3CA amplification in a large cohort of clinically well-characterized non-small cell lung cancer (NSCLC). Results Highly frequent promoter methylation was observed in NSCLC. With 100% diagnostic specificity, excellent sensitivity, ranging from 45.8 to 84.1%, was found for each of the 6 genes. The promoter methylation was associated with histologic type. Methylation of CALCA, CDH1, DAPK1, and EVX2 was more common in squamous cell carcinomas (SCC) compared to adenocarcinomas (ADC). Conversely, there was a trend toward a higher frequency of RASSF1A methylation in ADC than SCC. In addition, PIK3CA amplification was frequently found in NSCLC, and was associated with certain clinicopathologic features, such as smoking history, histologic type and pleural indentation. Importantly, aberrant promoter methylation of certain genes was significantly associated with PIK3CA amplification. Conclusions Our data showed highly frequent promoter methylation and PIK3CA amplification in Chinese NSCLC population, and first demonstrated the associations of gene methylation with PIK3CA amplification, suggesting that these epigenetic events may be a consequence of overactivation of PI3K/Akt pathway.
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Affiliation(s)
- Meiju Ji
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University College of Medicine, Xi'an 710061, the People's Republic of China
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Chik F, Szyf M. Effects of specific DNMT gene depletion on cancer cell transformation and breast cancer cell invasion; toward selective DNMT inhibitors. Carcinogenesis 2011; 32:224-32. [PMID: 20980350 DOI: 10.1093/carcin/bgq221] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
A hallmark of cancer is aberrant DNA methylation, consisting of global hypomethylation and regional hypermethylation of tumor suppressor genes. DNA methyltransferase inhibitors have been recognized as promising candidate anticancer drugs. Drug development has focused on DNA methylation inhibitors with the goal of activating tumor suppressor genes silenced by DNA methylation. 5-azacytidine (5-AC; Vidaza), a global DNA methyltransferase inhibitor, was Food and Drug Administration approved to treat myelodysplastic syndromes and is clinically tested for solid tumors. In this paper, it was demonstrated that 5'-aza-2'-deoxycytidine (5-azaCdR) activated both silenced tumor suppressor genes and pro-metastatic genes by demethylation, raising the concern that it would promote metastasis. 5-AzaCdR treatment increased the invasiveness of non-invasive breast cancer cell lines MCF-7 cells and ZR-75-1 and dramatically induced pro-metastatic genes; Urokinase plasminogen activator (uPA), matrix metalloproteinase 2 (MMP2), metastasis-associated gene (H-MTS1; S100A4) and C-X-C chemokine receptor 4 (CXCR4). The hypothesis that the blocking of cellular transformation activity of DNA methyltransferase inhibitor could be separated from the pro-metastatic activity was tested using short interfering RNA (siRNA) targeted to the different DNA methyltransferase (DNMT) genes. Although depletion of DNMT1 had the strongest effect on colony growth suppression in cellular transformation assays, it did not result in demethylation and activation of uPA, S100A4, MMP2 and CXCR4 in MCF-7 cells. Depletion of DNMT1 did not induce cellular invasion in MCF-7 and ZR-75-1 non-invasive breast cancer cell lines. These data have implications on the design of new DNA methyltransferase inhibitor and on the proper utilization of current inhibitors.
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Affiliation(s)
- Flora Chik
- Department of Pharmacology and Therapeutics, McGill University Medical School, Montreal, Quebec, Canada
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Kinney SRM, Pradhan S. Regulation of expression and activity of DNA (cytosine-5) methyltransferases in mammalian cells. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 101:311-33. [PMID: 21507356 DOI: 10.1016/b978-0-12-387685-0.00009-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Three active DNA (cytosine-5) methyltransferases (DNMTs) have been identified in mammalian cells, Dnmt1, Dnmt3a, and Dnmt3b. DNMT1 is primarily a maintenance methyltransferase, as it prefers to methylate hemimethylated DNA during DNA replication and in vitro. DNMT3A and DNMT3B are de novo methyltransferases and show similar activity on unmethylated and hemimethylated DNA. DNMT3L, which lacks the catalytic domain, binds to DNMT3A and DNMT3B variants and facilitates their chromatin targeting, presumably for de novo methylation. There are several mechanisms by which mammalian cells regulate DNMT levels, including varied transcriptional activation of the respective genes and posttranslational modifications of the enzymes that can affect catalytic activity, targeting, and enzyme degradation. In addition, binding of miRNAs or RNA-binding proteins can also alter the expression of DNMTs. These regulatory processes can be disrupted in disease or by environmental factors, resulting in altered DNMT expression and aberrant DNA methylation patterns.
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