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Wu DD, Lau ATY, Xu YM, Reinders-Luinge M, Koncz M, Kiss A, Timens W, Rots MG, Hylkema MN. Targeted epigenetic silencing of UCHL1 expression suppresses collagen-1 production in human lung epithelial cells. Epigenetics 2023; 18:2175522. [PMID: 38016026 PMCID: PMC9980648 DOI: 10.1080/15592294.2023.2175522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/17/2022] [Accepted: 01/11/2023] [Indexed: 02/24/2023] Open
Abstract
Ubiquitin carboxyl-terminal hydrolase L1 (UCHL1) is highly expressed in smokers, but little is known about the molecular mechanism of UCHL1 in airway epithelium and its possible role in affecting extracellular matrix (ECM) remodelling in the underlying submucosa. Since cigarette smoking is a major cause of lung diseases, we studied its effect on UCHL1 expression and DNA methylation patterns in human bronchial epithelial cells, obtained after laser capture micro-dissection (LCM) or isolated from residual tracheal/main stem bronchial tissue. Targeted regulation of UCHL1 expression via CRISPR/dCas9 based-epigenetic editing was used to explore the function of UCHL1 in lung epithelium. Our results show that cigarette smoke extract (CSE) stimulated the expression of UCHL1 in vitro. The methylation status of the UCHL1 gene was negatively associated with UCHL1 transcription in LCM-obtained airway epithelium at specific sites. Treatment with a UCHL1 inhibitor showed that the TGF-β1-induced upregulation of the ECM gene COL1A1 can be prevented by the inhibition of UCHL1 activity in cell lines. Furthermore, upon downregulation of UCHL1 by epigenetic editing using CRISPR/dCas-EZH2, mRNA expression of COL1A1 and fibronectin was reduced. In conclusion, we confirmed higher UCHL1 expression in current smokers compared to non- and ex-smokers, and induced downregulation of UCHL1 by epigenetic editing. The subsequent repression of genes encoding ECM proteins suggest a role for UCHL1 as a therapeutic target in fibrosis-related disease.
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Affiliation(s)
- Dan-Dan Wu
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, P. R. China
| | - Andy T. Y. Lau
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, P. R. China
| | - Yan-Ming Xu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, P. R. China
| | - Marjan Reinders-Luinge
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mihaly Koncz
- Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Antal Kiss
- Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marianne G. Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Machteld N. Hylkema
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Theys C, Ibrahim J, Mateiu L, Mposhi A, García-Pupo L, De Pooter T, De Rijk P, Strazisar M, İnce İA, Vintea I, Rots MG, Vanden Berghe W. Mitochondrial GpC and CpG DNA Hypermethylation Cause Metabolic Stress-Induced Mitophagy and Cholestophagy. Int J Mol Sci 2023; 24:16412. [PMID: 38003603 PMCID: PMC10671279 DOI: 10.3390/ijms242216412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/30/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) is characterized by a constant accumulation of lipids in the liver. This hepatic lipotoxicity is associated with a dysregulation of the first step in lipid catabolism, known as beta oxidation, which occurs in the mitochondrial matrix. Eventually, this dysregulation will lead to mitochondrial dysfunction. To evaluate the possible involvement of mitochondrial DNA methylation in this lipid metabolic dysfunction, we investigated the functional metabolic effects of mitochondrial overexpression of CpG (MSssI) and GpC (MCviPI) DNA methyltransferases in relation to gene expression and (mito)epigenetic signatures. Overall, the results show that mitochondrial GpC and, to a lesser extent, CpG methylation increase bile acid metabolic gene expression, inducing the onset of cholestasis through mito-nuclear epigenetic reprogramming. Moreover, both increase the expression of metabolic nuclear receptors and thereby induce basal overactivation of mitochondrial respiration. The latter promotes mitochondrial swelling, favoring lipid accumulation and metabolic-stress-induced mitophagy and autophagy stress responses. In conclusion, both mitochondrial GpC and CpG methylation create a metabolically challenging environment that induces mitochondrial dysfunction, which may contribute to the progression of MASLD.
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Affiliation(s)
- Claudia Theys
- Lab Protein Chemistry, Proteomics & Epigenetic Signaling (PPES), Department Biomedical Sciences, University of Antwerp, Wilrijk, 2610 Antwerp, Belgium; (C.T.)
| | - Joe Ibrahim
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
- Center for Oncological Research, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
| | - Ligia Mateiu
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, 2650 Edegem, Belgium
| | - Archibold Mposhi
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Laura García-Pupo
- Lab Protein Chemistry, Proteomics & Epigenetic Signaling (PPES), Department Biomedical Sciences, University of Antwerp, Wilrijk, 2610 Antwerp, Belgium; (C.T.)
| | - Tim De Pooter
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Wilrijk, 2610 Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Wirlijk, 2610 Antwerp, Belgium
| | - Peter De Rijk
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Wilrijk, 2610 Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Wirlijk, 2610 Antwerp, Belgium
| | - Mojca Strazisar
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Wilrijk, 2610 Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Wirlijk, 2610 Antwerp, Belgium
| | - İkbal Agah İnce
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
- Department of Medical Microbiology, School of Medicine, Acıbadem Mehmet, Ali Aydınlar University, 34752 Ataşehir, İstanbul, Türkiye
| | - Iuliana Vintea
- Pathophysiology Lab, Infla-Med Centre of Excellence, Department of Biomedical Sciences, University of Antwerp, Wilrijk, 2610 Antwerp, Belgium
| | - Marianne G. Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Wim Vanden Berghe
- Lab Protein Chemistry, Proteomics & Epigenetic Signaling (PPES), Department Biomedical Sciences, University of Antwerp, Wilrijk, 2610 Antwerp, Belgium; (C.T.)
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Coussement L, Oosterhof MM, Guryev V, Reitsema VA, Bruintjes JJ, Goris M, Bouma HR, de Meyer T, Rots MG, Henning RH. Liver transcriptomic and methylomic analyses identify transcriptional mitogen-activated protein kinase regulation in facultative hibernation of Syrian hamster. Proc Biol Sci 2023; 290:20230368. [PMID: 37221849 DOI: 10.1098/rspb.2023.0368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
Hibernation consists of alternating torpor-arousal phases, during which animals cope with repetitive hypothermia and ischaemia-reperfusion. Due to limited transcriptomic and methylomic information for facultative hibernators, we here conducted RNA and whole-genome bisulfide sequencing in liver of hibernating Syrian hamster (Mesocricetus auratus). Gene ontology analysis was performed on 844 differentially expressed genes and confirmed the shift in metabolic fuel utilization, inhibition of RNA transcription and cell cycle regulation as found in seasonal hibernators. Additionally, we showed a so far unreported suppression of mitogen-activated protein kinase (MAPK) and protein phosphatase 1 pathways during torpor. Notably, hibernating hamsters showed upregulation of MAPK inhibitors (dual-specificity phosphatases and sproutys) and reduced levels of MAPK-induced transcription factors (TFs). Promoter methylation was found to modulate the expression of genes targeted by these TFs. In conclusion, we document gene regulation between hibernation phases, which may aid the identification of pathways and targets to prevent organ damage in transplantation or ischaemia-reperfusion.
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Affiliation(s)
- Louis Coussement
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
| | - Marloes M Oosterhof
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Vera A Reitsema
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Jojanneke J Bruintjes
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Maaike Goris
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Hjalmar R Bouma
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
- Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Tim de Meyer
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
| | - Marianne G Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Robert H Henning
- Department of Clinical Pharmacy and Pharmacology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
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Mposhi A, Cortés-Mancera F, Heegsma J, de Meijer VE, van de Sluis B, Sydor S, Bechmann LP, Theys C, de Rijk P, De Pooter T, Vanden Berghe W, İnce İA, Faber KN, Rots MG. Mitochondrial DNA methylation in metabolic associated fatty liver disease. Front Nutr 2023; 10:964337. [PMID: 37305089 PMCID: PMC10249072 DOI: 10.3389/fnut.2023.964337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 02/07/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Hepatic lipid accumulation and mitochondrial dysfunction are hallmarks of metabolic associated fatty liver disease (MAFLD), yet molecular parameters underlying MAFLD progression are not well understood. Differential methylation within the mitochondrial DNA (mtDNA) has been suggested to be associated with dysfunctional mitochondria, also during progression to Metabolic Steatohepatitis (MeSH). This study further investigates whether mtDNA methylation is associated with hepatic lipid accumulation and MAFLD. Methods HepG2 cells were constructed to stably express mitochondria-targeted viral and prokaryotic cytosine DNA methyltransferases (mtM.CviPI or mtM.SssI for GpC or CpG methylation, respectively). A catalytically inactive variant (mtM.CviPI-Mut) was constructed as a control. Mouse and human patients' samples were also investigated. mtDNA methylation was assessed by pyro- or nanopore sequencing. Results and discussion Differentially induced mtDNA hypermethylation impaired mitochondrial gene expression and metabolic activity in HepG2-mtM.CviPI and HepG2-mtM.SssI cells and was associated with increased lipid accumulation, when compared to the controls. To test whether lipid accumulation causes mtDNA methylation, HepG2 cells were subjected to 1 or 2 weeks of fatty acid treatment, but no clear differences in mtDNA methylation were detected. In contrast, hepatic Nd6 mitochondrial gene body cytosine methylation and Nd6 gene expression were increased in mice fed a high-fat high cholesterol diet (HFC for 6 or 20 weeks), when compared to controls, while mtDNA content was unchanged. For patients with simple steatosis, a higher ND6 methylation was confirmed using Methylation Specific PCR, but no additional distinctive cytosines could be identified using pyrosequencing. This study warrants further investigation into a role for mtDNA methylation in promoting mitochondrial dysfunction and impaired lipid metabolism in MAFLD.
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Affiliation(s)
- Archibold Mposhi
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Fabian Cortés-Mancera
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Departamento de Ciencias Aplicadas, Instituto Tecnológico Metropolitano, Medellín, Colombia
| | - Janette Heegsma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Vincent E. de Meijer
- Department of Surgery, Division of Hepato-Pancreato-Biliary Surgery and Liver Transplantation, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Bart van de Sluis
- Section of Molecular Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Svenja Sydor
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Bochum, Germany
- Ruhr-University Bochum, Bochum, Germany
| | - Lars P. Bechmann
- Department of Internal Medicine, University Hospital Knappschaftskrankenhaus, Bochum, Germany
- Ruhr-University Bochum, Bochum, Germany
| | - Claudia Theys
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Peter de Rijk
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Neuromics Support Facility, VIB-UAntwerp Center for Molecular Neurology, University of Antwerp, Antwerp, Belgium
| | - Tim De Pooter
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Neuromics Support Facility, VIB-UAntwerp Center for Molecular Neurology, University of Antwerp, Antwerp, Belgium
| | - Wim Vanden Berghe
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - İkbal Agah İnce
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Medical Microbiology, School of Medicine, Acıbadem Mehmet Ali Aydınlar University, Istanbul, Türkiye
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Marianne G. Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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5
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Chen H, Yang QL, Xu JX, Deng X, Zhang YJ, Liu T, Rots MG, Xu GL, Huang KY. Efficient methods for multiple types of precise gene-editing in Chlamydomonas. Plant J 2023. [PMID: 37310200 DOI: 10.1111/tpj.16265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 06/14/2023]
Abstract
Precise gene-editing using CRISPR/Cas9 technology remains a long-standing challenge, especially for genes with low expression and no selectable phenotypes in Chlamydomonas reinhardtii, a classic model for photosynthesis and cilia research. Here, we developed a multi-type and precise genetic manipulation method in which a DNA break was generated by Cas9 nuclease and the repair was mediated using a homologous DNA template. The efficacy of this method was demonstrated for several types of gene editing, including inactivation of two low-expression genes (CrTET1 and CrKU80), the introduction of a FLAG-HA epitope tag into VIPP1, IFT46, CrTET1 and CrKU80 genes, and placing a YFP tag into VIPP1 and IFT46 for live-cell imaging. We also successfully performed a single amino acid substitution for the FLA3, FLA10 and FTSY genes, and documented the attainment of the anticipated phenotypes. Lastly, we demonstrated that precise fragment deletion from the 3'-UTR of MAA7 and VIPP1 resulted in a stable knock-down effect. Overall, our study has established efficient methods for multiple types of precise gene editing in Chlamydomonas, enabling substitution, insertion and deletion at the base resolution, thus improving the potential of this alga in both basic research and industrial applications.
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Affiliation(s)
- Hui Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qing-Lin Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jia-Xi Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuan Deng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yun-Jie Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ting Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Marianne G Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, The Netherlands
| | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Shanghai Key Laboratory of Medical Epigenetics, Laboratory of Cancer Epigenetics, Institutes of Biomedical Sciences, Medical College of Fudan University, Chinese Academy of Medical Sciences (RU069), Shanghai, China
| | - Kai-Yao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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Mposhi A, Liang L, Mennega KP, Yildiz D, Kampert C, Hof IH, Jellema PG, de Koning TJ, Faber KN, Ruiters MHJ, Niezen-Koning KE, Rots MG. The Mitochondrial Epigenome: An Unexplored Avenue to Explain Unexplained Myopathies? Int J Mol Sci 2022; 23:ijms23042197. [PMID: 35216315 PMCID: PMC8879787 DOI: 10.3390/ijms23042197] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/01/2022] [Accepted: 02/07/2022] [Indexed: 02/01/2023] Open
Abstract
Mutations in either mitochondrial DNA (mtDNA) or nuclear genes that encode mitochondrial proteins may lead to dysfunctional mitochondria, giving rise to mitochondrial diseases. Some mitochondrial myopathies, however, present without a known underlying cause. Interestingly, methylation of mtDNA has been associated with various clinical pathologies. The present study set out to assess whether mtDNA methylation could explain impaired mitochondrial function in patients diagnosed with myopathy without known underlying genetic mutations. Enhanced mtDNA methylation was indicated by pyrosequencing for muscle biopsies of 14 myopathy patients compared to four healthy controls, at selected cytosines in the Cytochrome B (CYTB) gene, but not within the displacement loop (D-loop) region. The mtDNA methylation patterns of the four healthy muscle biopsies were highly consistent and showed intriguing tissue-specific differences at particular cytosines with control skin fibroblasts cultured in vitro. Within individual myopathy patients, the overall mtDNA methylation pattern correlated well between muscle and skin fibroblasts. Despite this correlation, a pilot analysis of four myopathy and five healthy fibroblast samples did not reveal a disease-associated difference in mtDNA methylation. We did, however, detect increased expression of solute carrier family 25A26 (SLC25A26), encoding the importer of S-adenosylmethionine, together with enhanced mtDNA copy numbers in myopathy fibroblasts compared to healthy controls. To confirm that pyrosequencing indeed reflected DNA methylation and not bisulfite accessibility, mass spectrometry was employed. Although no myopathy-related differences in total amount of methylated cytosines were detected at this stage, a significant contribution of contaminating nuclear DNA (nDNA) was revealed, and steps to improve enrichment for mtDNA are reported. In conclusion, in this explorative study we show that analyzing the mitochondrial genome beyond its sequence opens novel avenues to identify potential molecular biomarkers assisting in the diagnosis of unexplained myopathies.
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Affiliation(s)
- Archibold Mposhi
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (A.M.); (L.L.); (K.P.M.); (P.G.J.); (M.H.J.R.)
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands;
| | - Lin Liang
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (A.M.); (L.L.); (K.P.M.); (P.G.J.); (M.H.J.R.)
| | - Kevin P. Mennega
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (A.M.); (L.L.); (K.P.M.); (P.G.J.); (M.H.J.R.)
- Department of Laboratory Medicine, Laboratory of Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (D.Y.); (C.K.); (I.H.H.); (K.E.N.-K.)
| | - Dilemin Yildiz
- Department of Laboratory Medicine, Laboratory of Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (D.Y.); (C.K.); (I.H.H.); (K.E.N.-K.)
| | - Crista Kampert
- Department of Laboratory Medicine, Laboratory of Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (D.Y.); (C.K.); (I.H.H.); (K.E.N.-K.)
| | - Ingrid H. Hof
- Department of Laboratory Medicine, Laboratory of Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (D.Y.); (C.K.); (I.H.H.); (K.E.N.-K.)
| | - Pytrick G. Jellema
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (A.M.); (L.L.); (K.P.M.); (P.G.J.); (M.H.J.R.)
| | - Tom J. de Koning
- Department of Genetics, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands;
- Department of Clinical Sciences, Lund University, Lasarettgatan 40, 221 85 Lund, Sweden
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands;
| | - Marcel H. J. Ruiters
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (A.M.); (L.L.); (K.P.M.); (P.G.J.); (M.H.J.R.)
| | - Klary E. Niezen-Koning
- Department of Laboratory Medicine, Laboratory of Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (D.Y.); (C.K.); (I.H.H.); (K.E.N.-K.)
| | - Marianne G. Rots
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (A.M.); (L.L.); (K.P.M.); (P.G.J.); (M.H.J.R.)
- Correspondence:
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Cortés-Mancera FM, Sarno F, Goubert D, Rots MG. Gene-Targeted DNA Methylation: Towards Long-Lasting Reprogramming of Gene Expression? Advances in Experimental Medicine and Biology 2022; 1389:515-533. [DOI: 10.1007/978-3-031-11454-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Tognoli ML, Vlahov N, Steenbeek S, Grawenda AM, Eyres M, Cano‐Rodriguez D, Scrace S, Kartsonaki C, von Kriegsheim A, Willms E, Wood MJ, Rots MG, van Rheenen J, O'Neill E, Pankova D. RASSF1C oncogene elicits amoeboid invasion, cancer stemness, and extracellular vesicle release via a SRC/Rho axis. EMBO J 2021; 40:e107680. [PMID: 34532864 PMCID: PMC8521318 DOI: 10.15252/embj.2021107680] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/20/2022] Open
Abstract
Cell plasticity is a crucial hallmark leading to cancer metastasis. Upregulation of Rho/ROCK pathway drives actomyosin contractility, protrusive forces, and contributes to the occurrence of highly invasive amoeboid cells in tumors. Cancer stem cells are similarly associated with metastasis, but how these populations arise in tumors is not fully understood. Here, we show that the novel oncogene RASSF1C drives mesenchymal-to-amoeboid transition and stem cell attributes in breast cancer cells. Mechanistically, RASSF1C activates Rho/ROCK via SRC-mediated RhoGDI inhibition, resulting in generation of actomyosin contractility. Moreover, we demonstrate that RASSF1C-induced amoeboid cells display increased expression of cancer stem-like markers such as CD133, ALDH1, and Nanog, and are accompanied by higher invasive potential in vitro and in vivo. Further, RASSF1C-induced amoeboid cells employ extracellular vesicles to transfer the invasive phenotype to target cells and tissue. Importantly, the underlying RASSF1C-driven biological processes concur to explain clinical data: namely, methylation of the RASSF1C promoter correlates with better survival in early-stage breast cancer patients. Therefore, we propose the use of RASSF1 gene promoter methylation status as a biomarker for patient stratification.
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Affiliation(s)
| | | | - Sander Steenbeek
- Molecular PathologyOncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | | | | | - David Cano‐Rodriguez
- University of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Simon Scrace
- Department of OncologyUniversity of OxfordOxfordUK
| | | | - Alex von Kriegsheim
- Cancer Research UK Edinburgh CentreMRC Institute of Genetics & Molecular MedicineThe University of EdinburghWestern General HospitalEdinburghUK
| | - Eduard Willms
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
- La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVic.Australia
| | | | - Marianne G Rots
- University of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Jacco van Rheenen
- Molecular PathologyOncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Eric O'Neill
- Department of OncologyUniversity of OxfordOxfordUK
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9
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Wu DD, Xu YM, Chen DJ, Liang ZL, Chen XL, Hylkema MN, Rots MG, Li SQ, Lau ATY. Ubiquitin carboxyl-terminal hydrolase isozyme L1/UCHL1 suppresses epithelial-mesenchymal transition and is under-expressed in cadmium-transformed human bronchial epithelial cells. Cell Biol Toxicol 2021; 37:497-513. [PMID: 33040242 DOI: 10.1007/s10565-020-09560-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/23/2020] [Indexed: 02/05/2023]
Abstract
Cadmium (Cd), a highly toxic heavy metal, is widespreadly distributed in the environment. Chronic exposure to Cd is associated with the development of several diseases including cancers. Over the decade, many researches have been carried on various models to examine the acute effects of Cd; yet, limited knowledge is known about the long-term Cd exposure, especially in the human lung cells. Previously, we showed that chronic Cd-exposed human bronchial epithelial BEAS-2B cells exhibited transformed cell properties, such as anchorage-independent growth, augmented cell migration, and epithelial-mesenchymal transition (EMT). To study these Cd-transformed cells more comprehensively, here, we further characterized their subproteomes. Overall, a total of 63 differentially expressed proteins between Cd-transformed and passage-matched control cells among the five subcellular fractions (cytoplasmic, membrane, nuclear-soluble, chromatin-bound, and cytoskeletal) were identified by mass spectrometric analysis and database searching. Interestingly, we found that the thiol protease ubiquitin carboxyl-terminal hydrolase isozyme L1 (UCHL1) is one of the severely downregulated proteins in the Cd-transformed cells. Notably, the EMT phenotype of Cd-transformed cells can be suppressed by forced ectopic expression of UCHL1, suggesting UCHL1 as a crucial modulator in the maintenance of the proper differentiation status in lung epithelial cells. Since EMT is considered as a critical step during malignant cell transformation, finding novel cellular targets that can antagonize this transition may lead to more efficient strategies to inhibit cancer development. Our data report for the first time that UCHL1 may play a function in the suppression of EMT in Cd-transformed human lung epithelial cells, indicating that UCHL1 might be a new therapeutic target for chronic Cd-induced carcinogenesis. Graphical abstract.
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Affiliation(s)
- Dan-Dan Wu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, Guangdong, People's Republic of China
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713, GZ, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, 9713, GZ, Groningen, The Netherlands
| | - Yan-Ming Xu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, Guangdong, People's Republic of China
| | - De-Ju Chen
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, Guangdong, People's Republic of China
| | - Zhan-Ling Liang
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, Guangdong, People's Republic of China
| | - Xu-Li Chen
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, Guangdong, People's Republic of China
| | - Machteld N Hylkema
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713, GZ, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, 9713, GZ, Groningen, The Netherlands
| | - Marianne G Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713, GZ, Groningen, The Netherlands
| | - Sheng-Qing Li
- Department of Pulmonary and Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, People's Republic of China
| | - Andy T Y Lau
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, 515041, Guangdong, People's Republic of China.
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10
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Fledderus J, Vanchin B, Rots MG, Krenning G. The Endothelium as a Target for Anti-Atherogenic Therapy: A Focus on the Epigenetic Enzymes EZH2 and SIRT1. J Pers Med 2021; 11:jpm11020103. [PMID: 33562658 PMCID: PMC7915331 DOI: 10.3390/jpm11020103] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 12/11/2022] Open
Abstract
Endothelial cell inflammatory activation and dysfunction are key events in the pathophysiology of atherosclerosis, and are associated with an elevated risk of cardiovascular events. Yet, therapies specifically targeting the endothelium and atherosclerosis are lacking. Here, we review how endothelial behaviour affects atherogenesis and pose that the endothelium may be an efficacious cellular target for antiatherogenic therapies. We discuss the contribution of endothelial inflammatory activation and dysfunction to atherogenesis and postulate that the dysregulation of specific epigenetic enzymes, EZH2 and SIRT1, aggravate endothelial dysfunction in a pleiotropic fashion. Moreover, we propose that commercially available drugs are available to clinically explore this postulation.
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Affiliation(s)
- Jolien Fledderus
- Medical Biology Section, Laboratory for Cardiovascular Regenerative Medicine, Department Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 (EA11), 9713 GZ Groningen, The Netherlands; (J.F.); (B.V.)
| | - Byambasuren Vanchin
- Medical Biology Section, Laboratory for Cardiovascular Regenerative Medicine, Department Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 (EA11), 9713 GZ Groningen, The Netherlands; (J.F.); (B.V.)
- Department Cardiology, School of Medicine, Mongolian National University of Medical Sciences, Jamyan St 3, Ulaanbaatar 14210, Mongolia
| | - Marianne G. Rots
- Epigenetic Editing, Medical Biology Section, Department Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 (EA11), 9713 GZ Groningen, The Netherlands;
| | - Guido Krenning
- Medical Biology Section, Laboratory for Cardiovascular Regenerative Medicine, Department Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 (EA11), 9713 GZ Groningen, The Netherlands; (J.F.); (B.V.)
- Correspondence: ; Tel.: +31-50-361-8043; Fax: +31-50-361-9911
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11
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Abstract
Epigenetic editing refers to the locus-specific targeting of epigenetic enzymes to rewrite the local epigenetic landscape of an endogenous genomic site, often with the aim of transcriptional reprogramming. Implementing clustered regularly interspaced short palindromic repeat-dCas9 greatly accelerated the advancement of epigenetic editing, yielding preclinical therapeutic successes using a variety of epigenetic enzymes. Here, we review the current applications of these epigenetic editing tools in mammals and shed light on biochemical improvements that facilitate versatile applications.
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Affiliation(s)
- Rutger A F Gjaltema
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Marianne G Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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12
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Mossel DM, Moganti K, Riabov V, Weiss C, Kopf S, Cordero J, Dobreva G, Rots MG, Klüter H, Harmsen MC, Kzhyshkowska J. Epigenetic Regulation of S100A9 and S100A12 Expression in Monocyte-Macrophage System in Hyperglycemic Conditions. Front Immunol 2020; 11:1071. [PMID: 32582175 PMCID: PMC7280556 DOI: 10.3389/fimmu.2020.01071] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 05/04/2020] [Indexed: 12/13/2022] Open
Abstract
The number of diabetic patients in Europe and world-wide is growing. Diabetes confers a 2-fold higher risk for vascular disease. Lack of insulin production (Type 1 diabetes, T1D) or lack of insulin responsiveness (Type 2 diabetes, T2D) causes systemic metabolic changes such as hyperglycemia (HG) which contribute to the pathology of diabetes. Monocytes and macrophages are key innate immune cells that control inflammatory reactions associated with diabetic vascular complications. Inflammatory programming of macrophages is regulated and maintained by epigenetic mechanisms, in particular histone modifications. The aim of our study was to identify the epigenetic mechanisms involved in the hyperglycemia-mediated macrophage activation. Using Affymetrix microarray profiling and RT-qPCR we identified that hyperglycemia increased the expression of S100A9 and S100A12 in primary human macrophages. Expression of S100A12 was sustained after glucose levels were normalized. Glucose augmented the response of macrophages to Toll-like receptor (TLR)-ligands Palmatic acid (PA) and Lipopolysaccharide (LPS) i.e., pro-inflammatory stimulation. The abundance of activating histone Histone 3 Lysine 4 methylation marks (H3K4me1, H3K4me3) and general acetylation on histone 3 (AceH3) with the promoters of these genes was analyzed by chromatin immunoprecipitation. Hyperglycemia increased acetylation of histones bound to the promoters of S100A9 and S100A12 in M1 macrophages. In contrast, hyperglycemia caused a reduction in total H3 which correlated with the increased expression of both S100 genes. The inhibition of histone methyltransferases SET domain-containing protein (SET)7/9 and SET and MYND domain-containing protein (SMYD)3 showed that these specifically regulated S100A12 expression. We conclude that hyperglycemia upregulates expression of S100A9, S100A12 via epigenetic regulation and induces an activating histone code on the respective gene promoters in M1 macrophages. Mechanistically, this regulation relies on action of histone methyltransferases SMYD3 and SET7/9. The results define an important role for epigenetic regulation in macrophage mediated inflammation in diabetic conditions.
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Affiliation(s)
- Dieuwertje M Mossel
- Medical Faculty Mannheim, Institute of Transfusion Medicine and Immunology, Heidelberg University, Mannheim, Germany
| | - Kondaiah Moganti
- Medical Faculty Mannheim, Institute of Transfusion Medicine and Immunology, Heidelberg University, Mannheim, Germany.,Department of Dermatology, University of Münster, Münster, Germany
| | - Vladimir Riabov
- Medical Faculty Mannheim, Institute of Transfusion Medicine and Immunology, Heidelberg University, Mannheim, Germany
| | - Christel Weiss
- Department of Medical Statistics, Biomathematics and Information Processing, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Stefan Kopf
- Department of Medicine I: Endocrinology and Clinical Chemistry, University Hospital Heidelberg, Heidelberg, Germany
| | - Julio Cordero
- Anatomy and Developmental Biology, CBTM, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Gergana Dobreva
- Anatomy and Developmental Biology, CBTM, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Marianne G Rots
- Department Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Harald Klüter
- Medical Faculty Mannheim, Institute of Transfusion Medicine and Immunology, Heidelberg University, Mannheim, Germany.,German Red Cross Blood Service Baden-Württemberg - Hessen, Mannheim, Germany
| | - Martin C Harmsen
- Department Pathology and Medical Biology, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
| | - Julia Kzhyshkowska
- Medical Faculty Mannheim, Institute of Transfusion Medicine and Immunology, Heidelberg University, Mannheim, Germany.,German Red Cross Blood Service Baden-Württemberg - Hessen, Mannheim, Germany
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13
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Gjaltema RAF, Goubert D, Huisman C, del Pilar García Tobilla C, Koncz M, Jellema PG, Wu D, Brouwer U, Kiss A, Verschure PJ, Bank RA, Rots MG. KRAB-Induced Heterochromatin Effectively Silences PLOD2 Gene Expression in Somatic Cells and is Resilient to TGFβ1 Activation. Int J Mol Sci 2020; 21:ijms21103634. [PMID: 32455614 PMCID: PMC7279273 DOI: 10.3390/ijms21103634] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/03/2020] [Accepted: 05/07/2020] [Indexed: 12/22/2022] Open
Abstract
Epigenetic editing, an emerging technique used for the modulation of gene expression in mammalian cells, is a promising strategy to correct disease-related gene expression. Although epigenetic reprogramming results in sustained transcriptional modulation in several in vivo models, further studies are needed to develop this approach into a straightforward technology for effective and specific interventions. Important goals of current research efforts are understanding the context-dependency of successful epigenetic editing and finding the most effective epigenetic effector(s) for specific tasks. Here we tested whether the fibrosis- and cancer-associated PLOD2 gene can be repressed by the DNA methyltransferase M.SssI, or by the non-catalytic Krüppel associated box (KRAB) repressor directed to the PLOD2 promoter via zinc finger- or CRISPR-dCas9-mediated targeting. M.SssI fusions induced de novo DNA methylation, changed histone modifications in a context-dependent manner, and led to 50%–70% reduction in PLOD2 expression in fibrotic fibroblasts and in MDA-MB-231 cancer cells. Targeting KRAB to PLOD2 resulted in the deposition of repressive histone modifications without DNA methylation and in almost complete PLOD2 silencing. Interestingly, both long-term TGFβ1-induced, as well as unstimulated PLOD2 expression, was completely repressed by KRAB, while M.SssI only prevented the TGFβ1-induced PLOD2 expression. Targeting transiently expressed dCas9-KRAB resulted in sustained PLOD2 repression in HEK293T and MCF-7 cells. Together, these findings point to KRAB outperforming DNA methylation as a small potent targeting epigenetic effector for silencing TGFβ1-induced and uninduced PLOD2 expression.
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Affiliation(s)
- Rutger A. F. Gjaltema
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
- MATRIX Research Group, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Désirée Goubert
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
| | - Christian Huisman
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
| | - Consuelo del Pilar García Tobilla
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
| | - Mihály Koncz
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (M.K.); (A.K.)
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Pytrick G. Jellema
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
- MATRIX Research Group, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Dandan Wu
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
| | - Uilke Brouwer
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
- MATRIX Research Group, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Antal Kiss
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary; (M.K.); (A.K.)
| | - Pernette J. Verschure
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands;
| | - Ruud A. Bank
- MATRIX Research Group, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands;
| | - Marianne G. Rots
- Epigenetic Editing Laboratory, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1 EA11, 9713 GZ Groningen, The Netherlands; (R.A.F.G.); (D.G.); (C.H.); (C.d.P.G.T.); (P.G.J.); (D.W.); (U.B.)
- Correspondence: ; Tel.: +31-50-3610153
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14
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Abstract
Gene therapy is currently considered as the optimal treatment for inborn errors of metabolism (IEMs), as it aims to permanently compensate for the primary genetic defect. However, emerging gene editing approaches such as CRISPR-Cas9, in which the DNA of the host organism is edited at a precise location, may have outperforming therapeutic potential. Gene editing strategies aim to correct the actual genetic mutation, while circumventing issues associated with conventional compensation gene therapy. Such strategies can also be repurposed to normalize gene expression changes that occur secondary to the genetic defect. Moreover, besides the genetic causes of IEMs, it is increasingly recognized that their clinical phenotypes are associated with epigenetic changes. Because epigenetic alterations are principally reversible, this may offer new opportunities for treatment of IEM patients. Here, we present an overview of the promises of epigenetics in eventually treating IEMs. We discuss the concepts of gene and epigenetic editing, and the advantages and disadvantages of current and upcoming gene-based therapies for treatment of IEMs.
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Affiliation(s)
- Martijn G. S. Rutten
- Department of PediatricsUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Marianne G. Rots
- Department of Pathology and Medical BiologyUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
| | - Maaike H. Oosterveer
- Department of PediatricsUniversity of Groningen, University Medical Center GroningenGroningenThe Netherlands
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15
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Ganesan A, Arimondo PB, Rots MG, Jeronimo C, Berdasco M. The timeline of epigenetic drug discovery: from reality to dreams. Clin Epigenetics 2019; 11:174. [PMID: 31791394 PMCID: PMC6888921 DOI: 10.1186/s13148-019-0776-0] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/05/2019] [Indexed: 12/14/2022] Open
Abstract
The flexibility of the epigenome has generated an enticing argument to explore its reversion through pharmacological treatments as a strategy to ameliorate disease phenotypes. All three families of epigenetic proteins—readers, writers, and erasers—are druggable targets that can be addressed through small-molecule inhibitors. At present, a few drugs targeting epigenetic enzymes as well as analogues of epigenetic modifications have been introduced into the clinic use (e.g. to treat haematological malignancies), and a wide range of epigenetic-based drugs are undergoing clinical trials. Here, we describe the timeline of epigenetic drug discovery and development beginning with the early design based solely on phenotypic observations to the state-of-the-art rational epigenetic drug discovery using validated targets. Finally, we will highlight some of the major aspects that need further research and discuss the challenges that need to be overcome to implement epigenetic drug discovery into clinical management of human disorders. To turn into reality, researchers from various disciplines (chemists, biologists, clinicians) need to work together to optimise the drug engineering, read-out assays, and clinical trial design.
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Affiliation(s)
- A Ganesan
- School of Pharmacy, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Paola B Arimondo
- Epigenetic Chemical Biology, Institut Pasteur, CNRS UMR3523, 28 rue du Docteur Roux, 75724, Paris, France
| | - Marianne G Rots
- Epigenetic Editing, Dept. Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713, GZ, Groningen, The Netherlands
| | - Carmen Jeronimo
- Cancer Biology & Epigenetics Group, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - María Berdasco
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain. .,Epigenetic Therapies, Josep Carreras Leukaemia Research Institute (IJC), IJC Building, Campus ICO-Germans Trias i Pujol, Ctra de Can Ruti, Camí de les Escoles s/n 08916 Badalona, Barcelona, Catalonia, Spain.
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16
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Geersing A, de Vries RH, Jansen G, Rots MG, Roelfes G. Folic acid conjugates of a bleomycin mimic for selective targeting of folate receptor positive cancer cells. Bioorg Med Chem Lett 2019; 29:1922-1927. [DOI: 10.1016/j.bmcl.2019.05.047] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 10/26/2022]
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17
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Verkuijl SAN, Rots MG. The influence of eukaryotic chromatin state on CRISPR–Cas9 editing efficiencies. Curr Opin Biotechnol 2019; 55:68-73. [DOI: 10.1016/j.copbio.2018.07.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/15/2018] [Accepted: 07/22/2018] [Indexed: 12/14/2022]
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18
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Geersing A, Ségaud N, van der Wijst MGP, Rots MG, Roelfes G. Importance of Metal-Ion Exchange for the Biological Activity of Coordination Complexes of the Biomimetic Ligand N4Py. Inorg Chem 2018; 57:7748-7756. [PMID: 29916702 PMCID: PMC6030684 DOI: 10.1021/acs.inorgchem.8b00714] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Indexed: 12/24/2022]
Abstract
Metal coordination complexes can display interesting biological activity, as illustrated by the bleomycins (BLMs), a family of natural antibiotics that when coordinated to a redox-active metal ion, show antitumor activity. Yet, which metal ion is required for the activity in cells is still subject to debate. In this study, we described how different metal ions affect the intracellular behavior and activity of the synthetic BLM-mimic N, N-bis(2-pyridylmethyl)- N-bis(2-pyridyl)methylamine (N4Py). Our study shows that a mixture of iron(II), copper(II), and zinc(II) complexes can be generated when N4Py is added to cell cultures but that the metal ion can also be exchanged by other metal ions present in cells. Moreover, the combination of chemical data, together with the performed biological experiments, shows that the active complex causing oxidative damage to cells is the FeII-N4Py complex and not per se the metal complex that was initially added to the cell culture medium. Finally, it is proposed that the high activity observed upon the addition of the free N4Py ligand is the result of a combination of scavenging of biologically relevant metals and oxidative damage caused by the iron(II) complex.
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Affiliation(s)
- Arjan Geersing
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Nathalie Ségaud
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Monique G. P. van der Wijst
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Marianne G. Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute
for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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19
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Geel TM, Ruiters MHJ, Cool RH, Halby L, Voshart DC, Andrade Ruiz L, Niezen-Koning KE, Arimondo PB, Rots MG. The past and presence of gene targeting: from chemicals and DNA via proteins to RNA. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170077. [PMID: 29685979 PMCID: PMC5915719 DOI: 10.1098/rstb.2017.0077] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2017] [Indexed: 12/19/2022] Open
Abstract
The ability to target DNA specifically at any given position within the genome allows many intriguing possibilities and has inspired scientists for decades. Early gene-targeting efforts exploited chemicals or DNA oligonucleotides to interfere with the DNA at a given location in order to inactivate a gene or to correct mutations. We here describe an example towards correcting a genetic mutation underlying Pompe's disease using a nucleotide-fused nuclease (TFO-MunI). In addition to the promise of gene correction, scientists soon realized that genes could be inactivated or even re-activated without inducing potentially harmful DNA damage by targeting transcriptional modulators to a particular gene. However, it proved difficult to fuse protein effector domains to the first generation of programmable DNA-binding agents. The engineering of gene-targeting proteins (zinc finger proteins (ZFPs), transcription activator-like effectors (TALEs)) circumvented this problem. The disadvantage of protein-based gene targeting is that a fusion protein needs to be engineered for every locus. The recent introduction of CRISPR/Cas offers a flexible approach to target a (fusion) protein to the locus of interest using cheap designer RNA molecules. Many research groups now exploit this platform and the first human clinical trials have been initiated: CRISPR/Cas has kicked off a new era of gene targeting and is revolutionizing biomedical sciences.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- T M Geel
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - M H J Ruiters
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - R H Cool
- Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - L Halby
- CNRS FRE3600 ETaC, bât IBCG, 31062 Toulouse, France
| | - D C Voshart
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - L Andrade Ruiz
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - K E Niezen-Koning
- Laboratory of Metabolic Diseases, Dept Laboratory Medicine, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - P B Arimondo
- CNRS FRE3600 ETaC, bât IBCG, 31062 Toulouse, France
| | - M G Rots
- Epigenetic Editing, Dept Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
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20
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Liang ZL, Wu DD, Yao Y, Yu FY, Yang L, Tan HW, Hylkema MN, Rots MG, Xu YM, Lau ATY. Epiproteome profiling of cadmium-transformed human bronchial epithelial cells by quantitative histone post-translational modification-enzyme-linked immunosorbent assay. J Appl Toxicol 2018; 38:888-895. [PMID: 29423916 DOI: 10.1002/jat.3597] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/18/2017] [Accepted: 01/01/2018] [Indexed: 02/05/2023]
Abstract
Cadmium (Cd), a carcinogenic toxic metal, is pervasively distributed in the soil, water and air. Chronic exposure to Cd has been correlated to lung disease development including cancers. Although many studies have been conducted to investigate the proteome response of cells challenged with Cd, the epiproteomic responses (i.e., global histone post-translational modifications [PTMs]), particularly in human lung cells, are largely unexplored. Here, we provide an epiproteome profiling of human bronchial epithelial cells (BEAS-2B) chronically treated with cadmium chloride (CdCl2 ), with the aim of identifying global epiproteomic signatures in response to Cd epigenotoxicity. Total histone proteins from Cd-treated and untreated BEAS-2B cells were isolated and subject to quantitative histone PTM-enzyme-linked immunosorbent assay using 18 histone PTM antibodies. Our results unveiled that chronic Cd treatment led to the marked downregulation of H3K4me2 and H3K36me3 and upregulation of H3K9acS10ph, H4K5ac, H4K8ac and H4K12ac PTM marks. Cd-treated cells exhibit transformed cell properties as evidenced by enhanced cell migration and the ability of anchorage-independent growth on soft agar. Notably, treatment of Cd-transformed cells with C646, a potent histone acetyltransferase inhibitor, suppressed the expression of mesenchymal marker genes and cell migration ability of these cells. Taken together, our studies provide for the first time the global epiproteomic interrogation of chronic Cd-exposed human lung cells. The identified aberrant histone PTM alterations associated with Cd-induced epigenotoxicity likely account for the epithelial-mesenchymal transition and neoplastic survival of these cells.
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Affiliation(s)
- Zhan-Ling Liang
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, 515041, People's Republic of China
| | - Dan-Dan Wu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, 515041, People's Republic of China
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Yue Yao
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, 515041, People's Republic of China
| | - Fei-Yuan Yu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, 515041, People's Republic of China
| | - Lei Yang
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, 515041, People's Republic of China
| | - Heng Wee Tan
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, 515041, People's Republic of China
| | - Machteld N Hylkema
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marianne G Rots
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Yan-Ming Xu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, 515041, People's Republic of China
| | - Andy T Y Lau
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, 515041, People's Republic of China
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21
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Wu DD, Song J, Bartel S, Krauss-Etschmann S, Rots MG, Hylkema MN. The potential for targeted rewriting of epigenetic marks in COPD as a new therapeutic approach. Pharmacol Ther 2018; 182:1-14. [PMID: 28830839 DOI: 10.1016/j.pharmthera.2017.08.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is an age and smoking related progressive, pulmonary disorder presenting with poorly reversible airflow limitation as a result of chronic bronchitis and emphysema. The prevalence, disease burden for the individual, and mortality of COPD continues to increase, whereas no effective treatment strategies are available. For many years now, a combination of bronchodilators and anti-inflammatory corticosteroids has been most widely used for therapeutic management of patients with persistent COPD. However, this approach has had disappointing results as a large number of COPD patients are corticosteroid resistant. In patients with COPD, there is emerging evidence showing aberrant expression of epigenetic marks such as DNA methylation, histone modifications and microRNAs in blood, sputum and lung tissue. Therefore, novel therapeutic approaches may exist using epigenetic therapy. This review aims to describe and summarize current knowledge of aberrant expression of epigenetic marks in COPD. In addition, tools available for restoration of epigenetic marks are described, as well as delivery mechanisms of epigenetic editors to cells. Targeting epigenetic marks might be a very promising tool for treatment and lung regeneration in COPD in the future.
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Affiliation(s)
- Dan-Dan Wu
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands; Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, P.R. China
| | - Juan Song
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands; Tianjin Medical University, School of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Department of Immunology, Tianjin, China
| | - Sabine Bartel
- Early Life Origins of Chronic Lung Disease, Priority Area Asthma & Allergy, Leibnitz Center for Medicine and Biosciences, Research Center Borstel and Christian Albrechts University Kiel; Airway Research Center North, member of the German Center for Lung Research (DZL), Germany
| | - Susanne Krauss-Etschmann
- Early Life Origins of Chronic Lung Disease, Priority Area Asthma & Allergy, Leibnitz Center for Medicine and Biosciences, Research Center Borstel and Christian Albrechts University Kiel; Airway Research Center North, member of the German Center for Lung Research (DZL), Germany
| | - Marianne G Rots
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - Machteld N Hylkema
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands; University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, The Netherlands.
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22
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Abstract
Epigenetic editing is a promising approach to modulate the local chromatin environment of target genes with the ultimate goal of stable gene expression reprogramming. Epigenetic editing tools minimally consist of a DNA-binding domain and an effector domain. The CRISPR/dCas9 platform, where mutations in the nuclease domains render the Cas9 protein inactive, is widely used to guide epigenetic effectors to their intended genomic loci. Its flexible nature, simple use, and relatively low cost have revolutionized the research field of epigenetic editing. Although effective expression modulation is readily achieved, only a few studies have addressed the maintenance of the induced effects on endogenous loci. Here, we describe a detailed protocol to engineer cells that stably express the CRISPR/dCas9-effectors. The protocol involves modification of published dCas9-based plasmid vectors for easy transfer of the effector domain between the vector designed for transient transfection and the vector used for establishing cell lines stably expressing the dCas9-effector fusion protein. Transient transfection of the dCas9-effector-producing cells with sgRNA-expressing plasmids allows studying of the maintenance of epigenetic editing. Targeting various genes in different chromatin contexts and/or co-targeting multiple CRISPR/dCas9-effectors can be used to unravel rules underlying maintained gene expression reprogramming.
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Affiliation(s)
- Désirée Goubert
- Epigenetic Editing, Department of Pathology and Medical Biology, University of Groningen, University Medical CenterGroningen, Groningen, The Netherlands
| | - Mihály Koncz
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Antal Kiss
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Marianne G Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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23
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24
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Bustos FJ, Ampuero E, Jury N, Aguilar R, Falahi F, Toledo J, Ahumada J, Lata J, Cubillos P, Henríquez B, Guerra MV, Stehberg J, Neve RL, Inestrosa NC, Wyneken U, Fuenzalida M, Härtel S, Sena-Esteves M, Varela-Nallar L, Rots MG, Montecino M, van Zundert B. Epigenetic editing of the Dlg4/PSD95 gene improves cognition in aged and Alzheimer's disease mice. Brain 2017; 140:3252-3268. [PMID: 29155979 DOI: 10.1093/brain/awx272] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/27/2017] [Indexed: 12/31/2022] Open
Abstract
The Dlg4 gene encodes for post-synaptic density protein 95 (PSD95), a major synaptic protein that clusters glutamate receptors and is critical for plasticity. PSD95 levels are diminished in ageing and neurodegenerative disorders, including Alzheimer's disease and Huntington's disease. The epigenetic mechanisms that (dys)regulate transcription of Dlg4/PSD95, or other plasticity genes, are largely unknown, limiting the development of targeted epigenome therapy. We analysed the Dlg4/PSD95 epigenetic landscape in hippocampal tissue and designed a Dlg4/PSD95 gene-targeting strategy: a Dlg4/PSD95 zinc finger DNA-binding domain was engineered and fused to effector domains to either repress (G9a, Suvdel76, SKD) or activate (VP64) transcription, generating artificial transcription factors or epigenetic editors (methylating H3K9). These epi-editors altered critical histone marks and subsequently Dlg4/PSD95 expression, which, importantly, impacted several hippocampal neuron plasticity processes. Intriguingly, transduction of the artificial transcription factor PSD95-VP64 rescued memory deficits in aged and Alzheimer's disease mice. Conclusively, this work validates PSD95 as a key player in memory and establishes epigenetic editing as a potential therapy to treat human neurological disorders.
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Affiliation(s)
- Fernando J Bustos
- Center for Biomedical Research, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Avenida Republica 217, Santiago, Chile.,FONDAP Center for Genome Regulation, Chile
| | - Estibaliz Ampuero
- Center for Biomedical Research, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Avenida Republica 217, Santiago, Chile
| | - Nur Jury
- Center for Biomedical Research, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Avenida Republica 217, Santiago, Chile
| | - Rodrigo Aguilar
- Center for Biomedical Research, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Avenida Republica 217, Santiago, Chile.,FONDAP Center for Genome Regulation, Chile
| | - Fahimeh Falahi
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jorge Toledo
- Anatomy and Developmental Biology, SCIAN-Lab, Institute of Biomedical Sciences, Biomedical Neuroscience Institute, Center for Medical Informatics and Telemedicine CIMT, National Center for Health Information Systems CENS, Santiago, Chile.,Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Juan Ahumada
- Centro de Neurobiología y Plasticidad Cerebral, Departamento de Fisiología, Facultad de Ciencias, Universidad Valparaíso, Chile
| | - Jaclyn Lata
- Department of Neurology and Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - Paula Cubillos
- Center for Biomedical Research, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Avenida Republica 217, Santiago, Chile
| | - Berta Henríquez
- Center for Biomedical Research, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Avenida Republica 217, Santiago, Chile
| | - Miguel V Guerra
- Center for Biomedical Research, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Avenida Republica 217, Santiago, Chile
| | - Jimmy Stehberg
- Center for Biomedical Research, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Avenida Republica 217, Santiago, Chile
| | - Rachael L Neve
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Nibaldo C Inestrosa
- CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Chile
| | - Ursula Wyneken
- Laboratorio de Neurociencias, Universidad de Los Andes, Santiago, Chile
| | - Marco Fuenzalida
- Centro de Neurobiología y Plasticidad Cerebral, Departamento de Fisiología, Facultad de Ciencias, Universidad Valparaíso, Chile
| | - Steffen Härtel
- Anatomy and Developmental Biology, SCIAN-Lab, Institute of Biomedical Sciences, Biomedical Neuroscience Institute, Center for Medical Informatics and Telemedicine CIMT, National Center for Health Information Systems CENS, Santiago, Chile.,Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Miguel Sena-Esteves
- Department of Neurology and Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lorena Varela-Nallar
- Center for Biomedical Research, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Avenida Republica 217, Santiago, Chile
| | - Marianne G Rots
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Martin Montecino
- Center for Biomedical Research, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Avenida Republica 217, Santiago, Chile.,FONDAP Center for Genome Regulation, Chile
| | - Brigitte van Zundert
- Center for Biomedical Research, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Avenida Republica 217, Santiago, Chile
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25
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Cano-Rodriguez D, Campagnoli S, Grandi A, Parri M, Camilli ED, Song C, Jin B, Lacombe A, Pierleoni A, Bombaci M, Cordiglieri C, Ruiters MH, Viale G, Terracciano L, Sarmientos P, Abrignani S, Grandi G, Pileri P, Rots MG, Grifantini R. TCTN2: a novel tumor marker with oncogenic properties. Oncotarget 2017; 8:95256-95269. [PMID: 29221125 PMCID: PMC5707019 DOI: 10.18632/oncotarget.20438] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 07/25/2017] [Indexed: 12/21/2022] Open
Abstract
Tectonic family member 2 (TCTN2) encodes a transmembrane protein that belongs to the tectonic family, which is involved in ciliary functions. Previous studies have demonstrated the role of tectonics in regulating a variety of signaling pathways at the transition zone of cilia. However, the role of tectonics in cancer is still unclear. Here we identify that TCTN2 is overexpressed in colorectal, lung and ovary cancers. We show that different cancer cell lines express the protein that localizes at the plasma membrane, facing the intracellular milieu. TCTN2 over-expression in cancer cells resulted in an increased ability to form colonies in an anchorage independent way. On the other hand, downregulation of TCTN2 using targeted epigenetic editing in cancer cells significantly reduced colony formation, cell invasiveness, increased apoptosis and impaired assembly of primary cilia. Taken together, our results indicate that TCTN2 acts as an oncogene, making it an interesting cancer-associated protein and a potential candidate for therapeutic applications.
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Affiliation(s)
- David Cano-Rodriguez
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center, Groningen, The Netherlands
| | | | | | | | - Elisa De Camilli
- Department of Pathology, European Institute of Oncology, Milan, Italy
| | - Chaojun Song
- Department of Immunology, The Fourth Military Medical University, Xi'an, China
| | - Boquan Jin
- Department of Immunology, The Fourth Military Medical University, Xi'an, China
| | - Aurelien Lacombe
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Andrea Pierleoni
- Externautics SpA, Siena, Italy.,Present affiliation: European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Mauro Bombaci
- Istituto Nazionale Genetica Molecolare, Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Chiara Cordiglieri
- Istituto Nazionale Genetica Molecolare, Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Marcel Hj Ruiters
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Giuseppe Viale
- Department of Pathology, European Institute of Oncology, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Luigi Terracciano
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Sergio Abrignani
- Istituto Nazionale Genetica Molecolare, Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Guido Grandi
- Centre for Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | | | - Marianne G Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Renata Grifantini
- Externautics SpA, Siena, Italy.,Istituto Nazionale Genetica Molecolare, Padiglione Romeo ed Enrica Invernizzi, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
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26
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Hensel KO, Rendon JC, Navas MC, Rots MG, Postberg J. Virus-host interplay in hepatitis B virus infection and epigenetic treatment strategies. FEBS J 2017; 284:3550-3572. [PMID: 28457020 DOI: 10.1111/febs.14094] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/25/2017] [Accepted: 04/26/2017] [Indexed: 12/11/2022]
Abstract
Worldwide, chronic hepatitis B virus (HBV) infection is a major health problem and no cure exists. Importantly, hepatocyte intrusion by HBV particles results in a complex deregulation of both viral and host cellular genetic and epigenetic processes. Among the attempts to develop novel therapeutic approaches against HBV infection, several options targeting the epigenomic regulation of HBV replication are gaining attention. These include the experimental treatment with 'epidrugs'. Moreover, as a targeted approach, the principle of 'epigenetic editing' recently is being exploited to control viral replication. Silencing of HBV by specific rewriting of epigenetic marks might diminish viral replication, viremia, and infectivity, eventually controlling the disease and its complications. Additionally, epigenetic editing can be used as an experimental tool to increase our limited understanding regarding the role of epigenetic modifications in viral infections. Aiming for permanent epigenetic reprogramming of the viral genome without unspecific side effects, this breakthrough may pave the roads for an ambitious technological pursuit: to start designing a curative approach utilizing manipulative molecular therapies for viral infections in vivo.
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Affiliation(s)
- Kai O Hensel
- HELIOS Medical Centre Wuppertal, Paediatrics Centre, Centre for Clinical & Translational Research (CCTR), Faculty of Health, Centre for Biomedical Education & Research (ZBAF), Witten/Herdecke University, Germany
| | - Julio C Rendon
- Epigenetic Editing, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), The Netherlands.,Grupo de Gastrohepatologia, Facultad de Medicina, Universidad de Antioquia (UdeA), Medellin, Colombia
| | - Maria-Cristina Navas
- Grupo de Gastrohepatologia, Facultad de Medicina, Universidad de Antioquia (UdeA), Medellin, Colombia
| | - Marianne G Rots
- Epigenetic Editing, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), The Netherlands
| | - Jan Postberg
- HELIOS Medical Centre Wuppertal, Paediatrics Centre, Centre for Clinical & Translational Research (CCTR), Faculty of Health, Centre for Biomedical Education & Research (ZBAF), Witten/Herdecke University, Germany
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27
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Song J, Heijink IH, Kistemaker LEM, Reinders-Luinge M, Kooistra W, Noordhoek JA, Gosens R, Brandsma CA, Timens W, Hiemstra PS, Rots MG, Hylkema MN. Aberrant DNA methylation and expression of SPDEF and FOXA2 in airway epithelium of patients with COPD. Clin Epigenetics 2017; 9:42. [PMID: 28450970 PMCID: PMC5404321 DOI: 10.1186/s13148-017-0341-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 04/12/2017] [Indexed: 12/20/2022] Open
Abstract
Background Goblet cell metaplasia, a common feature of chronic obstructive pulmonary disease (COPD), is associated with mucus hypersecretion which contributes to the morbidity and mortality among patients. Transcription factors SAM-pointed domain-containing Ets-like factor (SPDEF) and forkhead box protein A2 (FOXA2) regulate goblet cell differentiation. This study aimed to (1) investigate DNA methylation and expression of SPDEF and FOXA2 during goblet cell differentiation and (2) compare this in airway epithelial cells from patients with COPD and controls during mucociliary differentiation. Methods To assess DNA methylation and expression of SPDEF and FOXA2 during goblet cell differentiation, primary airway epithelial cells, isolated from trachea (non-COPD controls) and bronchial tissue (patients with COPD), were differentiated by culture at the air-liquid interface (ALI) in the presence of cytokine interleukin (IL)-13 to promote goblet cell differentiation. Results We found that SPDEF expression was induced during goblet cell differentiation, while FOXA2 expression was decreased. Importantly, CpG number 8 in the SPDEF promoter was hypermethylated upon differentiation, whereas DNA methylation of FOXA2 promoter was not changed. In the absence of IL-13, COPD-derived ALI-cultured cells displayed higher SPDEF expression than control-derived ALI cultures, whereas no difference was found for FOXA2 expression. This was accompanied with hypomethylation of CpG number 6 in the SPDEF promoter and also hypomethylation of CpG numbers 10 and 11 in the FOXA2 promoter. Conclusions These findings suggest that aberrant DNA methylation of SPDEF and FOXA2 is one of the factors underlying mucus hypersecretion in COPD, opening new avenues for epigenetic-based inhibition of mucus hypersecretion. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0341-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J Song
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - I H Heijink
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - L E M Kistemaker
- GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands
| | - M Reinders-Luinge
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - W Kooistra
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - J A Noordhoek
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - R Gosens
- GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands
| | - C A Brandsma
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - W Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - P S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - M G Rots
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - M N Hylkema
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Pathology and Medical Biology EA10, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
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Nolte IM, van der Most PJ, Alizadeh BZ, de Bakker PI, Boezen HM, Bruinenberg M, Franke L, van der Harst P, Navis G, Postma DS, Rots MG, Stolk RP, Swertz MA, Wolffenbuttel BH, Wijmenga C, Snieder H. Missing heritability: is the gap closing? An analysis of 32 complex traits in the Lifelines Cohort Study. Eur J Hum Genet 2017; 25:877-885. [PMID: 28401901 DOI: 10.1038/ejhg.2017.50] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 02/03/2017] [Accepted: 02/14/2017] [Indexed: 01/08/2023] Open
Abstract
Despite the recent explosive rise in number of genetic markers for complex disease traits identified in genome-wide association studies, there is still a large gap between the known heritability of these traits and the part explained by these markers. To gauge whether this 'heritability gap' is closing, we first identified genome-wide significant SNPs from the literature and performed replication analyses for 32 highly relevant traits from five broad disease areas in 13 436 subjects of the Lifelines Cohort. Next, we calculated the variance explained by multi-SNP genetic risk scores (GRSs) for each trait, and compared it to their broad- and narrow-sense heritabilities captured by all common SNPs. The majority of all previously-associated SNPs (median=75%) were significantly associated with their respective traits. All GRSs were significant, with unweighted GRSs generally explaining less phenotypic variance than weighted GRSs, for which the explained variance was highest for height (15.5%) and varied between 0.02 and 6.7% for the other traits. Broad-sense common-SNP heritability estimates were significant for all traits, with the additive effect of common SNPs explaining 48.9% of the variance for height and between 5.6 and 39.2% for the other traits. Dominance effects were uniformly small (0-1.5%) and not significant. On average, the variance explained by the weighted GRSs accounted for only 10.7% of the common-SNP heritability of the 32 traits. These results indicate that GRSs may not yet be ready for accurate personalized prediction of complex disease traits limiting widespread adoption in clinical practice.
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Affiliation(s)
- Ilja M Nolte
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter J van der Most
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Behrooz Z Alizadeh
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Paul Iw de Bakker
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - H Marike Boezen
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerjan Navis
- Department of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dirkje S Postma
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marianne G Rots
- Department of Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ronald P Stolk
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Bruce Hr Wolffenbuttel
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Harold Snieder
- Unit of Genetic Epidemiology and Bioinformatics, Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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30
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31
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Song J, Cano-Rodriquez D, Winkle M, Gjaltema RAF, Goubert D, Jurkowski TP, Heijink IH, Rots MG, Hylkema MN. Targeted epigenetic editing of SPDEF reduces mucus production in lung epithelial cells. Am J Physiol Lung Cell Mol Physiol 2016; 312:L334-L347. [PMID: 28011616 DOI: 10.1152/ajplung.00059.2016] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 12/20/2016] [Accepted: 12/20/2016] [Indexed: 11/22/2022] Open
Abstract
Airway mucus hypersecretion contributes to the morbidity and mortality in patients with chronic inflammatory lung diseases. Reducing mucus production is crucial for improving patients' quality of life. The transcription factor SAM-pointed domain-containing Ets-like factor (SPDEF) plays a critical role in the regulation of mucus production and, therefore, represents a potential therapeutic target. This study aims to reduce lung epithelial mucus production by targeted silencing SPDEF using the novel strategy, epigenetic editing. Zinc fingers and CRISPR/dCas platforms were engineered to target repressors (KRAB, DNA methyltransferases, histone methyltransferases) to the SPDEF promoter. All constructs were able to effectively suppress both SPDEF mRNA and protein expression, which was accompanied by inhibition of downstream mucus-related genes [anterior gradient 2 (AGR2), mucin 5AC (MUC5AC)]. For the histone methyltransferase G9A, and not its mutant or other effectors, the obtained silencing was mitotically stable. These results indicate efficient SPDEF silencing and downregulation of mucus-related gene expression by epigenetic editing, in human lung epithelial cells. This opens avenues for epigenetic editing as a novel therapeutic strategy to induce long-lasting mucus inhibition.
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Affiliation(s)
- Juan Song
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,Tianjin Medical University, School of Basic Medical Sciences, Department of Biochemistry and Molecular Biology, Department of Immunology, Tianjin, China; and
| | - David Cano-Rodriquez
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - Melanie Winkle
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - Rutger A F Gjaltema
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - Désirée Goubert
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - Tomasz P Jurkowski
- Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Stuttgart, Germany
| | - Irene H Heijink
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Marianne G Rots
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands
| | - Machteld N Hylkema
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, The Netherlands; .,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
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Affiliation(s)
- Lucia Altucci
- Seconda Università degli Studi di Napoli, Dipartimento di Biochimica, Biofisica e Patologia generale, Vico L. De Crecchio 7, Napoli, 80138 Italy
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Huisman C, van der Wijst MGP, Schokker M, Blancafort P, Terpstra MM, Kok K, van der Zee AGJ, Schuuring E, Wisman GBA, Rots MG. Re-expression of Selected Epigenetically Silenced Candidate Tumor Suppressor Genes in Cervical Cancer by TET2-directed Demethylation. Mol Ther 2015; 24:536-47. [PMID: 26686387 DOI: 10.1038/mt.2015.226] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/11/2015] [Indexed: 12/18/2022] Open
Abstract
DNA hypermethylation is extensively explored as therapeutic target for gene expression modulation in cancer. Here, we re-activated hypermethylated candidate tumor suppressor genes (TSGs) (C13ORF18, CCNA1, TFPI2, and Maspin) by TET2-induced demethylation in cervical cancer cell lines. To redirect TET2 to hypermethylated TSGs, we engineered zinc finger proteins (ZFPs), which were first fused to the transcriptional activator VP64 to validate effective gene re-expression and confirm TSG function. ChIP-Seq not only revealed enriched binding of ZFPs to their intended sequence, but also considerable off-target binding, especially at promoter regions. Nevertheless, results obtained by targeted re-expression using ZFP-VP64 constructs were in line with cDNA overexpression; both revealed strong growth inhibition for C13ORF18 and TFPI2, but not for CCNA1 and Maspin. To explore effectivity of locus-targeted demethylation, ZFP-TET2 fusions were constructed which efficiently demethylated genes with subsequent gene re-activation. Moreover, targeting TET2 to TFPI2 and C13ORF18, but not CCNA1, significantly decreased cell growth, viability, and colony formation in cervical cancer cells compared to a catalytically inactive mutant of TET2. These data underline that effective re-activation of hypermethylated genes can be achieved through targeted DNA demethylation by TET2, which can assist in realizing sustained re-expression of genes of interest.
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Affiliation(s)
- Christian Huisman
- Department of Pathology and Medical Biology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands.,Current address: Department of Pediatrics, Oregon Health and Science University, Portland, Oregon, USA
| | - Monique G P van der Wijst
- Department of Pathology and Medical Biology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Matthijs Schokker
- Department of Pathology and Medical Biology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Pilar Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute for Medical Research, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Martijn M Terpstra
- Department of Genetics, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Klaas Kok
- Department of Genetics, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Ate G J van der Zee
- Department of Gynecological Oncology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - G Bea A Wisman
- Department of Gynecological Oncology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Marianne G Rots
- Department of Pathology and Medical Biology, University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
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Gjaltema RAF, de Rond S, Rots MG, Bank RA. Procollagen Lysyl Hydroxylase 2 Expression Is Regulated by an Alternative Downstream Transforming Growth Factor β-1 Activation Mechanism. J Biol Chem 2015; 290:28465-28476. [PMID: 26432637 DOI: 10.1074/jbc.m114.634311] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Indexed: 11/06/2022] Open
Abstract
PLOD2 (procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2) hydroxylates lysine residues in collagen telopeptides and is essential for collagen pyridinoline cross-link formation. PLOD2 expression and subsequent pyridinoline cross-links are increased in fibrotic pathologies by transforming growth factor β-1 (TGFβ1). In this report we examined the molecular processes underlying TGFβ1-induced PLOD2 expression. We found that binding of the TGFβ1 pathway related transcription factors SMAD3 and SP1-mediated TGFβ1 enhanced PLOD2 expression and could be correlated to an increase of acetylated histone H3 and H4 at the PLOD2 promoter. Interestingly, the classical co-activators of SMAD3 complexes, p300 and CBP, were not responsible for the enhanced H3 and H4 acetylation. Depletion of SMAD3 reduced PLOD2 acetylated H3 and H4, indicating that another as of yet unidentified histone acetyltransferase binds to SMAD3 at PLOD2. Assessing histone methylation marks at the PLOD2 promoter depicted an increase of the active histone mark H3K79me2, a decrease of the repressive H4K20me3 mark, but no role for the generally strong transcription-related modifications: H3K4me3, H3K9me3 and H3K27me3. Collectively, our findings reveal that TGFβ1 induces a SP1- and SMAD3-dependent recruitment of histone modifying enzymes to the PLOD2 promoter other than the currently known TGFβ1 downstream co-activators and epigenetic modifications. This also suggests that additional activation strategies are used downstream of the TGFβ1 pathway, and hence their unraveling could be of great importance to fully understand TGFβ1 activation of genes.
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Affiliation(s)
- Rutger A F Gjaltema
- MATRIX Research Group, Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; Epigenetic Editing Research Group, Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Saskia de Rond
- MATRIX Research Group, Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Marianne G Rots
- Epigenetic Editing Research Group, Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Ruud A Bank
- MATRIX Research Group, Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands.
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Abstract
Despite decades of research, mitochondrial epigenetics remains a controversial notion. Recent findings, however, indicate that dysfunctional mitochondrial DNA (mtDNA) methylation could underlie aging and disease. Unraveling such a level of regulation will be essential in the understanding of and in interfering with the role of mitochondria in many physiological and pathophysiological processes.
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Affiliation(s)
- Monique G P van der Wijst
- Epigenetic Editing, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Marianne G Rots
- Epigenetic Editing, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Hanzeplein 1, 9713 GZ Groningen, The Netherlands.
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36
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Huisman C, van der Wijst MGP, Falahi F, Overkamp J, Karsten G, Terpstra MM, Kok K, van der Zee AGJ, Schuuring E, Wisman GBA, Rots MG. Prolonged re-expression of the hypermethylated gene EPB41L3 using artificial transcription factors and epigenetic drugs. Epigenetics 2015; 10:384-96. [PMID: 25830725 DOI: 10.1080/15592294.2015.1034415] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Epigenetic silencing of tumor suppressor genes (TSGs) is considered a significant event in the progression of cancer. For example, EPB41L3, a potential biomarker in cervical cancer, is often silenced by cancer-specific promoter methylation. Artificial transcription factors (ATFs) are unique tools to re-express such silenced TSGs to functional levels; however, the induced effects are considered transient. Here, we aimed to improve the efficiency and sustainability of gene re-expression using engineered zinc fingers fused to VP64 (ZF-ATFs) or DNA methylation modifiers (ZF-Tet2 or ZF-TDG) and/or by co-treatment with epigenetic drugs [5-aza-2'-deoxycytidine or Trichostatin A (TSA)]. The EPB41L3-ZF effectively bound its methylated endogenous locus, as also confirmed by ChIP-seq. ZF-ATFs reactivated the epigenetically silenced target gene EPB41L3 (∼ 10-fold) in breast, ovarian, and cervical cancer cell lines. Prolonged high levels of EPB41L3 (∼ 150-fold) induction could be achieved by short-term co-treatment with epigenetic drugs. Interestingly, for otherwise ineffective ZF-Tet2 or ZF-TDG treatments, TSA facilitated re-expression of EPB41L3 up to twofold. ATF-mediated re-expression demonstrated a tumor suppressive role for EPB41L3 in cervical cancer cell lines. In conclusion, epigenetic reprogramming provides a novel way to improve sustainability of re-expression of epigenetically silenced promoters.
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van der Wijst MGP, Huisman C, Mposhi A, Roelfes G, Rots MG. Targeting Nrf2 in healthy and malignant ovarian epithelial cells: Protection versus promotion. Mol Oncol 2015; 9:1259-73. [PMID: 25841766 DOI: 10.1016/j.molonc.2015.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 03/09/2015] [Accepted: 03/11/2015] [Indexed: 12/30/2022] Open
Abstract
Risk factors indicate the importance of oxidative stress during ovarian carcinogenesis. To tolerate oxidative stress, cells activate the transcription factor Nrf2 (Nfe2l2), the master regulator of antioxidant and cytoprotective genes. Indeed, for most cancers, hyperactivity of Nrf2 is observed, and siRNA studies assigned Nrf2 as therapeutic target. However, the cancer-protective role of Nrf2 in healthy cells highlights the requirement for an adequate therapeutic window. We engineered artificial transcription factors to assess the role of Nrf2 in healthy (OSE-C2) and malignant ovarian cells (A2780). Successful NRF2 up- and downregulation correlated with decreased, respectively increased, sensitivity toward oxidative stress. Inhibition of NRF2 reduced the colony forming potential to the same extent in wild-type and BRCA1 knockdown A2780 cells. Only in BRCA1 knockdown A2780 cells, the effect of Nrf2 inhibition could be enhanced when combined with PARP inhibitors. Therefore, we propose that this combination therapy of PARP inhibitors and Nrf2 inhibition can further improve treatment efficacy specifically in BRCA1 mutant cancer cells without acquiring the side-effects associated with previously studied Nrf2 inhibition combinations with either chemotherapy or radiation. Our findings stress the dual role of Nrf2 in carcinogenesis, while offering approaches to exploit Nrf2 as a potent therapeutic target in ovarian cancer.
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Affiliation(s)
- Monique G P van der Wijst
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Hanzeplein 1 9713 GZ Groningen, The Netherlands.
| | - Christian Huisman
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Hanzeplein 1 9713 GZ Groningen, The Netherlands.
| | - Archibold Mposhi
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Hanzeplein 1 9713 GZ Groningen, The Netherlands.
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
| | - Marianne G Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Hanzeplein 1 9713 GZ Groningen, The Netherlands.
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van der Wijst MGP, Venkiteswaran M, Chen H, Xu GL, Plösch T, Rots MG. Local chromatin microenvironment determines DNMT activity: from DNA methyltransferase to DNA demethylase or DNA dehydroxymethylase. Epigenetics 2015; 10:671-6. [PMID: 26098813 PMCID: PMC4622917 DOI: 10.1080/15592294.2015.1062204] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 06/03/2015] [Accepted: 06/09/2015] [Indexed: 12/22/2022] Open
Abstract
Insights on active DNA demethylation disproved the original assumption that DNA methylation is a stable epigenetic modification. Interestingly, mammalian DNA methyltransferases 3A and 3B (DNMT-3A and -3B) have also been reported to induce active DNA demethylation, in addition to their well-known function in catalyzing methylation. In situations of extremely low levels of S-adenosyl methionine (SAM), DNMT-3A and -3B might demethylate C-5 methyl cytosine (5mC) via deamination to thymine, which is subsequently replaced by an unmodified cytosine through the base excision repair (BER) pathway. Alternatively, 5mC when converted to 5- hydroxymethylcytosine (5hmC) by TET enzymes, might be further modified to an unmodified cytosine by DNMT-3A and -3B under oxidized redox conditions, although exact pathways are yet to be elucidated. Interestingly, even direct conversion of 5mC to cytosine might be catalyzed by DNMTs. Here, we summarize the evidence on the DNA dehydroxymethylase and demethylase activity of DNMT-3A and -3B. Although physiological relevance needs to be demonstrated, the current indications on the 5mC- and 5hmC-modifying activities of de novo DNA C-5 methyltransferases shed a new light on these enzymes. Despite the extreme circumstances required for such unexpected reactions to occur, we here put forward that the chromatin microenvironment can be locally exposed to extreme conditions, and hypothesize that such waves of extremes allow enzymes to act in differential ways.
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Key Words
- 5caC, 5-carboxylcytosine
- 5fC, 5-formylcytosine
- 5hmC, 5 hydroxymethylcytosine
- 5mC, 5-methylcytosine
- AID, activation-induced cytidine deaminase
- APOBEC, apolipoprotein B mRNA editing enzyme catalytic polypeptide-like
- BER, base excision and repair
- C, cytosine
- CGI, CpG islands
- DNA dehydroxymethylation
- DNA demethylation
- DNMT, DNA methyltransferase
- DNMTs
- GADD45, growth arrest and DNA-damage-inducible protein 45
- RARE, retinoic acid response element
- S-adenosyl methionine (SAM)
- SAM, S-adenosyl methionine
- TDG, thymine DNA glycosylase
- TET, ten-eleven translocation.
- chromatin microenvironment
- oxidizing redox state
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Affiliation(s)
- Monique G P van der Wijst
- Epigenetic Editing; Department of Pathology and Medical Biology; University Medical Center Groningen; University of Groningen; Groningen, The Netherlands
| | - Muralidhar Venkiteswaran
- Epigenetic Editing; Department of Pathology and Medical Biology; University Medical Center Groningen; University of Groningen; Groningen, The Netherlands
| | - Hui Chen
- Epigenetic Editing; Department of Pathology and Medical Biology; University Medical Center Groningen; University of Groningen; Groningen, The Netherlands
- Group of DNA Metabolism; The State Key Laboratory of Molecular Biology; Institute of Biochemistry and Cell Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai, China
| | - Guo-Liang Xu
- Group of DNA Metabolism; The State Key Laboratory of Molecular Biology; Institute of Biochemistry and Cell Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai, China
| | - Torsten Plösch
- Department of Obstetrics and Gynecology; University Medical Center Groningen; University of Groningen; Groningen, The Netherlands
| | - Marianne G Rots
- Epigenetic Editing; Department of Pathology and Medical Biology; University Medical Center Groningen; University of Groningen; Groningen, The Netherlands
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Dekker AD, De Deyn PP, Rots MG. Epigenetics: The neglected key to minimize learning and memory deficits in Down syndrome. Neurosci Biobehav Rev 2014; 45:72-84. [DOI: 10.1016/j.neubiorev.2014.05.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/04/2014] [Accepted: 05/13/2014] [Indexed: 10/25/2022]
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Falahi F, van Kruchten M, Martinet N, Hospers GAP, Rots MG. Current and upcoming approaches to exploit the reversibility of epigenetic mutations in breast cancer. Breast Cancer Res 2014; 16:412. [PMID: 25410383 PMCID: PMC4303227 DOI: 10.1186/s13058-014-0412-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 07/11/2014] [Indexed: 01/02/2023] Open
Abstract
DNA methylation and histone modifications are important epigenetic modifications associated with gene (dys)regulation. The epigenetic modifications are balanced by epigenetic enzymes, so-called writers and erasers, such as DNA (de)methylases and histone (de)acetylases. Aberrant epigenetic alterations have been associated with various diseases, including breast cancer. Since aberrant epigenetic modifications are potentially reversible, they might represent targets for breast cancer therapy. Indeed, several drugs have been designed to inhibit epigenetic enzymes (epi-drugs), thereby reversing epigenetic modifications. US Food and Drug Administration approval has been obtained for some epi-drugs for hematological malignancies. However, these drugs have had very modest anti-tumor efficacy in phase I and II clinical trials in breast cancer patients as monotherapy. Therefore, current clinical trials focus on the combination of epi-drugs with other therapies to enhance or restore the sensitivity to such therapies. This approach has yielded some promising results in early phase II trials. The disadvantage of epi-drugs, however, is genome-wide effects, which may cause unwanted upregulation of, for example, pro-metastatic genes. Development of gene-targeted epigenetic modifications (epigenetic editing) in breast cancer can provide a novel approach to prevent such unwanted events. In this context, identification of crucial epigenetic modifications regulating key genes in breast cancer is of critical importance. In this review, we first describe aberrant DNA methylation and histone modifications as two important classes of epigenetic mutations in breast cancer. Then we focus on the preclinical and clinical epigenetic-based therapies currently being explored for breast cancer. Finally, we describe epigenetic editing as a promising new approach for possible applications towards more targeted breast cancer treatment.
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Li Q, van der Wijst MG, Kazemier HG, Rots MG, Roelfes G. Efficient nuclear DNA cleavage in human cancer cells by synthetic bleomycin mimics. ACS Chem Biol 2014; 9:1044-51. [PMID: 24527883 DOI: 10.1021/cb500057n] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Iron complexes of N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)-methylamine (N4Py) have proven to be excellent synthetic mimics of the Bleomycins (BLMs), which are a family of natural antibiotics used clinically in the treatment of certain cancers. However, most investigations of DNA cleavage activity of these and related metal complexes were carried out in cell-free systems using plasmid DNA as substrate. The present study evaluated nuclear DNA cleavage activity and cell cytotoxicity of BLM and its synthetic mimics based on the ligand N4Py. The N4Py-based reagents induced nuclear DNA cleavage in living cells as efficiently as BLM and Fe(II)-BLM. Treatment of 2 cancer cell lines and 1 noncancerous cell line indicated improved cytotoxicity of N4Py when compared to BLM. Moreover, some level of selectivity was observed for N4Py on cancerous versus noncancerous cells. It was demonstrated that N4Py-based reagents and BLM induce cell death via different mechanistic pathways. BLM was shown to induce cell cycle arrest, ultimately resulting in mitotic catastrophe. In contrast, N4Py-based reagents were shown to induce apoptosis effectively. To the best of our knowledge, the present study is the first demonstration of efficient nuclear DNA cleavage activity of a synthetic BLM mimic within cells. The results presented here show that it is possible to design synthetic bioinorganic model complexes that are at least as active as the parent natural product and thereby are potentially interesting alternatives for BLM to induce antitumor activity.
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Affiliation(s)
- Qian Li
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Monique G.P. van der Wijst
- Department
of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713
GZ Groningen, The Netherlands
| | - Hinke G. Kazemier
- Department
of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713
GZ Groningen, The Netherlands
| | - Marianne G. Rots
- Department
of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713
GZ Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Chen H, Kazemier HG, de Groote ML, Ruiters MHJ, Xu GL, Rots MG. Induced DNA demethylation by targeting Ten-Eleven Translocation 2 to the human ICAM-1 promoter. Nucleic Acids Res 2013; 42:1563-74. [PMID: 24194590 PMCID: PMC3919596 DOI: 10.1093/nar/gkt1019] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Increasing evidence indicates that active DNA demethylation is involved in several processes in mammals, resulting in developmental stage-specificity and cell lineage-specificity. The recently discovered Ten-Eleven Translocation (TET) dioxygenases are accepted to be involved in DNA demethylation by initiating 5-mC oxidation. Aberrant DNA methylation profiles are associated with many diseases. For example in cancer, hypermethylation results in silencing of tumor suppressor genes. Such silenced genes can be re-expressed by epigenetic drugs, but this approach has genome-wide effects. In this study, fusions of designer DNA binding domains to TET dioxygenase family members (TET1, -2 or -3) were engineered to target epigenetically silenced genes (ICAM-1, EpCAM). The effects on targeted CpGs’ methylation and on expression levels of the target genes were assessed. The results indicated demethylation of targeted CpG sites in both promoters for targeted TET2 and to a lesser extent for TET1, but not for TET3. Interestingly, we observed re-activation of transcription of ICAM-1. Thus, our work suggests that we provided a mechanism to induce targeted DNA demethylation, which facilitates re-activation of expression of the target genes. Furthermore, this Epigenetic Editing approach is a powerful tool to investigate functions of epigenetic writers and erasers and to elucidate consequences of epigenetic marks.
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Affiliation(s)
- Hui Chen
- Epigenetic Editing, Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein1, 9713 GZ Groningen, The Netherlands, The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China and Synvolux Therapeutics Inc., LJ. Zielstraweg 1, 9713 GX Groningen, The Netherlands
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Rots MG, Petersen-Mahrt SK. The 2012 IMB Conference: DNA demethylation, repair and beyond. Institute of Molecular Biology, Mainz, Germany, 18-21 October 2012. Epigenomics 2013; 5:25-8. [PMID: 23414316 DOI: 10.2217/epi.12.73] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Headline-grabbing attention has been given to DNA demethylation pathways as new epigenetic mechanisms, with reviews and hypotheses outnumbering research papers. As candidate proteins for DNA demethylation include well-known DNA repair enzymes, it was timely to join epigenetics and DNA repair experts at the first international meeting on DNA Demethylation, Repair and Beyond. New mechanistic insights were presented for known players orchestrating the symphony on cytosine - 'the symphony on C' (TET1, 2, 3; GADD45; AID; and TDG), while new instruments and classical themes were pulled into the amalgamation. What may appear as just an unintentional cacophony of random oxidative lesions and abasic sites in a bed of chromatin noise may turn out to be a gene-expressing regulatory melody.
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Affiliation(s)
- Marianne G Rots
- Epigenetic Editing, Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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Falahi F, Huisman C, Kazemier HG, van der Vlies P, Kok K, Hospers GAP, Rots MG. Towards sustained silencing of HER2/neu in cancer by epigenetic editing. Mol Cancer Res 2013; 11:1029-39. [PMID: 23814024 DOI: 10.1158/1541-7786.mcr-12-0567] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
UNLABELLED The human epidermal growth factor receptor-2 (HER2/neu/ERBB2) is overexpressed in several cancer types. Although therapies targeting the HER2/neu protein result in inhibition of cell proliferation, the anticancer effect might be further optimized by limiting HER2/neu expression at the DNA level. Towards this aim, epigenetic editing was performed to suppress HER2/neu expression by inducing epigenetic silencing marks on the HER2/neu promoter.HER2/neu expression and HER2/neu promoter epigenetic modification status were determined in a panel of ovarian and breast cancer cell lines. HER2/neu-overexpressing cancer cells were transduced to express a zinc finger protein (ZFP), targeting the HER2/neugene, fused to histone methyltransferases (G9a, SUV39-H1)/super KRAB domain (SKD). Epigenetic assessment of the HER2/neu promoter showed that HER2/neu-ZFP fused to G9a efficiently induced the intended silencing histone methylation mark (H3K9me2). Importantly, H3K9me2 induction was associated with a dramatic downregulation of HER2/neu expression in HER2/neu- overexpressing cells. Downregulation by SKD, traditionally considered transient in nature, was associated with removal of the histone acetylation mark (H3ac). The downregulation of HER2/neu by induced H3K9 methylation and/or reduced H3 acetylation was sufficient to effectively inhibit cellular metabolic activity and clonogenicity. Furthermore, genome-wide analysis indicated preferential binding of the ZFP to its target sequence. These results not only show that H3K9 methylation can be induced but also that this epigenetic mark was instructive in promoting downregulation of HER2/neu expression. IMPLICATIONS Epigenetic editing provides a novel (synergistic) approach to modulate expression of oncogenes.
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Affiliation(s)
- Fahimeh Falahi
- University Medical Center Groningen, Groningen, 9713 GZ, the Netherlands.
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de Groote ML, Kazemier HG, Huisman C, van der Gun BT, Faas MM, Rots MG. Upregulation of endogenous ICAM-1 reduces ovarian cancer cell growth in the absence of immune cells. Int J Cancer 2013; 134:280-90. [DOI: 10.1002/ijc.28375] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 05/25/2013] [Accepted: 06/12/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Marloes L. de Groote
- Epigenetic Editing; Department of Pathology and Medical Biology; University Medical Center Groningen, University of Groningen; Groningen The Netherlands
| | - Hinke G. Kazemier
- Epigenetic Editing; Department of Pathology and Medical Biology; University Medical Center Groningen, University of Groningen; Groningen The Netherlands
| | - Christian Huisman
- Epigenetic Editing; Department of Pathology and Medical Biology; University Medical Center Groningen, University of Groningen; Groningen The Netherlands
| | - Bernardina T.F. van der Gun
- Epigenetic Editing; Department of Pathology and Medical Biology; University Medical Center Groningen, University of Groningen; Groningen The Netherlands
| | - Marijke M. Faas
- Immunoendocrinology; Department of Pathology and Medical Biology; University Medical Center Groningen, University of Groningen; Groningen The Netherlands
| | - Marianne G. Rots
- Epigenetic Editing; Department of Pathology and Medical Biology; University Medical Center Groningen, University of Groningen; Groningen The Netherlands
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Huisman C, Wisman GBA, Kazemier HG, van Vugt MATM, van der Zee AGJ, Schuuring E, Rots MG. Functional validation of putative tumor suppressor gene C13ORF18 in cervical cancer by Artificial Transcription Factors. Mol Oncol 2013; 7:669-79. [PMID: 23522960 DOI: 10.1016/j.molonc.2013.02.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 02/03/2013] [Accepted: 02/21/2013] [Indexed: 01/04/2023] Open
Abstract
C13ORF18 is frequently hypermethylated in cervical cancer but not in normal cervix and might serve as a biomarker for the early detection of cervical cancer in scrapings. As hypermethylation is often observed for silenced tumor suppressor genes (TSGs), hypermethylated biomarker genes might exhibit tumor suppressive activities upon re-expression. Epigenetic drugs are successfully exploited to reverse TSG silencing, but act genome-wide. Artificial Transcription Factors (ATFs) provide a gene-specific approach for re-expression of silenced genes. Here, we investigated the potential tumor suppressive role of C13ORF18 in cervical cancer by ATF-induced re-expression. Five zinc finger proteins were engineered to bind the C13ORF18 promoter and fused to a strong transcriptional activator. C13ORF18 expression could be induced in cervical cell lines: ranging from >40-fold in positive (C13ORF18-unmethylated) cells to >110-fold in negative (C13ORF18-methylated) cells. Re-activation of C13ORF18 resulted in significant cell growth inhibition and/or induction of apoptosis. Co-treatment of cell lines with ATFs and epigenetic drugs further enhanced the ATF-induced effects. Interestingly, re-activation of C13ORF18 led to partial demethylation of the C13ORF18 promoter and decreased repressive histone methylation. These data demonstrate the potency of ATFs to re-express and potentially demethylate hypermethylated silenced genes. Concluding, we show that C13ORF18 has a TSG function in cervical cancer and may serve as a therapeutic anti-cancer target. As the amount of epimutations in cancer exceeds the number of gene mutations, ATFs provide promising tools to validate hypermethylated marker genes as therapeutic targets.
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Affiliation(s)
- Christian Huisman
- Dept. of Pathology and Medical Biology, University Medical Centre Groningen (UMCG), University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands.
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Falahi F, Huisman C, Diaz EG, Kazemier HG, Hospers GAP, Rots MG. Gene specific overwriting of epigenetic signatures to modulate the expression of selected tumor-promoting genes in cancer. Epigenetics Chromatin 2013. [PMCID: PMC3600697 DOI: 10.1186/1756-8935-6-s1-p15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Siddique AN, Nunna S, Rajavelu A, Zhang Y, Jurkowska RZ, Reinhardt R, Rots MG, Ragozin S, Jurkowski TP, Jeltsch A. Targeted methylation and gene silencing of VEGF-A in human cells by using a designed Dnmt3a-Dnmt3L single-chain fusion protein with increased DNA methylation activity. J Mol Biol 2012; 425:479-91. [PMID: 23220192 DOI: 10.1016/j.jmb.2012.11.038] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 11/27/2012] [Accepted: 11/28/2012] [Indexed: 02/08/2023]
Abstract
The C-terminal domain of the Dnmt3a de novo DNA methyltransferase (Dnmt3a-C) forms a complex with the C-terminal domain of Dnmt3L, which stimulates its catalytic activity. We generated and characterized single-chain (sc) fusion proteins of both these domains with linker lengths between 16 and 30 amino acid residues. The purified sc proteins showed about 10-fold higher DNA methylation activities than Dnmt3a-C in vitro and were more active in bacterial cells as well. After fusing the Dnmt3a-3L sc enzyme to an artificial zinc-finger protein targeting the vascular endothelial cell growth factor A (VEGF-A) promoter, we demonstrate successful targeting of DNA methylation to the VEGF-A promoter in human cells and observed that almost complete methylation of 12 CpG sites in the gene promoter could be achieved. Targeted methylation by the Dnmt3a-3L sc enzymes was about twofold higher than that of Dnmt3a-C, indicating that Dnmt3a-3L sc variants are more efficient as catalytic modules in chimeric DNA methyltransfeases than Dnmt3a-C. Targeted methylation of the VEGF-A promoter with the Dnmt3a-3L sc variant led to a strong silencing of VEGF-A expression, indicating that the artificial DNA methylation of an endogenous promoter is a powerful strategy to achieve silencing of the corresponding gene in human cells.
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Affiliation(s)
- Abu Nasar Siddique
- Biochemistry Laboratory, School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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de Groote ML, Verschure PJ, Rots MG. Epigenetic Editing: targeted rewriting of epigenetic marks to modulate expression of selected target genes. Nucleic Acids Res 2012; 40:10596-613. [PMID: 23002135 PMCID: PMC3510492 DOI: 10.1093/nar/gks863] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Despite significant advances made in epigenetic research in recent decades, many questions remain unresolved, especially concerning cause and consequence of epigenetic marks with respect to gene expression modulation (GEM). Technologies allowing the targeting of epigenetic enzymes to predetermined DNA sequences are uniquely suited to answer such questions and could provide potent (bio)medical tools. Toward the goal of gene-specific GEM by overwriting epigenetic marks (Epigenetic Editing, EGE), instructive epigenetic marks need to be identified and their writers/erasers should then be fused to gene-specific DNA binding domains. The appropriate epigenetic mark(s) to change in order to efficiently modulate gene expression might have to be validated for any given chromatin context and should be (mitotically) stable. Various insights in such issues have been obtained by sequence-specific targeting of epigenetic enzymes, as is presented in this review. Features of such studies provide critical aspects for further improving EGE. An example of this is the direct effect of the edited mark versus the indirect effect of recruited secondary proteins by targeting epigenetic enzymes (or their domains). Proof-of-concept of expression modulation of an endogenous target gene is emerging from the few EGE studies reported. Apart from its promise in correcting disease-associated epi-mutations, EGE represents a powerful tool to address fundamental epigenetic questions.
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Affiliation(s)
- Marloes L de Groote
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1 EA11, 9713 GZ, Groningen, The Netherlands
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Stolzenburg S, Rots MG, Beltran AS, Rivenbark AG, Yuan X, Qian H, Strahl BD, Blancafort P. Targeted silencing of the oncogenic transcription factor SOX2 in breast cancer. Nucleic Acids Res 2012; 40:6725-40. [PMID: 22561374 PMCID: PMC3413152 DOI: 10.1093/nar/gks360] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The transcription factor (TF) SOX2 is essential for the maintenance of pluripotency and self-renewal in embryonic stem cells. In addition to its normal stem cell function, SOX2 over-expression is associated with cancer development. The ability to selectively target this and other oncogenic TFs in cells, however, remains a significant challenge due to the ‘undruggable’ characteristics of these molecules. Here, we employ a zinc finger (ZF)-based artificial TF (ATF) approach to selectively suppress SOX2 gene expression in cancer cells. We engineered four different proteins each composed of 6ZF arrays designed to bind 18 bp sites in the SOX2 promoter and enhancer region, which controls SOX2 methylation. The 6ZF domains were linked to the Kruppel Associated Box (SKD) repressor domain. Three engineered proteins were able to bind their endogenous target sites and effectively suppress SOX2 expression (up to 95% repression efficiencies) in breast cancer cells. Targeted down-regulation of SOX2 expression resulted in decreased tumor cell proliferation and colony formation in these cells. Furthermore, induced expression of an ATF in a mouse model inhibited breast cancer cell growth. Collectively, these findings demonstrate the effectiveness and therapeutic potential of engineered ATFs to mediate potent and long-lasting down-regulation of oncogenic TF expression in cancer cells.
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Affiliation(s)
- Sabine Stolzenburg
- Epigenetic Editing, Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
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