151
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Epigenetic regulation of skeletal muscle metabolism. Clin Sci (Lond) 2017; 130:1051-63. [PMID: 27215678 DOI: 10.1042/cs20160115] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 03/15/2016] [Indexed: 01/04/2023]
Abstract
Normal skeletal muscle metabolism is essential for whole body metabolic homoeostasis and disruptions in muscle metabolism are associated with a number of chronic diseases. Transcriptional control of metabolic enzyme expression is a major regulatory mechanism for muscle metabolic processes. Substantial evidence is emerging that highlights the importance of epigenetic mechanisms in this process. This review will examine the importance of epigenetics in the regulation of muscle metabolism, with a particular emphasis on DNA methylation and histone acetylation as epigenetic control points. The emerging cross-talk between metabolism and epigenetics in the context of health and disease will also be examined. The concept of inheritance of skeletal muscle metabolic phenotypes will be discussed, in addition to emerging epigenetic therapies that could be used to alter muscle metabolism in chronic disease states.
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152
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Chamessian AG, Qadri YJ, Cummins M, Hendrickson M, Berta T, Buchheit T, Van de Ven T. 5-Hydroxymethylcytosine (5hmC) and Ten-eleven translocation 1-3 (TET1-3) proteins in the dorsal root ganglia of mouse: Expression and dynamic regulation in neuropathic pain. Somatosens Mot Res 2017; 34:72-79. [PMID: 28276837 DOI: 10.1080/08990220.2017.1292237] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Epigenetic mechanisms are increasingly implicated in chronic pain pathology. In this study, we demonstrate that the novel epigenetic mark 5-hydroxymethylcytosine (5hmC) is present in dorsal root ganglia (DRG) neurons and glia, and its levels increase following nerve injury. Furthermore, we show that the 5hmC-generating Ten-eleven translocation 1-3 (TET1-3) proteins are expressed in a cell-type specific manner in the DRG, with Tet3 displaying differential upregulation after injury, suggesting a potential role in neuropathic pain.
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Affiliation(s)
- Alexander G Chamessian
- a Department of Anesthesiology , Duke University Medical Center , Durham , NC , USA.,b Department of Pharmacology and Cancer Biology , Duke University , Durham , NC , USA.,c Medical Scientist Training Program , Duke University School of Medicine , Durham , NC , USA
| | - Yawar J Qadri
- a Department of Anesthesiology , Duke University Medical Center , Durham , NC , USA
| | - Matthew Cummins
- a Department of Anesthesiology , Duke University Medical Center , Durham , NC , USA
| | - Michele Hendrickson
- e Department of Anesthesiology , Cincinnati Children's Hospital , Cincinnati , OH , USA
| | - Temugin Berta
- d Department of Anesthesiology , University of Cincinnati Medical Center , Cincinnati , OH , USA
| | - Thomas Buchheit
- a Department of Anesthesiology , Duke University Medical Center , Durham , NC , USA
| | - Thomas Van de Ven
- a Department of Anesthesiology , Duke University Medical Center , Durham , NC , USA
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153
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Kuzniar A, Laffeber C, Eppink B, Bezstarosti K, Dekkers D, Woelders H, Zwamborn APM, Demmers J, Lebbink JHG, Kanaar R. Semi-quantitative proteomics of mammalian cells upon short-term exposure to non-ionizing electromagnetic fields. PLoS One 2017; 12:e0170762. [PMID: 28234898 PMCID: PMC5325209 DOI: 10.1371/journal.pone.0170762] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 01/10/2017] [Indexed: 01/26/2023] Open
Abstract
The potential effects of non-ionizing electromagnetic fields (EMFs), such as those emitted by power-lines (in extremely low frequency range), mobile cellular systems and wireless networking devices (in radio frequency range) on human health have been intensively researched and debated. However, how exposure to these EMFs may lead to biological changes underlying possible health effects is still unclear. To reveal EMF-induced molecular changes, unbiased experiments (without a priori focusing on specific biological processes) with sensitive readouts are required. We present the first proteome-wide semi-quantitative mass spectrometry analysis of human fibroblasts, osteosarcomas and mouse embryonic stem cells exposed to three types of non-ionizing EMFs (ELF 50 Hz, UMTS 2.1 GHz and WiFi 5.8 GHz). We performed controlled in vitro EMF exposures of metabolically labeled mammalian cells followed by reliable statistical analyses of differential protein- and pathway-level regulations using an array of established bioinformatics methods. Our results indicate that less than 1% of the quantitated human or mouse proteome responds to the EMFs by small changes in protein abundance. Further network-based analysis of the differentially regulated proteins did not detect significantly perturbed cellular processes or pathways in human and mouse cells in response to ELF, UMTS or WiFi exposure. In conclusion, our extensive bioinformatics analyses of semi-quantitative mass spectrometry data do not support the notion that the short-time exposures to non-ionizing EMFs have a consistent biologically significant bearing on mammalian cells in culture.
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Affiliation(s)
- Arnold Kuzniar
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
- Netherlands eScience Center, Amsterdam, The Netherlands
- * E-mail: (RK); (AK)
| | - Charlie Laffeber
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Berina Eppink
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Karel Bezstarosti
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Dick Dekkers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Henri Woelders
- Wageningen Livestock Research, Wageningen, The Netherlands
| | | | - Jeroen Demmers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
- Netherlands Proteomics Center, Rotterdam, The Netherlands
| | - Joyce H. G. Lebbink
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Radiation Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Radiation Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
- * E-mail: (RK); (AK)
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154
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Morales-Lara D, De-la-Peña C, Murillo-Rodríguez E. Dad's Snoring May Have Left Molecular Scars in Your DNA: the Emerging Role of Epigenetics in Sleep Disorders. Mol Neurobiol 2017; 55:2713-2724. [PMID: 28155201 DOI: 10.1007/s12035-017-0409-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/13/2017] [Indexed: 12/16/2022]
Abstract
The sleep-wake cycle is a biological phenomena under the orchestration of neurophysiological, neurochemical, neuroanatomical, and genetical mechanisms. Moreover, homeostatic and circadian processes participate in the regulation of sleep across the light-dark period. Further complexity of the understanding of the genesis of sleep engages disturbances which have been characterized and classified in a variety of sleep-wake cycle disorders. The most prominent sleep alterations include insomnia as well as excessive daytime sleepiness. On the other side, several human diseases have been linked with direct changes in DNA, such as chromatin configuration, genomic imprinting, DNA methylation, histone modifications (acetylation, methylation, ubiquitylation or sumoylation, etc.), and activating RNA molecules that are transcribed from DNA but not translated into proteins. Epigenetic theories primarily emphasize the interaction between the environment and gene expression. According to these approaches, the environment to which mammals are exposed has a significant role in determining the epigenetic modifications occurring in chromosomes that ultimately would influence not only development but also the descendants' physiology and behavior. Thus, what makes epigenetics intriguing is that, unlike genetic variation, modifications in DNA are altered directly by the environment and, in some cases, these epigenetic changes may be inherited by future generations. Thus, it is likely that epigenetic phenomena might contribute to the homeostatic and/or circadian control of sleep and, possibly, have an undescribed link with sleep disorders. An exciting new horizon of research is arising between sleep and epigenetics since it represents the relevance of the study of how the genome learns from its experiences and modulates behavior, including sleep.
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Affiliation(s)
- Daniela Morales-Lara
- Laboratorio de Neurociencias Moleculares e Integrativas, Escuela de Medicina, División Ciencias de la Salud, Universidad Anáhuac Mayab, Carretera Mérida-Progreso Km. 15.5, A.P. 96 Cordemex, C.P. 97310, Mérida, Yucatán, Mexico.,Grupo de Investigación en Envejecimiento, División Ciencias de la Salud, Universidad Anáhuac Mayab, Mérida, Yucatán, Mexico.,Intercontinental Neuroscience Research Group, Mérida, Yucatán, Mexico
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C, Mérida, Yucatán, Mexico
| | - Eric Murillo-Rodríguez
- Laboratorio de Neurociencias Moleculares e Integrativas, Escuela de Medicina, División Ciencias de la Salud, Universidad Anáhuac Mayab, Carretera Mérida-Progreso Km. 15.5, A.P. 96 Cordemex, C.P. 97310, Mérida, Yucatán, Mexico. .,Grupo de Investigación en Envejecimiento, División Ciencias de la Salud, Universidad Anáhuac Mayab, Mérida, Yucatán, Mexico. .,Intercontinental Neuroscience Research Group, Mérida, Yucatán, Mexico. .,Grupo de Investigación Desarrollos Tecnológicos para la Salud, División de Ingeniería y Ciencias Exactas, Universidad Anáhuac Mayab, Mérida, Yucatán, Mexico.
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155
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Zhang W, Xu J. DNA methyltransferases and their roles in tumorigenesis. Biomark Res 2017; 5:1. [PMID: 28127428 PMCID: PMC5251331 DOI: 10.1186/s40364-017-0081-z] [Citation(s) in RCA: 225] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/03/2017] [Indexed: 01/13/2023] Open
Abstract
DNA methylation plays an important role in gene expression, chromatin stability, and genetic imprinting. In mammals, DNA methylation patterns are written and regulated by DNA methyltransferases (DNMTs), including DNMT1, DNMT3A and DNMT3B. Recent emerging evidence shows that defects in DNMTs are involved in tumor transformation and progression, thus indicating that epigenetic disruptions caused by DNMT abnormalities are associated with tumorigenesis. Herein, we review the latest findings related to DNMT alterations in cancer cells and discuss the contributions of these effects to oncogenic phenotypes.
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Affiliation(s)
- Wu Zhang
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital affiliated to Shanghai Jiao-Tong University School of Medicine, 197 Rui Jin Er Road, 200025 Shanghai, China
| | - Jie Xu
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital affiliated to Shanghai Jiao-Tong University School of Medicine, 197 Rui Jin Er Road, 200025 Shanghai, China
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156
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Huang C, Liu H, Gong XL, Wu LY, Wen B. Effect of evodiamine and berberine on the interaction between DNMTs and target microRNAs during malignant transformation of the colon by TGF-β1. Oncol Rep 2017; 37:1637-1645. [PMID: 28098901 DOI: 10.3892/or.2017.5379] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/07/2016] [Indexed: 11/05/2022] Open
Abstract
The tissue microenvironment functions as a crucial player in carcinogenesis, and transforming growth factor-β1 (TGF-β1) within the microenvironment stimulates the formation of neoplasms. Using an in vitro model of malignancy induced by TGF-β1, we assessed the effect of evodiamine and berberine on the interaction between DNA methyltransferases (DNMTs) and target microRNAs (miRNAs) in the model. Colon tissues from neonatal rats 7 days of age were cultured and malignancy was induced by TGF-β1 in vitro for 48 h, and then the tissues were respectively treated with evodiamine and berberine for 24 h. Morphological alteration of tissues was observed by an inverted microscope, histological structures were observed using hematoxylin and eosin staining, and the expression levels of DNMTs and targeted miRNAs screened by bioinformatics software combined with Gene chip analysis in our previous study were detected by immunohistochemistry and quantified by real-time PCR. Twenty-four hours after treatment with TGF-β1, expression levels of DNMT1, DNMT3A, DNMT3B and miR-152 (target DNMT1), miR-429 (target DNMT3A) and miR-29a (target DNMT3A/3B) were markedly decreased; however, after 48 h, the expression levels of DNMT1 and DNMT3A were significantly increased, but their target miRNAs were still decreased. After treatment with a DNMT inhibitor (5-Aza-dC), expression levels of the miRNAs were increased to a larger extent, but did not reach normal levels. After treatment with berberine and evodiamine for 24 h, respectively, increased expression of DNMT1, DNMT3A, DNMT3B and miR-152, miR-429, miR-29a was noted. In conclusion, the results of the present study suggest that miRNAs can also be post-transcriptionally regulated by their corresponding DNMTs and that berberine and evodiamine regulate the expression of these genes, which provides early epigenetic evidence for the prevention and therapy of colorectal cancer.
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Affiliation(s)
- Chao Huang
- Pi-Wei Institute, Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong 510000, P.R. China
| | - Hong Liu
- Pi-Wei Institute, Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong 510000, P.R. China
| | - Xiu-Li Gong
- Pi-Wei Institute, Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong 510000, P.R. China
| | - Li-Yun Wu
- Pi-Wei Institute, Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong 510000, P.R. China
| | - Bin Wen
- Pi-Wei Institute, Guangzhou University of Traditional Chinese Medicine, Guangzhou, Guangdong 510000, P.R. China
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157
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Wang Z, Wang C, Wu Z, Xue J, Shen B, Zuo W, Wang Z, Wang SL. Artesunate Suppresses the Growth of Prostatic Cancer Cells through Inhibiting Androgen Receptor. Biol Pharm Bull 2017; 40:479-485. [DOI: 10.1248/bpb.b16-00908] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Zhenzhong Wang
- School of Public Health, Nanjing Medical University
- Department of Urology, the Second Affiliated Hospital of Nanjing Medical University
| | - Chao Wang
- School of Public Health, Nanjing Medical University
| | - Ziyu Wu
- Department of Urology, Huai’an Hospital Affiliated with Xuzhou Medical University
| | - Jun Xue
- Department of Urology, the Second Affiliated Hospital of Nanjing Medical University
| | - Baixin Shen
- Department of Urology, the Second Affiliated Hospital of Nanjing Medical University
| | - Wei Zuo
- Department of Urology, the Second Affiliated Hospital of Nanjing Medical University
| | - Zengjun Wang
- Department of Urology, the First Affiliated Hospital of Nanjing Medical University
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158
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Liu W. Epigenetics in Schistosomes: What We Know and What We Need Know. Front Cell Infect Microbiol 2016; 6:149. [PMID: 27891322 PMCID: PMC5104962 DOI: 10.3389/fcimb.2016.00149] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/28/2016] [Indexed: 01/26/2023] Open
Abstract
Schistosomes are metazoan parasites and can cause schistosomiasis. Epigenetic modifications include DNA methylation, histone modifications and non-coding RNAs. Some enzymes involved in epigenetic modification and microRNA processes have been developed as drugs to treat the disease. Compared with humans and vertebrates, an in-depth understanding of epigenetic modifications in schistosomes is starting to be realized. DNA methylation, histone modifications and non-coding RNAs play important roles in the development and reproduction of schistosomes and in interactions between the host and schistosomes. Therefore, exploring and investigating the epigenetic modifications in schistosomes will facilitate drug development and therapy for schistosomiasis. Here, we review the role of epigenetic modifications in the development, growth and reproduction of schistosomes, and the interactions between the host and schistosome. We further discuss potential epigenetic targets for drug discovery for the treatment of schistosomiasis.
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Affiliation(s)
- Weiwei Liu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science Shanghai, China
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159
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Rechavi E, Lev A, Eyal E, Barel O, Kol N, Barhom SF, Pode-Shakked B, Anikster Y, Somech R, Simon AJ. A Novel Mutation in a Critical Region for the Methyl Donor Binding in DNMT3B Causes Immunodeficiency, Centromeric Instability, and Facial Anomalies Syndrome (ICF). J Clin Immunol 2016; 36:801-809. [PMID: 27734333 DOI: 10.1007/s10875-016-0340-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/21/2016] [Indexed: 10/20/2022]
Abstract
PURPOSE Immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome is an extremely rare autosomal recessive disease. The immune phenotype is characterized by hypogammaglobulinemia in the presence of B cells. T cell lymphopenia also develops in some patients. We sought to further investigate the immune defect in an ICF patient with a novel missense mutation in DNMT3B and a severe phenotype. METHODS Patient lymphocytes were examined for subset counts, immunoglobulin levels, T and B cell de novo production (via excision circles) and receptor repertoire diversity. Mutated DNMT3B protein structure was modeled to assess the effect of a mutation located outside of the catalytic region on protein function. RESULTS A novel homozygous missense mutation, Ala585Thr, was found in DNMT3B. The patient had decreased B cell counts with hypogammaglobulinemia, and normal T cell counts. CD4+ T cells decreased over time, leading to an inversion of the CD4+ to CD8+ ratio. Excision circle copy numbers were normal, signifying normal de novo lymphocyte production, but the ratio between naïve and total B cells was low, indicating decreased in vivo B cell replication. T and B cell receptor repertoires displayed normal diversity. Computerized modeling of the mutated Ala585 residue suggested reduced thermostability, possibly affecting the enzyme kinetics. CONCLUSIONS Our results highlight the existence of a T cell defect that develops over time in ICF patient, in addition to the known B cell dysfunction. With intravenous immunoglobulin (IVIG) treatment ameliorating the B cell defect, the extent of CD4+ lymphopenia may determine the severity of ICF immunodeficiency.
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Affiliation(s)
- Erez Rechavi
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Edmond and Lily Safra Children's Hospital, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Atar Lev
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Eran Eyal
- Cancer Research Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Ortal Barel
- Cancer Research Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Nitzan Kol
- Cancer Research Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Sarit Farage Barhom
- Cancer Research Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Ben Pode-Shakked
- Edmond and Lily Safra Children's Hospital, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Yair Anikster
- Edmond and Lily Safra Children's Hospital, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Metabolic Disease Unit, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel
| | - Raz Somech
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
- Edmond and Lily Safra Children's Hospital, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
| | - Amos J Simon
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
- Cancer Research Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
- Institute of Hematology, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
- Sheba Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel-Hashomer, Ramat Gan, Israel.
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160
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Zhao H, Ning S, Scicinski J, Oronsky B, Knox SJ, Peehl DM. Epigenetic effects of RRx-001: a possible unifying mechanism of anticancer activity. Oncotarget 2016; 6:43172-81. [PMID: 26657731 PMCID: PMC4791224 DOI: 10.18632/oncotarget.6526] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 11/27/2015] [Indexed: 12/26/2022] Open
Abstract
RRx-001 is a novel aerospace-derived compound currently under investigation in several ongoing Phase II studies. In a Phase I trial, it demonstrated anti-cancer activity and evidence of resensitization to formerly effective therapies in heavily pre-treated patients with relapsed/refractory solid tumors. RRx-001 generates reactive oxygen and nitrogen species (ROS and RNS) and nitric oxide (NO), elicits changes in intracellular redox status, modulates tumor blood flow, hypoxia and vascular function and triggers apoptosis in cancer cells. We investigated the effect of RRx-001 on the epigenome of SCC VII cancer cells. RRx-001 at 0.5 and 2 μM significantly decreased global DNA methylation, i.e., 5-methylcytosine levels, in SCC VII cells. Consistently, 0.5-5 μM RRx-001 significantly decreased Dnmt1 and Dnmt3a protein expression in a dose- and time-dependent manner. In addition, global methylation profiling identified differentially methylated genes in SCC VII cells treated with 0.5, 2, and 5 μM RRx-001 compared to control cells. Twenty-three target sites were hypomethylated and 22 hypermethylated by >10% in the presence of at least two different concentrations of RRx-001. Moreover, RRx-001 at 2 μM significantly increased global acetylated histone H3 and H4 levels in SCC VII cells after 24 hour treatment, suggesting that RRx-001 regulates global acetylation in cancer cells. These results demonstrate that, in contrast to the traditional "one drug one target" paradigm, RRx-001 has multi(epi)target features, which contribute to its anti-cancer activity and may rationalize the resensitization to previously effective therapies observed in clinical trials and serve as a unifying mechanism for its anticancer activity.
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Affiliation(s)
- Hongjuan Zhao
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shoucheng Ning
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Susan J Knox
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Donna M Peehl
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA
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161
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Zhang Q, Yin S, Liu L, Liu Z, Cao W. Rhein reversal of DNA hypermethylation-associated Klotho suppression ameliorates renal fibrosis in mice. Sci Rep 2016; 6:34597. [PMID: 27703201 PMCID: PMC5050540 DOI: 10.1038/srep34597] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 09/15/2016] [Indexed: 11/15/2022] Open
Abstract
Renal fibrosis is the hallmark of chronic kidney diseases (CKD) and its development and progression are significantly affected by epigenetic modifications. Rhein, a plant-derived anthraquinone, displays strong anti-fibrosis properties, but its protective mode of action remains incompletely understood. Here we explore the mechanism of Rhein anti-renal fibrosis by investigating its regulation of Klotho, a known renal anti-fibrotic protein whose suppression after renal injury reportedly involves aberrant DNA methylation. We report that Rhein is an impressive up-regulator of Klotho and it markedly reversed Klotho down-regulation in unilateral ureteral occlusion-induced fibrotic kidney. Further examinations revealed that Klotho loss in fibrotic kidney is associated with Klotho promoter hypermethylation due to aberrant methyltransferase 1 and 3a expressions. However, Rhein significantly corrected all these epigenetic alterations and subsequently alleviated pro-fibrotic protein expression and renal fibrosis, whereas Klotho knockdown via RNA interferences largely abrogated the anti-renal fibrotic effects of Rhein, suggesting that Rhein epigenetic reversal of Klotho loss represents a critical mode of action that confers Rhein’s anti- renal fibrotic functions. Altogether our studies uncover a novel hypomethylating character of Rhein in preventing Klotho loss and renal fibrosis, and demonstrate the efficacy of Klotho-targeted epigenetic intervention in potential treatment of renal fibrosis-associated kidney diseases.
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Affiliation(s)
- Qin Zhang
- Division of Nephrology, Jinling Hospital, Southern Medical University, Nanjing, 210016, China.,National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China
| | - Shasha Yin
- The Key lab of Jiangsu molecular Medicine, Nanjing University School of Medicine, Nanjing, 210093, China
| | - Lin Liu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China
| | - Zhihong Liu
- Division of Nephrology, Jinling Hospital, Southern Medical University, Nanjing, 210016, China.,National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China
| | - Wangsen Cao
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China.,The Key lab of Jiangsu molecular Medicine, Nanjing University School of Medicine, Nanjing, 210093, China
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162
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Li M, Du W, Shao F, Wang W. Cognitive dysfunction and epigenetic alterations of the BDNF gene are induced by social isolation during early adolescence. Behav Brain Res 2016; 313:177-183. [DOI: 10.1016/j.bbr.2016.07.025] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 07/11/2016] [Accepted: 07/15/2016] [Indexed: 10/21/2022]
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163
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Tsang SY, Ahmad T, Mat FWK, Zhao C, Xiao S, Xia K, Xue H. Variation of global DNA methylation levels with age and in autistic children. Hum Genomics 2016; 10:31. [PMID: 27663196 PMCID: PMC5035466 DOI: 10.1186/s40246-016-0086-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/07/2016] [Indexed: 11/22/2022] Open
Abstract
Background The change in epigenetic signatures, in particular DNA methylation, has been proposed as risk markers for various age-related diseases. However, the course of variation in methylation levels with age, the difference in methylation between genders, and methylation-disease association at the whole genome level is unclear. In the present study, genome-wide methylation levels in DNA extracted from peripheral blood for 2116 healthy Chinese in the 2–97 age range and 280 autistic trios were examined using the fluorescence polarization-based genome-wide DNA methylation quantification method developed by us. Results Genome-wide or global DNA methylation levels proceeded through multiple phases of variation with age, consisting of a steady increase from age 2 to 25 (r = 0.382) and another rise from age 41 to 55 to reach a peak level of ~80 % (r = 0.265), followed by a sharp decrease to ~40 % in the mid-1970s (age 56 to 75; r = −0.395) and leveling off thereafter. Significant gender effect in methylation levels was observed only for the 41–55 age group in which methylation in females was significantly higher than in males (p = 0.010). In addition, global methylation level was significantly higher in autistic children than in age-matched healthy children (p < 0.001). Conclusions The multiphasic nature of changes in global methylation levels with age was delineated, and investigation into the factors underlying this profile will be essential to a proper understanding of the aging process. Furthermore, this first report of global hypermethylation in autistic children also illustrates the importance of age-matched controls in characterization of disease-associated variations in DNA methylation. Electronic supplementary material The online version of this article (doi:10.1186/s40246-016-0086-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shui-Ying Tsang
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Tanveer Ahmad
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Flora W K Mat
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Cunyou Zhao
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Department of Medical Genetics, School of Basic Medical Science, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Shifu Xiao
- Department of Geriatric Psychiatry, Shanghai Mental Health Center, Shanghai Jiaotong University School of Medicine, Shanghai, 200030, China.
| | - Kun Xia
- The State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, 410078, China.
| | - Hong Xue
- Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
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Abstract
DNA methylation alterations are common in urothelial carcinoma, a prevalent cancer worldwide caused predominantly by chemical carcinogens. Recent studies have proposed sets of hypermethylated genes as promising diagnostic and prognostic biomarkers from urine or tissue samples, which require validation. Other studies have revealed intriguing links between specific carcinogens and DNA methylation alterations in cancer tissues or blood that might clarify carcinogenesis mechanisms and aid prevention. Like DNA methylation alterations, mutations in chromatin regulators are frequent, underlining the importance of epigenetic changes. However, the relations between the two changes and their functions in urothelial carcinogenesis remain unclear. Transcription factor genes with altered methylation deserve particular interest. Elucidating the functional impact of methylation changes is a prerequisite for their therapeutic targeting.
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Affiliation(s)
- Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich Heine University Duesseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Wolfgang Goering
- Department of Pathology, Medical Faculty, Heinrich Heine University Duesseldorf, Germany
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165
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Cureau N, AlJahdali N, Vo N, Carbonero F. Epigenetic mechanisms in microbial members of the human microbiota: current knowledge and perspectives. Epigenomics 2016; 8:1259-73. [DOI: 10.2217/epi-2016-0057] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The human microbiota and epigenetic processes have both been shown to play a crucial role in health and disease. However, there is extremely scarce information on epigenetic modulation of microbiota members except for a few pathogens. Mainly DNA adenine methylation has been described extensively in modulating the virulence of pathogenic bacteria in particular. It would thus appear likely that such mechanisms are widespread for most bacterial members of the microbiota. This review will present briefly the current knowledge on epigenetic processes in bacteria, give examples of known methylation processes in microbial members of the human microbiota and summarize the knowledge on regulation of host epigenetic processes by the human microbiota.
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Affiliation(s)
- Natacha Cureau
- Department of Food Science, University of Arkansas, Fayetteville, AR 72704, USA
| | - Nesreen AlJahdali
- Cellular and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72704, USA
| | - Nguyen Vo
- Cellular and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72704, USA
| | - Franck Carbonero
- Department of Food Science, University of Arkansas, Fayetteville, AR 72704, USA
- Cellular and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72704, USA
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166
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Min HY, Lee SC, Woo JK, Jung HJ, Park KH, Jeong HM, Hyun SY, Cho J, Lee W, Park JE, Kwon SJ, Lee HJ, Ni X, Shin YK, Johnson FM, Duvic M, Lee HY. Essential Role of DNA Methyltransferase 1-mediated Transcription of Insulin-like Growth Factor 2 in Resistance to Histone Deacetylase Inhibitors. Clin Cancer Res 2016; 23:1299-1311. [PMID: 27582487 DOI: 10.1158/1078-0432.ccr-16-0534] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 07/06/2016] [Accepted: 08/03/2016] [Indexed: 12/22/2022]
Abstract
Purpose: Histone deacetylase inhibitors (HDI) are promising anticancer therapies; however, drug resistance limits their efficacy. Here, we investigated the molecular mechanisms underlying HDI resistance, focusing on the mechanism of HDI-mediated induction of insulin-like growth factor 2 (IGF2) based on our previous study.Experimental Design: The methylation status of CCCTC-binding factor (CTCF)-binding sites in the IGF2/H19 imprinting control region (ICR) were determined by methylation-specific PCR and bisulfite sequencing. The effectiveness of single or combinatorial blockade of DNA methyltransferase 1 (DNMT1) and histone deacetylase (HDAC) was evaluated using cell viability assay and patient-derived tumor xenograft (PDX) model.Results: HDAC inhibition by vorinostat increased acetylated STAT3 (K685), resulting in transcriptional upregulation of DNMT1 DNMT1-mediated hypermethylation of CTCF-binding sites in the IGF2/H19 ICR decreased CTCF insulator activity, leading to a transcriptional upregulation of IGF2 and activation of the insulin-like growth factor 1 receptor (IGF-1R) pathway in cells with acquired or de novo vorinostat resistance. Strategies targeting DNMT1 diminished the IGF2 expression and potentiated vorinostat sensitivity in preclinical models of lung cancer with hypermethylation in the H19/IGF2 ICR. The degree of ICR hypermethylation correlated with vorinostat resistance in patient-derived lung tumors and in patients with hematologic malignancies.Conclusions: DNMT1-mediated transcriptional upregulation of IGF2 is a novel mechanism of resistance to HDIs, highlighting the role of epigenetic deregulation of IGF2 in HDI resistance and the potential value of the H19/IGF2 ICR hypermethylation and DNMT1 expression as predictive biomarkers in HDI-based anticancer therapies. Clin Cancer Res; 23(5); 1299-311. ©2016 AACR.
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Affiliation(s)
- Hye-Young Min
- Creative Research Initiative Center for concurrent control of emphysema and lung cancer, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.,Department of Molecular Medicine and Biopharmaceutical Science, Graduate School of Convergence Science and Technology, Seoul National University, Suwon, Gyeonggi 16229, Republic of Korea
| | - Su-Chan Lee
- Creative Research Initiative Center for concurrent control of emphysema and lung cancer, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jong Kyu Woo
- Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyun Jin Jung
- Interdisciplinary Program in Genetic Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Kwan Hee Park
- Creative Research Initiative Center for concurrent control of emphysema and lung cancer, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.,Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Hae Min Jeong
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Seung Yeob Hyun
- Creative Research Initiative Center for concurrent control of emphysema and lung cancer, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaebeom Cho
- Creative Research Initiative Center for concurrent control of emphysema and lung cancer, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Wooin Lee
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Eun Park
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - So Jung Kwon
- College of Pharmacy, Inje University, Gimhae, Gyungnam 50834, Republic of Korea
| | - Hyo-Jong Lee
- College of Pharmacy, Inje University, Gimhae, Gyungnam 50834, Republic of Korea
| | - Xiao Ni
- Department of Dermatology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Young Kee Shin
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Faye M Johnson
- Department of Thoracic Head & Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Madeleine Duvic
- Department of Dermatology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Ho-Young Lee
- Creative Research Initiative Center for concurrent control of emphysema and lung cancer, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.,Department of Molecular Medicine and Biopharmaceutical Science, Graduate School of Convergence Science and Technology, Seoul National University, Suwon, Gyeonggi 16229, Republic of Korea.,Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea.,Interdisciplinary Program in Genetic Engineering, Seoul National University, Seoul 08826, Republic of Korea.,College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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167
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Solomon O, Kunik V, Simon A, Kol N, Barel O, Lev A, Amariglio N, Somech R, Rechavi G, Eyal E. G23D: Online tool for mapping and visualization of genomic variants on 3D protein structures. BMC Genomics 2016; 17:681. [PMID: 27565432 PMCID: PMC5002099 DOI: 10.1186/s12864-016-3028-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 08/19/2016] [Indexed: 11/10/2022] Open
Abstract
Background Evaluation of the possible implications of genomic variants is an increasingly important task in the current high throughput sequencing era. Structural information however is still not routinely exploited during this evaluation process. The main reasons can be attributed to the partial structural coverage of the human proteome and the lack of tools which conveniently convert genomic positions, which are the frequent output of genomic pipelines, to proteins and structure coordinates. Results We present G23D, a tool for conversion of human genomic coordinates to protein coordinates and protein structures. G23D allows mapping of genomic positions/variants on evolutionary related (and not only identical) protein three dimensional (3D) structures as well as on theoretical models. By doing so it significantly extends the space of variants for which structural insight is feasible. To facilitate interpretation of the variant consequence, pathogenic variants, functional sites and polymorphism sites are displayed on protein sequence and structure diagrams alongside the input variants. G23D also provides modeling of the mutant structure, analysis of intra-protein contacts and instant access to functional predictions and predictions of thermo-stability changes. G23D is available at http://www.sheba-cancer.org.il/G23D. Conclusions G23D extends the fraction of variants for which structural analysis is applicable and provides better and faster accessibility for structural data to biologists and geneticists who routinely work with genomic information.
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Affiliation(s)
- Oz Solomon
- Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel.,The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Vered Kunik
- Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel
| | - Amos Simon
- Pediatric Immunology Service, Jeffrey Modell Foundation, Sheba Medical Center, Ramat-Gan, Israel
| | - Nitzan Kol
- Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel
| | - Ortal Barel
- Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel
| | - Atar Lev
- Pediatric Immunology Service, Jeffrey Modell Foundation, Sheba Medical Center, Ramat-Gan, Israel
| | - Ninette Amariglio
- Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel.,The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Raz Somech
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat-Gan, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gidi Rechavi
- Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eran Eyal
- Cancer Research Center, Sheba Medical Center, Ramat-Gan, Israel.
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168
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Jeltsch A, Jurkowska RZ. Allosteric control of mammalian DNA methyltransferases - a new regulatory paradigm. Nucleic Acids Res 2016; 44:8556-8575. [PMID: 27521372 PMCID: PMC5062992 DOI: 10.1093/nar/gkw723] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 08/08/2016] [Indexed: 12/23/2022] Open
Abstract
In mammals, DNA methylation is introduced by the DNMT1, DNMT3A and DNMT3B methyltransferases, which are all large multi-domain proteins containing a catalytic C-terminal domain and an N-terminal part with regulatory functions. Recently, two novel regulatory principles of DNMTs were uncovered. It was shown that their catalytic activity is under allosteric control of N-terminal domains with autoinhibitory function, the RFT and CXXC domains in DNMT1 and the ADD domain in DNMT3. Moreover, targeting and activity of DNMTs were found to be regulated in a concerted manner by interactors and posttranslational modifications (PTMs). In this review, we describe the structures and domain composition of the DNMT1 and DNMT3 enzymes, their DNA binding, catalytic mechanism, multimerization and the processes controlling their stability in cells with a focus on their regulation and chromatin targeting by PTMs, interactors and chromatin modifications. We propose that the allosteric regulation of DNMTs by autoinhibitory domains acts as a general switch for the modulation of the function of DNMTs, providing numerous possibilities for interacting proteins, nucleic acids or PTMs to regulate DNMT activity and targeting. The combined regulation of DNMT targeting and catalytic activity contributes to the precise spatiotemporal control of DNMT function and genome methylation in cells.
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Affiliation(s)
- Albert Jeltsch
- Institute of Biochemistry, Pfaffenwaldring 55, Faculty of Chemistry, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Renata Z Jurkowska
- BioMed X Innovation Center, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
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169
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Zhang H, Qi J, Reyes JM, Li L, Rao PK, Li F, Lin CY, Perry JA, Lawlor MA, Federation A, De Raedt T, Li YY, Liu Y, Duarte MA, Zhang Y, Herter-Sprie GS, Kikuchi E, Carretero J, Perou CM, Reibel JB, Paulk J, Bronson RT, Watanabe H, Brainson CF, Kim CF, Hammerman PS, Brown M, Cichowski K, Long H, Bradner JE, Wong KK. Oncogenic Deregulation of EZH2 as an Opportunity for Targeted Therapy in Lung Cancer. Cancer Discov 2016; 6:1006-21. [PMID: 27312177 DOI: 10.1158/2159-8290.cd-16-0164] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 06/14/2016] [Indexed: 12/26/2022]
Abstract
UNLABELLED As a master regulator of chromatin function, the lysine methyltransferase EZH2 orchestrates transcriptional silencing of developmental gene networks. Overexpression of EZH2 is commonly observed in human epithelial cancers, such as non-small cell lung carcinoma (NSCLC), yet definitive demonstration of malignant transformation by deregulated EZH2 remains elusive. Here, we demonstrate the causal role of EZH2 overexpression in NSCLC with new genetically engineered mouse models of lung adenocarcinoma. Deregulated EZH2 silences normal developmental pathways, leading to epigenetic transformation independent of canonical growth factor pathway activation. As such, tumors feature a transcriptional program distinct from KRAS- and EGFR-mutant mouse lung cancers, but shared with human lung adenocarcinomas exhibiting high EZH2 expression. To target EZH2-dependent cancers, we developed a potent open-source EZH2 inhibitor, JQEZ5, that promoted the regression of EZH2-driven tumors in vivo, confirming oncogenic addiction to EZH2 in established tumors and providing the rationale for epigenetic therapy in a subset of lung cancer. SIGNIFICANCE EZH2 overexpression induces murine lung cancers that are similar to human NSCLC with high EZH2 expression and low levels of phosphorylated AKT and ERK, implicating biomarkers for EZH2 inhibitor sensitivity. Our EZH2 inhibitor, JQEZ5, promotes regression of these tumors, revealing a potential role for anti-EZH2 therapy in lung cancer. Cancer Discov; 6(9); 1006-21. ©2016 AACR.See related commentary by Frankel et al., p. 949This article is highlighted in the In This Issue feature, p. 932.
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Affiliation(s)
- Haikuo Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jaime M Reyes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Lewyn Li
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Prakash K Rao
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Fugen Li
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Charles Y Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Jennifer A Perry
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Matthew A Lawlor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alexander Federation
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Thomas De Raedt
- Department of Medicine, Harvard Medical School, Boston, Massachusetts. Genetics Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Yvonne Y Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Yan Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Melissa A Duarte
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Yanxi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Grit S Herter-Sprie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Eiki Kikuchi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Julian Carretero
- Department of Physiology, University of Valencia, Burjassot, Valencia, Spain
| | - Charles M Perou
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jacob B Reibel
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Joshiawa Paulk
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Roderick T Bronson
- Department of Microbiology and Immunobiology, Division of Immunology, Harvard Medical School, Boston, Massachusetts
| | - Hideo Watanabe
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Christine Fillmore Brainson
- Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts. Harvard Stem Cell Institute, Cambridge, Massachusetts. Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Carla F Kim
- Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts. Harvard Stem Cell Institute, Cambridge, Massachusetts. Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Peter S Hammerman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Myles Brown
- Department of Medicine, Harvard Medical School, Boston, Massachusetts. Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Karen Cichowski
- Department of Medicine, Harvard Medical School, Boston, Massachusetts. Genetics Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Henry Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts.
| | - Kwok-Kin Wong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medicine, Harvard Medical School, Boston, Massachusetts. Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts.
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170
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Stueve TR, Marconett CN, Zhou B, Borok Z, Laird-Offringa IA. The importance of detailed epigenomic profiling of different cell types within organs. Epigenomics 2016; 8:817-29. [PMID: 27305639 PMCID: PMC5066118 DOI: 10.2217/epi-2016-0005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The human body consists of hundreds of kinds of cells specified from a single genome overlaid with cell type-specific epigenetic information. Comprehensively profiling the body's distinct epigenetic landscapes will allow researchers to verify cell types used in regenerative medicine and to determine the epigenetic effects of disease, environmental exposures and genetic variation. Key marks/factors that should be investigated include regions of nucleosome-free DNA accessible to regulatory factors, histone marks defining active enhancers and promoters, DNA methylation levels, regulatory RNAs, and factors controlling the three-dimensional conformation of the genome. Here we use the lung to illustrate the importance of investigating an organ's purified cell epigenomes, and outline the challenges and promise of realizing a comprehensive catalog of primary cell epigenomes.
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Affiliation(s)
- Theresa Ryan Stueve
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Department of Biochemistry & Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Crystal N Marconett
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Beiyun Zhou
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Division of Pulmonary & Critical Care Medicine, Department of Medicine, Will Rogers Institute Pulmonary Research Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Zea Borok
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Department of Biochemistry & Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Division of Pulmonary & Critical Care Medicine, Department of Medicine, Will Rogers Institute Pulmonary Research Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Ite A Laird-Offringa
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.,Department of Biochemistry & Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
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171
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Li L, Li C, Mao H, Du Z, Chan WY, Murray P, Luo B, Chan AT, Mok TS, Chan FK, Ambinder RF, Tao Q. Epigenetic inactivation of the CpG demethylase TET1 as a DNA methylation feedback loop in human cancers. Sci Rep 2016; 6:26591. [PMID: 27225590 PMCID: PMC4880909 DOI: 10.1038/srep26591] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 05/05/2016] [Indexed: 12/17/2022] Open
Abstract
Promoter CpG methylation is a fundamental regulatory process of gene expression. TET proteins are active CpG demethylases converting 5-methylcytosine to 5-hydroxymethylcytosine, with loss of 5 hmC as an epigenetic hallmark of cancers, indicating critical roles of TET proteins in epigenetic tumorigenesis. Through analysis of tumor methylomes, we discovered TET1 as a methylated target, and further confirmed its frequent downregulation/methylation in cell lines and primary tumors of multiple carcinomas and lymphomas, including nasopharyngeal, esophageal, gastric, colorectal, renal, breast and cervical carcinomas, as well as non-Hodgkin, Hodgkin and nasal natural killer/T-cell lymphomas, although all three TET family genes are ubiquitously expressed in normal tissues. Ectopic expression of TET1 catalytic domain suppressed colony formation and induced apoptosis of tumor cells of multiple tissue types, supporting its role as a broad bona fide tumor suppressor. Furthermore, TET1 catalytic domain possessed demethylase activity in cancer cells, being able to inhibit the CpG methylation of tumor suppressor gene (TSG) promoters and reactivate their expression, such as SLIT2, ZNF382 and HOXA9. As only infrequent mutations of TET1 have been reported, compared to TET2, epigenetic silencing therefore appears to be the dominant mechanism for TET1 inactivation in cancers, which also forms a feedback loop of CpG methylation during tumorigenesis.
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Affiliation(s)
- Lili Li
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Chen Li
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Haitao Mao
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Zhenfang Du
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Wai Yee Chan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Paul Murray
- School of Cancer Sciences, University of Birmingham, Birmingham, UK
| | - Bing Luo
- Department of Medical Microbiology, Qingdao University Medical College, Shandong, China
| | - Anthony Tc Chan
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Tony Sk Mok
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Francis Kl Chan
- Institute of Digestive Disease and State Key Laboratory of Digestive Diseases, Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - Richard F Ambinder
- Johns Hopkins Singapore and Sydney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, USA
| | - Qian Tao
- Cancer Epigenetics Laboratory, Department of Clinical Oncology, State Key Laboratory of Oncology in South China, Sir YK Pao Center for Cancer, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong.,Johns Hopkins Singapore and Sydney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, USA
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Maloney B, Lahiri DK. Epigenetics of dementia: understanding the disease as a transformation rather than a state. Lancet Neurol 2016; 15:760-774. [PMID: 27302240 DOI: 10.1016/s1474-4422(16)00065-x] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 01/22/2016] [Accepted: 02/11/2016] [Indexed: 12/26/2022]
Abstract
Alzheimer's disease and other idiopathic dementias are associated with epigenetic transformations. These transformations connect the environment and genes to pathogenesis, and have led to the investigation of epigenetic-based therapeutic targes for the treatment of these diseases. Epigenetic changes occur over time in response to environmental effects. The epigenome-based latent early-life associated regulation (LEARn) hypothetical model indicates that accumulated environmental hits produce latent epigenetic changes. These hits can alter biochemical pathways until a pathological threshold is reached, which appears clinically as the onset of dementia. The hypotheses posed by LEARn are testable via longitudinal epigenome-wide, envirome-wide, and exposome-wide association studies (LEWAS) of the genome, epigenome, and environment. We posit that the LEWAS design could lead to effective prevention and treatments by identifying potential therapeutic strategies. Epigenetic evidence suggests that dementia is not a suddenly occurring and sharply delineated state, but rather a gradual change in crucial cellular pathways, that transforms an otherwise healthy state, as a result of neurodegeneration, to a dysfunctional state. Evidence from epigenetics could lead to ways to detect, prevent, and reverse such processes before clinical dementia.
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Affiliation(s)
- Bryan Maloney
- Department of Psychiatry, Institute of Psychiatric Research, Indiana University School of Medicine, Neuroscience Research Center, Indianapolis, IN, USA
| | - Debomoy K Lahiri
- Department of Psychiatry, Institute of Psychiatric Research, Indiana University School of Medicine, Neuroscience Research Center, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
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173
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Hoxa5 undergoes dynamic DNA methylation and transcriptional repression in the adipose tissue of mice exposed to high-fat diet. Int J Obes (Lond) 2016; 40:929-37. [PMID: 26980478 DOI: 10.1038/ijo.2016.36] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 12/28/2015] [Accepted: 01/24/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND/OBJECTIVES The genomic bases of the adipose tissue abnormalities induced by chronic positive calorie excess have been only partially elucidated. We adopted a genome-wide approach to directly test whether long-term high-fat diet (HFD) exposure affects the DNA methylation profile of the mouse adipose tissue and to identify the functional consequences of these changes. SUBJECTS/METHODS We have used epididymal fat of mice fed either high-fat (HFD) or regular chow (STD) diet for 5 months and performed genome-wide DNA methylation analyses by methylated DNA immunoprecipitation sequencing (MeDIP-seq). Mouse Homeobox (Hox) Gene DNA Methylation PCR, RT-qPCR and bisulphite sequencing analyses were then performed. RESULTS Mice fed the HFD progressively expanded their adipose mass accompanied by a significant decrease in glucose tolerance (P<0.001) and insulin sensitivity (P<0.05). MeDIP-seq data analysis revealed a uniform distribution of differentially methylated regions (DMR) through the entire adipocyte genome, with a higher number of hypermethylated regions in HFD mice (P<0.005). This different methylation profile was accompanied by increased expression of the Dnmt3a DNA methyltransferase (Dnmt; P<0.05) and the methyl-CpG-binding domain protein Mbd3 (P<0.05) genes in HFD mice. Gene ontology analysis revealed that, in the HFD-treated mice, the Hox family of development genes was highly enriched in differentially methylated genes (P=0.008). To validate this finding, Hoxa5, which is implicated in fat tissue differentiation and remodeling, has been selected and analyzed by bisulphite sequencing, confirming hypermethylation in the adipose tissue from the HFD mice. Hoxa5 hypermethylation was associated with downregulation of Hoxa5 mRNA and protein expression. Feeding animals previously exposed to the HFD with a standard chow diet for two further months improved the metabolic phenotype of the animals, accompanied by return of Hoxa5 methylation and expression levels (P<0.05) to values similar to those of the control mice maintained under standard chow. CONCLUSIONS HFD induces adipose tissue abnormalities accompanied by epigenetic changes at the Hoxa5 adipose tissue remodeling gene.
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174
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Jurkowska RZ, Jeltsch A. Mechanisms and Biological Roles of DNA Methyltransferases and DNA Methylation: From Past Achievements to Future Challenges. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:1-17. [DOI: 10.1007/978-3-319-43624-1_1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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175
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Dan J, Chen T. Genetic Studies on Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:123-150. [PMID: 27826837 DOI: 10.1007/978-3-319-43624-1_6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cytosine methylation at the C5-position, generating 5-methylcytosine (5mC), is a DNA modification found in many eukaryotic organisms, including fungi, plants, invertebrates, and vertebrates, albeit its levels vary greatly in different organisms. In mammals, cytosine methylation occurs predominantly in the context of CpG dinucleotides, with the majority (60-80 %) of CpG sites in their genomes being methylated. DNA methylation plays crucial roles in the regulation of chromatin structure and gene expression and is essential for mammalian development. Aberrant changes in DNA methylation levels and patterns are associated with various human diseases, including cancer and developmental disorders. DNA methylation is mediated by three active DNA methyltransferases (Dnmts), namely, Dnmt1, Dnmt3a, and Dnmt3b, in mammals. Over the last two decades, genetic manipulations of these enzymes, as well as their regulators, in mice have greatly contributed to our understanding of the biological functions of DNA methylation in mammals. In this chapter, we discuss genetic studies on mammalian Dnmts, focusing on their roles in embryogenesis, cellular differentiation, genomic imprinting, and X-chromosome inactivation.
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Affiliation(s)
- Jiameng Dan
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA.
- Graduate School of Biomedical Sciences at Houston, Houston, TX, 77030, USA.
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176
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Jurkowska RZ, Jeltsch A. Enzymology of Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:87-122. [PMID: 27826836 DOI: 10.1007/978-3-319-43624-1_5] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA methylation is currently one of the hottest topics in basic and biomedical research. Despite tremendous progress in understanding the structures and biochemical properties of the mammalian DNA nucleotide methyltransferases (DNMTs), principles of their regulation in cells have only begun to be uncovered. In mammals, DNA methylation is introduced by the DNMT1, DNMT3A, and DNMT3B enzymes, which are all large multi-domain proteins. These enzymes contain a catalytic C-terminal domain with a characteristic cytosine-C5 methyltransferase fold and an N-terminal part with different domains that interacts with other proteins and chromatin and is involved in targeting and regulation of the DNMTs. The subnuclear localization of the DNMT enzymes plays an important role in their biological function: DNMT1 is localized to replicating DNA via interaction with PCNA and UHRF1. DNMT3 enzymes bind to heterochromatin via protein multimerization and are targeted to chromatin by their ADD and PWWP domains. Recently, a novel regulatory mechanism has been discovered in DNMTs, as latest structural and functional data demonstrated that the catalytic activities of all three enzymes are under tight allosteric control of their N-terminal domains having autoinhibitory functions. This mechanism provides numerous possibilities for the precise regulation of the methyltransferases via controlling the binding and release of autoinhibitory domains by protein factors, noncoding RNAs, or by posttranslational modifications of the DNMTs. In this chapter, we summarize key enzymatic properties of DNMTs, including their specificity and processivity, and afterward we focus on the regulation of their activity and targeting via allosteric processes, protein interactors, and posttranslational modifications.
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Affiliation(s)
- Renata Z Jurkowska
- BioMed X Innovation Center, Im Neuenheimer Feld 583, Heidelberg, D-69120, Germany.
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Pfaffenwaldring 55, Stuttgart, D-70569, Germany.
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177
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Simon RP. Epigenetic modulation of gene expression governs the brain's response to injury. Neurosci Lett 2015; 625:16-9. [PMID: 26739198 DOI: 10.1016/j.neulet.2015.12.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/03/2015] [Accepted: 12/11/2015] [Indexed: 10/22/2022]
Abstract
Mild stress from ischemia, seizure, hypothermia, or infection can produce a transient neuroprotected state in the brain. In the neuroprotected state, the brain responds differently to a severe stress and sustains less injury. At the genomic level, the response of the neuroprotected brain to a severe stress is characterized by widespread differential regulation of genes with diverse functions. This reprogramming of gene expression observed in the neuroprotected brain in response to a stress is consistent with an epigenetic model of regulation mediated by changes in DNA methylation and histone modification. Here, we summarize our evolving understanding of the molecular basis for endogenous neuroprotection and review recent findings that implicate DNA methylation and protein mediators of histone modification as epigenetic regulators of the brain's response to injury.
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Affiliation(s)
- Roger P Simon
- Translational Stroke Program, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA, USA; Grady Memorial Hospital, Atlanta, GA, USA.
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178
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Landmarks in the Evolution of (t)-RNAs from the Origin of Life up to Their Present Role in Human Cognition. Life (Basel) 2015; 6:life6010001. [PMID: 26703740 PMCID: PMC4810232 DOI: 10.3390/life6010001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/07/2015] [Accepted: 12/15/2015] [Indexed: 01/28/2023] Open
Abstract
How could modern life have evolved? The answer to that question still remains unclear. However, evidence is growing that, since the origin of life, RNA could have played an important role throughout evolution, right up to the development of complex organisms and even highly sophisticated features such as human cognition. RNA mediated RNA-aminoacylation can be seen as a first landmark on the path from the RNA world to modern DNA- and protein-based life. Likewise, the generation of the RNA modifications that can be found in various RNA species today may already have started in the RNA world, where such modifications most likely entailed functional advantages. This association of modification patterns with functional features was apparently maintained throughout the further course of evolution, and particularly tRNAs can now be seen as paradigms for the developing interdependence between structure, modification and function. It is in this spirit that this review highlights important stepping stones of the development of (t)RNAs and their modifications (including aminoacylation) from the ancient RNA world up until their present role in the development and maintenance of human cognition. The latter can be seen as a high point of evolution at its present stage, and the susceptibility of cognitive features to even small alterations in the proper structure and functioning of tRNAs underscores the evolutionary relevance of this RNA species.
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179
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Chen J, Wang B, Chung JS, Chai H, Liu C, Ruan Y, Shi H. The role of promoter cis-element, mRNA capping, and ROS in the repression and salt-inducible expression of AtSOT12 in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2015; 6:974. [PMID: 26594223 PMCID: PMC4635225 DOI: 10.3389/fpls.2015.00974] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 10/23/2015] [Indexed: 05/28/2023]
Abstract
Inducible gene expression is a gene regulatory mechanism central to plant response to environmental cues. The inducible genes are often repressed under normal growth conditions while their expression levels are significantly elevated by conditions such as abiotic stresses. Induction of gene expression requires both cis-acting DNA elements and trans-acting proteins that are modulated through signal transduction pathways. Here we report several molecular events that affect salt induced expression of the Arabidopsis AtSOT12 gene. Promoter deletion analysis revealed that DNA elements residing in the 5' UTR are required for the salt induced expression of AtSOT12. Cytosine methylation in the promoter was low and salt stress slightly increased the DNA methylation level, suggesting that DNA methylation may not contribute to AtSOT12 gene repression. Co-transcriptional processing of AtSOT12 mRNA including capping and polyadenylation site selection was also affected by salt stress. The percentage of capped mRNA increased by salt treatment, and the polyadenylation sites were significantly different before and after exposure to salt stress. The expression level of AtSOT12 under normal growth conditions was markedly higher in the oxi1 mutant defective of reactive oxygen species (ROS) signaling than in the wild type. Moreover, AtSOT12 transcript level was elevated by treatments with DPI and DMTU, two chemicals preventing ROS accumulation. These results suggest that repression of AtSOT12 expression may require physiological level of ROS and ROS signaling.
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Affiliation(s)
- Jinhua Chen
- Pre-National Laboratory for Crop Germplasm Innovation and Resource Utilization, Hunan Agricultural UniversityChangsha, China
| | - Bangshing Wang
- Department of Chemistry and Biochemistry, Texas Tech University, LubbockTX, USA
| | - Jung-Sung Chung
- Department of Chemistry and Biochemistry, Texas Tech University, LubbockTX, USA
| | - Haoxi Chai
- Department of Chemistry and Biochemistry, Texas Tech University, LubbockTX, USA
| | - Chunlin Liu
- Pre-National Laboratory for Crop Germplasm Innovation and Resource Utilization, Hunan Agricultural UniversityChangsha, China
| | - Ying Ruan
- Pre-National Laboratory for Crop Germplasm Innovation and Resource Utilization, Hunan Agricultural UniversityChangsha, China
| | - Huazhong Shi
- Department of Chemistry and Biochemistry, Texas Tech University, LubbockTX, USA
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180
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Hu PP, Liu H, Zhen SJ, Li CM, Huang CZ. Nanosilver-based surface-enhanced Raman spectroscopic determination of DNA methyltransferase activity through real-time hybridization chain reaction. Biosens Bioelectron 2015; 73:228-233. [DOI: 10.1016/j.bios.2015.06.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/24/2015] [Accepted: 06/04/2015] [Indexed: 02/06/2023]
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181
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O' Callaghan C, Fanning LJ, Barry OP. Hypermethylation of MAPK13 Promoter in Oesophageal Squamous Cell Carcinoma Is Associated with Loss of p38δ MAPK Expression. Cancers (Basel) 2015; 7:2124-33. [PMID: 26512696 PMCID: PMC4695881 DOI: 10.3390/cancers7040881] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 10/14/2015] [Accepted: 10/15/2015] [Indexed: 12/26/2022] Open
Abstract
The loss of tumour suppressor gene function is a hallmark of malignant transformation and can occur by a variety of genetic and/or epigenetic alterations. We have previously characterised p38δ mitogen-activated protein kinase (MAPK) as a tumour suppressor in oesophageal squamous cell carcinoma (OESCC) and outlined how loss of p38δ MAPK expression promotes increased proliferation and migration, as well as reduced chemosensitivity. Our aim was to investigate the underlying molecular causes of loss of p38δ MAPK expression in OESCC. Sequence analysis of DNA from p38δ MAPK positive and p38δ MAPK negative OESCC cell lines was used to investigate potential loss of function causing mutations. Epigenetic control of p38δ expression in OESCC was examined using methylation-specific PCR and sequencing of bisulfite-converted DNA. We did not identify any mutations in the MAPK13 sequence in OESCC cell lines which lack p38δ MAPK expression. However, we identified a differential pattern of methylation between p38δ MAPK positive and p38δ MAPK negative cell lines. We outline here for the first time differential MAPK13 promoter methylation in OESCC. Our results suggest that epigenetic alterations are responsible, in part, for the suppression of p38δ MAPK expression and promotion of tumourigenesis in OESCC.
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Affiliation(s)
- Carol O' Callaghan
- Department of Pharmacology and Therapeutics, University College Cork, Room 3.89, Western Gateway Building, Western Road, Cork, Ireland.
| | - Liam J Fanning
- Molecular Virology Diagnostic and Research Laboratory, Department of Medicine, University College Cork and Cork University Hospital, Clinical Sciences Building, Cork, Ireland.
| | - Orla P Barry
- Department of Pharmacology and Therapeutics, University College Cork, Room 3.89, Western Gateway Building, Western Road, Cork, Ireland.
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182
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Yuan SX, Zhang J, Xu QG, Yang Y, Zhou WP. Long noncoding RNA, the methylation of genomic elements and their emerging crosstalk in hepatocellular carcinoma. Cancer Lett 2015; 379:239-44. [PMID: 26282784 DOI: 10.1016/j.canlet.2015.08.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 07/30/2015] [Accepted: 08/07/2015] [Indexed: 02/06/2023]
Abstract
The epigenetic mechanism that incorporates DNA methylation alterations, histone modifications, and non-coding RNA expression has been identified as a major characteristic in distinguishing physiological and pathological settings of cancers including hepatocellular carcinoma (HCC), the third leading cause of mortality related cancer. The advance in methylation modification of chromatin elements (for both genomic DNA and histone tails) and the emerging roles of long noncoding RNA (lncRNA) have given us a better understanding of molecular mechanisms underlying HCC. Recently, methods like genome-wide lncRNA profiling and histone hallmark detection were reported to discover mass tumor-associated lncRNAs epigenetically deregulated by differential chromosome modification, mainly by genomic DNA and histone methylation. Therefore, aberrant methylation modification of certain particular lncRNA genes could be crucial events correlating with unfavorable outcomes in HCC. In addition, amount of lncRNAs could act as a manipulator for DNA methylation or a scaffold for histone modification to affect key signaling pathways in hepatocarcinogenesis. This suggests that methylation modification of chromatin elements may have functional crosstalk with lncRNA. Here, we aim to outline the emerging role of the methylation and lncRNA, and their crosstalk of molecular mechanism.
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Affiliation(s)
- Sheng-Xian Yuan
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Hospital, Second Military Medical University, Shanghai, China
| | - Jin Zhang
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Hospital, Second Military Medical University, Shanghai, China
| | - Qing-Guo Xu
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Hospital, Second Military Medical University, Shanghai, China
| | - Yuan Yang
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Hospital, Second Military Medical University, Shanghai, China
| | - Wei-Ping Zhou
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Hospital, Second Military Medical University, Shanghai, China.
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