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Hsu E, Hutchison K, Liu Y, Nicolet CM, Schreiner S, Zemke N, Farnham P. Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters. Nucleic Acids Res 2024; 52:6850-6865. [PMID: 38726870 PMCID: PMC11229363 DOI: 10.1093/nar/gkae372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/21/2024] [Accepted: 04/25/2024] [Indexed: 07/09/2024] Open
Abstract
The ZFX transcriptional activator binds to CpG island promoters, with a major peak at ∼200-250 bp downstream from transcription start sites. Because ZFX binds within the transcribed region, we investigated whether it regulates transcriptional elongation. We used GRO-seq to show that loss or reduction of ZFX increased Pol2 pausing at ZFX-regulated promoters. To further investigate the mechanisms by which ZFX regulates transcription, we determined regions of the protein needed for transactivation and for recruitment to the chromatin. Interestingly, although ZFX has 13 grouped zinc fingers, deletion of the first 11 fingers produces a protein that can still bind to chromatin and activate transcription. We next used TurboID-MS to detect ZFX-interacting proteins, identifying ZNF593, as well as proteins that interact with the N-terminal transactivation domain (which included histone modifying proteins), and proteins that interact with ZFX when it is bound to the chromatin (which included TAFs and other histone modifying proteins). Our studies support a model in which ZFX enhances elongation at target promoters by recruiting H4 acetylation complexes and reducing pausing.
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Affiliation(s)
- Emily Hsu
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Katherine Hutchison
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Yao Liu
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Charles M Nicolet
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Shannon Schreiner
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Nathan R Zemke
- Department of Cellular and Molecular Medicine, UCSD School of Medicine, La Jolla, CA 92093, USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
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2
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Felipe Fumero E, Walter C, Frenz JM, Seifert F, Alla V, Hennig T, Angenendt L, Hartmann W, Wolf S, Serve H, Oellerich T, Lenz G, Müller-Tidow C, Schliemann C, Huber O, Dugas M, Mann M, Jayavelu AK, Mikesch JH, Arteaga MF. Epigenetic control over the cell-intrinsic immune response antagonizes self-renewal in acute myeloid leukemia. Blood 2024; 143:2284-2299. [PMID: 38457355 PMCID: PMC11181352 DOI: 10.1182/blood.2023021640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 02/16/2024] [Accepted: 02/18/2024] [Indexed: 03/10/2024] Open
Abstract
ABSTRACT Epigenetic modulation of the cell-intrinsic immune response holds promise as a therapeutic approach for leukemia. However, current strategies designed for transcriptional activation of endogenous transposons and subsequent interferon type-I (IFN-I) response, show limited clinical efficacy. Histone lysine methylation is an epigenetic signature in IFN-I response associated with suppression of IFN-I and IFN-stimulated genes, suggesting histone demethylation as key mechanism of reactivation. In this study, we unveil the histone demethylase PHF8 as a direct initiator and regulator of cell-intrinsic immune response in acute myeloid leukemia (AML). Site-specific phosphorylation of PHF8 orchestrates epigenetic changes that upregulate cytosolic RNA sensors, particularly the TRIM25-RIG-I-IFIT5 axis, thereby triggering the cellular IFN-I response-differentiation-apoptosis network. This signaling cascade largely counteracts differentiation block and growth of human AML cells across various disease subtypes in vitro and in vivo. Through proteome analysis of over 200 primary AML bone marrow samples, we identify a distinct PHF8/IFN-I signature in half of the patient population, without significant associations with known clinically or genetically defined AML subgroups. This profile was absent in healthy CD34+ hematopoietic progenitor cells, suggesting therapeutic applicability in a large fraction of patients with AML. Pharmacological support of PHF8 phosphorylation significantly impairs the growth in samples from patients with primary AML. These findings provide novel opportunities for harnessing the cell-intrinsic immune response in the development of immunotherapeutic strategies against AML.
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MESH Headings
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/metabolism
- Epigenesis, Genetic
- Animals
- Histone Demethylases/genetics
- Histone Demethylases/metabolism
- Mice
- Interferon Type I/metabolism
- Cell Self Renewal
- Gene Expression Regulation, Leukemic
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Affiliation(s)
| | - Carolin Walter
- Institute of Medical Informatics, Gerhard-Domagk-Institute for Pathology, University Hospital Muenster, Muenster, Germany
| | - Joris Maximillian Frenz
- Proteomics and Cancer Cell Signaling Group, German Cancer Research Center, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children’s Cancer Center, University of Heidelberg, Heidelberg, Germany
| | - Franca Seifert
- Department of Medicine A, University Hospital Muenster, Muenster, Germany
| | - Vijay Alla
- Department of Medicine A, University Hospital Muenster, Muenster, Germany
| | - Thorben Hennig
- Proteomics and Cancer Cell Signaling Group, German Cancer Research Center, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children’s Cancer Center, University of Heidelberg, Heidelberg, Germany
| | - Linus Angenendt
- Department of Medicine A, University Hospital Muenster, Muenster, Germany
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zurich, Basel, Switzerland
| | - Wolfgang Hartmann
- Division of Translational Pathology, Gerhard-Domagk-Institute for Pathology, University Hospital Muenster, Muenster, Germany
| | - Sebastian Wolf
- Department of Hematology/Oncology, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Hubert Serve
- Department of Hematology/Oncology, Johann Wolfgang Goethe University, Frankfurt, Germany
| | - Thomas Oellerich
- Department of Hematology/Oncology, Johann Wolfgang Goethe University, Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, Germany
| | - Georg Lenz
- Department of Medicine A, University Hospital Muenster, Muenster, Germany
| | | | | | - Otmar Huber
- Department of Biochemistry II, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University Hospital Heidelberg, Heidelberg, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ashok Kumar Jayavelu
- Proteomics and Cancer Cell Signaling Group, German Cancer Research Center, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children’s Cancer Center, University of Heidelberg, Heidelberg, Germany
| | - Jan-Henrik Mikesch
- Department of Medicine A, University Hospital Muenster, Muenster, Germany
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3
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Wu XN, Li JY, He Q, Li BQ, He YH, Pan X, Wang MY, Sang R, Ding JC, Gao X, Wu Z, Liu W. Targeting the PHF8/YY1 axis suppresses cancer cell growth through modulation of ROS. Proc Natl Acad Sci U S A 2024; 121:e2219352120. [PMID: 38165927 PMCID: PMC10786316 DOI: 10.1073/pnas.2219352120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 11/17/2023] [Indexed: 01/04/2024] Open
Abstract
High levels of mitochondrial reactive oxygen species (mROS) are linked to cancer development, which is tightly controlled by the electron transport chain (ETC). However, the epigenetic mechanisms governing ETC gene transcription to drive mROS production and cancer cell growth remain to be fully characterized. Here, we report that protein demethylase PHF8 is overexpressed in many types of cancers, including colon and lung cancer, and is negatively correlated with ETC gene expression. While it is well known to demethylate histones to activate transcription, PHF8 demethylates transcription factor YY1, functioning as a co-repressor for a large set of nuclear-coded ETC genes to drive mROS production and cancer development. In addition to genetically ablating PHF8, pharmacologically targeting PHF8 with a specific chemical inhibitor, iPHF8, is potent in regulating YY1 methylation, ETC gene transcription, mROS production, and cell growth in colon and lung cancer cells. iPHF8 exhibits potency and safety in suppressing tumor growth in cell-line- and patient-derived xenografts in vivo. Our data uncover a key epigenetic mechanism underlying ETC gene transcriptional regulation, demonstrating that targeting the PHF8/YY1 axis has great potential to treat cancers.
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Affiliation(s)
- Xiao-Nan Wu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
| | - Jia-yuan Li
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
| | - Qi He
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
| | - Bo-qun Li
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
| | - Yao-hui He
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
| | - Xu Pan
- Xiamen University-Amogene Joint Research and Development Center for Genetic Diagnostics, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
| | - Ming-yue Wang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
| | - Rui Sang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
| | - Jian-cheng Ding
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
| | - Xiang Gao
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
| | - Zhen Wu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
| | - Wen Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian361102, China
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Roy A, Niharika, Chakraborty S, Mishra J, Singh SP, Patra SK. Mechanistic aspects of reversible methylation modifications of arginine and lysine of nuclear histones and their roles in human colon cancer. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:261-302. [PMID: 37019596 DOI: 10.1016/bs.pmbts.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Developmental proceedings and maintenance of cellular homeostasis are regulated by the precise orchestration of a series of epigenetic events that eventually control gene expression. DNA methylation and post-translational modifications (PTMs) of histones are well-characterized epigenetic events responsible for fine-tuning gene expression. PTMs of histones bear molecular logic of gene expression at chromosomal territory and have become a fascinating field of epigenetics. Nowadays, reversible methylation on histone arginine and lysine is gaining increasing attention as a significant PTM related to reorganizing local nucleosomal structure, chromatin dynamics, and transcriptional regulation. It is now well-accepted and reported that histone marks play crucial roles in colon cancer initiation and progression by encouraging abnormal epigenomic reprogramming. It is becoming increasingly clear that multiple PTM marks at the N-terminal tails of the core histones cross-talk with one another to intricately regulate DNA-templated biological processes such as replication, transcription, recombination, and damage repair in several malignancies, including colon cancer. These functional cross-talks provide an additional layer of message, which spatiotemporally fine-tunes the overall gene expression regulation. Nowadays, it is evident that several PTMs instigate colon cancer development. How colon cancer-specific PTM patterns or codes are generated and how they affect downstream molecular events are uncovered to some extent. Future studies would address more about epigenetic communication, and the relationship between histone modification marks to define cellular functions in depth. This chapter will comprehensively highlight the importance of histone arginine and lysine-based methylation modifications and their functional cross-talk with other histone marks from the perspective of colon cancer development.
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Sobering AK, Bryant LM, Li D, McGaughran J, Maystadt I, Moortgat S, Graham JM, van Haeringen A, Ruivenkamp C, Cuperus R, Vogt J, Morton J, Brasch-Andersen C, Steenhof M, Hansen LK, Adler É, Lyonnet S, Pingault V, Sandrine M, Ziegler A, Donald T, Nelson B, Holt B, Petryna O, Firth H, McWalter K, Zyskind J, Telegrafi A, Juusola J, Person R, Bamshad MJ, Earl D, Tsai ACH, Yearwood KR, Marco E, Nowak C, Douglas J, Hakonarson H, Bhoj EJ. Variants in PHF8 cause a spectrum of X-linked neurodevelopmental disorders and facial dysmorphology. HGG ADVANCES 2022; 3:100102. [PMID: 35469323 PMCID: PMC9034099 DOI: 10.1016/j.xhgg.2022.100102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/18/2022] [Indexed: 01/25/2023] Open
Abstract
Loss-of-function variants in PHD Finger Protein 8 (PHF8) cause Siderius X-linked intellectual disability (ID) syndrome, hereafter called PHF8-XLID. PHF8 is a histone demethylase that is important for epigenetic regulation of gene expression. PHF8-XLID is an under-characterized disorder with only five previous reports describing different PHF8 predicted loss-of-function variants in eight individuals. Features of PHF8-XLID include ID and craniofacial dysmorphology. In this report we present 16 additional individuals with PHF8-XLID from 11 different families of diverse ancestry. We also present five individuals from four different families who have ID and a variant of unknown significance in PHF8 with no other explanatory variant in another gene. All affected individuals exhibited developmental delay and all but two had borderline to severe ID. Of the two who did not have ID, one had dyscalculia and the other had mild learning difficulties. Craniofacial findings such as hypertelorism, microcephaly, elongated face, ptosis, and mild facial asymmetry were found in some affected individuals. Orofacial clefting was seen in three individuals from our cohort, suggesting that this feature is less common than previously reported. Autism spectrum disorder and attention deficit hyperactivity disorder, which were not previously emphasized in PHF8-XLID, were frequently observed in affected individuals. This series expands the clinical phenotype of this rare ID syndrome caused by loss of PHF8 function.
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Affiliation(s)
- Andrew K. Sobering
- AU/UGA Medical Partnership, Department of Basic Sciences, University of Georgia Health Sciences Campus, Athens, GA 30602, USA
- St. George’s University, Department of Biochemistry, St. George’s, Grenada, West Indies
- Windward Islands Research and Education Foundation, True Blue, St. George’s, Grenada, West Indies
- Corresponding author
| | - Laura M. Bryant
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Dong Li
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Julie McGaughran
- Genetic Health Queensland, RBWH, Brisbane and The University of Queensland School of Medicine, Brisbane, QLD 4029, Australia
| | - Isabelle Maystadt
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, 6041 Gosselies, Belgium
| | - Stephanie Moortgat
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, 6041 Gosselies, Belgium
| | - John M. Graham
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, CA 90048, USA
| | | | | | - Roos Cuperus
- Juliana Children’s Hospital, HAGA Medical Center, The Hague, the Netherlands
| | - Julie Vogt
- Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham Women’s Hospital, Birmingham B15 2TG, UK
| | - Jenny Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women’s Hospital NHS Foundation Trust, Birmingham B15 2TG, UK
| | - Charlotte Brasch-Andersen
- Department of Clinical Genetics, Odense University Hospital, Odense 5000, Denmark
- Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense 5000, Denmark
| | - Maria Steenhof
- Department of Clinical Genetics, Odense University Hospital, Odense 5000, Denmark
| | | | - Élodie Adler
- Fédération de Médecine Génomique and Imagine Institute, Université de Paris, Hôpital Necker-Enfants Malades, APHP, 75015 Paris, France
| | - Stanislas Lyonnet
- Fédération de Médecine Génomique and Imagine Institute, Université de Paris, Hôpital Necker-Enfants Malades, APHP, 75015 Paris, France
| | - Veronique Pingault
- Fédération de Médecine Génomique and Imagine Institute, Université de Paris, Hôpital Necker-Enfants Malades, APHP, 75015 Paris, France
| | - Marlin Sandrine
- Reference Center for Genetic Deafness, Fédération de Médecine Génomique and Imagine Institute, Université de Paris, Hôpital Necker-Enfants Malades, APHP, 75015 Paris, France
| | - Alban Ziegler
- Reference Center for Genetic Deafness, Fédération de Médecine Génomique and Imagine Institute, Université de Paris, Hôpital Necker-Enfants Malades, APHP, 75015 Paris, France
| | - Tyhiesia Donald
- Clinical Teaching Unit, St. George’s University School of Medicine, St. George’s, Grenada, West Indies
| | - Beverly Nelson
- Clinical Teaching Unit, St. George’s University School of Medicine, St. George’s, Grenada, West Indies
| | - Brandon Holt
- Department of Anatomical Sciences, St. George’s University, Grenada, West Indies
| | - Oleksandra Petryna
- Hackensack University Ocean Medical Center, Department of Psychiatry, Hackensack, NJ 08724, USA
| | - Helen Firth
- Department of Clinical Genetics, Cambridge University Hospitals, Box 134, Cambridge CB2 0QQ, UK
| | | | - Jacob Zyskind
- Clinical Genomics, GeneDx, Gaithersburg, MD 20877, USA
| | | | - Jane Juusola
- Clinical Genomics, GeneDx, Gaithersburg, MD 20877, USA
| | | | - Michael J. Bamshad
- Seattle Children’s Hospital, Seattle, WA 98105, USA
- Departments of Pediatrics and Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman-Baty Institute, Seattle, WA 98195, USA
| | - Dawn Earl
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | | | - Anne Chun-Hui Tsai
- University of Oklahoma, Section of Genetics, 800 Stanton L Young Boulevard, Oklahoma City, OK 73117, USA
| | | | - Elysa Marco
- Cortica Healthcare, Marin Center, 4000 Civic Center Dr, Ste 100, San Rafael, CA 94903, USA
| | - Catherine Nowak
- Boston Children’s Hospital, Division of Genetics and Genomics, 60 Temple Place, 2nd Floor, Boston, MA 02111, USA
| | - Jessica Douglas
- Boston Children’s Hospital, Division of Genetics and Genomics, 60 Temple Place, 2nd Floor, Boston, MA 02111, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Elizabeth J. Bhoj
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Corresponding author
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Li H, Zimmerman SE, Weyemi U. Genomic instability and metabolism in cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:241-265. [PMID: 34507785 DOI: 10.1016/bs.ircmb.2021.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Genomic instability and metabolic reprogramming are among the key hallmarks discriminating cancer cells from normal cells. The two phenomena contribute to the robust and evasive nature of cancer, particularly when cancer cells are exposed to chemotherapeutic agents. Genomic instability is defined as the increased frequency of mutations within the genome, while metabolic reprogramming is the alteration of metabolic pathways that cancer cells undergo to adapt to increased bioenergetic demand. An underlying source of these mutations is the aggregate product of damage to the DNA, and a defective repair pathway, both resulting in the expansion of genomic lesions prior to uncontrolled proliferation and survival of cancer cells. Exploitation of DNA damage and the subsequent DNA damage response (DDR) have aided in defining therapeutic approaches in cancer. Studies have demonstrated that targeting metabolic reprograming yields increased sensitivity to chemo- and radiotherapies. In the past decade, it has been shown that these two key features are interrelated. Metabolism impacts DNA damage and DDR via regulation of metabolite pools. Conversely, DDR affects the response of metabolic pathways to therapeutic agents. Because of the interplay between genomic instability and metabolic reprogramming, we have compiled findings which more selectively highlight the dialog between metabolism and DDR, with a particular focus on glucose metabolism and double-strand break (DSB) repair pathways. Decoding this dialog will provide significant clues for developing combination cancer therapies.
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Affiliation(s)
- Haojian Li
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Susan E Zimmerman
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Urbain Weyemi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States.
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Inflammation, epigenetics, and metabolism converge to cell senescence and ageing: the regulation and intervention. Signal Transduct Target Ther 2021; 6:245. [PMID: 34176928 PMCID: PMC8236488 DOI: 10.1038/s41392-021-00646-9] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/09/2021] [Accepted: 05/13/2021] [Indexed: 02/05/2023] Open
Abstract
Remarkable progress in ageing research has been achieved over the past decades. General perceptions and experimental evidence pinpoint that the decline of physical function often initiates by cell senescence and organ ageing. Epigenetic dynamics and immunometabolic reprogramming link to the alterations of cellular response to intrinsic and extrinsic stimuli, representing current hotspots as they not only (re-)shape the individual cell identity, but also involve in cell fate decision. This review focuses on the present findings and emerging concepts in epigenetic, inflammatory, and metabolic regulations and the consequences of the ageing process. Potential therapeutic interventions targeting cell senescence and regulatory mechanisms, using state-of-the-art techniques are also discussed.
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Chen LL, Huang JQ, Wu YY, Chen LB, Li SP, Zhang X, Wu S, Ren FZ, Lei XG. Loss of Selenov predisposes mice to extra fat accumulation and attenuated energy expenditure. Redox Biol 2021; 45:102048. [PMID: 34167027 PMCID: PMC8227834 DOI: 10.1016/j.redox.2021.102048] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/13/2021] [Accepted: 06/14/2021] [Indexed: 12/13/2022] Open
Abstract
Selenoprotein V (SELENOV) is a new and the least conserved member of the selenoprotein family. Herein we generated Selenov knockout (KO) mice to determine its in vivo function. The KO led to 16-19% increases (P < 0.05) in body weight that were largely due to 54% higher (P < 0.05) fat mass accumulation, compared with the wild-type (WT) controls. The extra fat accumulation in the KO mice was mediated by up-regulations of genes and proteins involved in lipogenesis (Acc, Fas, Dgat, and Lpl; up by 40%-1.1-fold) and down-regulations of lipolysis (Atgl, Hsl, Ces1d, and Cpt1a; down by 36-89%) in the adipose tissues. The KO also decreased (P < 0.05) VO2 consumption (14-21%), VCO2 production (14-16%), and energy expenditure (14-23%), compared with the WT controls. SELENOV and O-GlcNAc transferase (OGT) exhibited a novel protein-protein interaction that explained the KO-induced decreases (P < 0.05) of OGT protein (15-29%), activity (33%), and function (O-GlcNAcylation, 10-21%) in the adipose tissues. A potential cascade of SELENOV-OGT-AMP-activated protein kinase might serve as a central mechanism to link the biochemical and molecular responses to the KO. Overall, our data revealed a novel in vivo function and mechanism of SELENOV as a new inhibitor of body fat accumulation, activator of energy expenditure, regulator of O-GlcNAcylation, and therapeutic target of such related disorders.
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Affiliation(s)
- Ling-Li Chen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China; Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China; College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, 330045, China
| | - Jia-Qiang Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China; Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Yuan-Yuan Wu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Liang-Bing Chen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China; Life Science and Agriculture Department, Zhoukou Normal University, Zhoukou, Henan, 466001, China
| | - Shu-Ping Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Xu Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Sen Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Fa-Zheng Ren
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China; Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China.
| | - Xin-Gen Lei
- Department of Animal Science, Cornell University, Ithaca, NY, 14853, USA.
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9
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Histone Methylation Regulation in Neurodegenerative Disorders. Int J Mol Sci 2021; 22:ijms22094654. [PMID: 33925016 PMCID: PMC8125694 DOI: 10.3390/ijms22094654] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022] Open
Abstract
Advances achieved with molecular biology and genomics technologies have permitted investigators to discover epigenetic mechanisms, such as DNA methylation and histone posttranslational modifications, which are critical for gene expression in almost all tissues and in brain health and disease. These advances have influenced much interest in understanding the dysregulation of epigenetic mechanisms in neurodegenerative disorders. Although these disorders diverge in their fundamental causes and pathophysiology, several involve the dysregulation of histone methylation-mediated gene expression. Interestingly, epigenetic remodeling via histone methylation in specific brain regions has been suggested to play a critical function in the neurobiology of psychiatric disorders, including that related to neurodegenerative diseases. Prominently, epigenetic dysregulation currently brings considerable interest as an essential player in neurodegenerative disorders, such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), Amyotrophic lateral sclerosis (ALS) and drugs of abuse, including alcohol abuse disorder, where it may facilitate connections between genetic and environmental risk factors or directly influence disease-specific pathological factors. We have discussed the current state of histone methylation, therapeutic strategies, and future perspectives for these disorders. While not somatically heritable, the enzymes responsible for histone methylation regulation, such as histone methyltransferases and demethylases in neurons, are dynamic and reversible. They have become promising potential therapeutic targets to treat or prevent several neurodegenerative disorders. These findings, along with clinical data, may provide links between molecular-level changes and behavioral differences and provide novel avenues through which the epigenome may be targeted early on in people at risk for neurodegenerative disorders.
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10
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Stelman CR, Smith BM, Chandra B, Roberts-Galbraith RH. CBP/p300 homologs CBP2 and CBP3 play distinct roles in planarian stem cell function. Dev Biol 2021; 473:130-143. [PMID: 33607113 DOI: 10.1016/j.ydbio.2021.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 11/19/2022]
Abstract
Chromatin modifications function as critical regulators of gene expression and cellular identity, especially in the regulation and maintenance of the pluripotent state. However, many studies of chromatin modification in stem cells-and pluripotent stem cells in particular-are performed in mammalian stem cell culture, an in vitro condition mimicking a very transient state during mammalian development. Thus, new models for studying pluripotent stem cells in vivo could be helpful for understanding the roles of chromatin modification, for confirming prior in vitro studies, and for exploring evolution of the pluripotent state. The freshwater flatworm, Schmidtea mediterranea, is an excellent model for studying adult pluripotent stem cells, particularly in the context of robust, whole-body regeneration. To identify chromatin modifying and remodeling enzymes critical for planarian regeneration and stem cell maintenance, we took a candidate approach and screened planarian homologs of 25 genes known to regulate chromatin biology in other organisms. Through our study, we identified six genes with novel functions in planarian homeostasis, regeneration, and behavior. Of the list of genes characterized, we identified five planarian homologs of the mammalian CREB-Binding Protein (CBP) and p300 family of histone acetyltransferases, representing an expansion of this family in planarians. We find that two planarian CBP family members are required for planarian survival, with knockdown of Smed-CBP2 and Smed-CBP3 causing distinct defects in stem cell maintenance or function. Loss of CBP2 causes a quick, dramatic loss of stem cells, while knockdown of CBP3 affects stem cells more narrowly, influencing differentiation of several cell types that include neuronal subtypes and cells of the eye. Further, we find that Smed-CBP1 is required for planarian fissioning behavior. We propose that the division of labor among a diversified CBP family in planarians presents an opportunity to dissect specific functions of a broadly important histone acetyltransferase family.
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Affiliation(s)
- Clara R Stelman
- Department of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Britessia M Smith
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Bidushi Chandra
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Rachel H Roberts-Galbraith
- Department of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Cellular Biology, University of Georgia, Athens, GA, USA.
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11
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Chaturvedi SS, Ramanan R, Hu J, Hausinger RP, Christov CZ. Atomic and Electronic Structure Determinants Distinguish between Ethylene Formation and l-Arginine Hydroxylation Reaction Mechanisms in the Ethylene-Forming Enzyme. ACS Catal 2021. [DOI: 10.1021/acscatal.0c03349] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Shobhit S. Chaturvedi
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Rajeev Ramanan
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | | | | | - Christo Z. Christov
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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12
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Müller S, Sindikubwabo F, Cañeque T, Lafon A, Versini A, Lombard B, Loew D, Wu TD, Ginestier C, Charafe-Jauffret E, Durand A, Vallot C, Baulande S, Servant N, Rodriguez R. CD44 regulates epigenetic plasticity by mediating iron endocytosis. Nat Chem 2020; 12:929-938. [DOI: 10.1038/s41557-020-0513-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 06/16/2020] [Indexed: 01/06/2023]
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13
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Chaturvedi S, Ramanan R, Lehnert N, Schofield CJ, Karabencheva-Christova TG, Christov CZ. Catalysis by the Non-Heme Iron(II) Histone Demethylase PHF8 Involves Iron Center Rearrangement and Conformational Modulation of Substrate Orientation. ACS Catal 2020; 10:1195-1209. [PMID: 31976154 PMCID: PMC6970271 DOI: 10.1021/acscatal.9b04907] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/10/2019] [Indexed: 02/07/2023]
Abstract
PHF8 (KDM7B) is a human non-heme 2-oxoglutarate (2OG) JmjC domain oxygenase that catalyzes the demethylation of the di/mono-Nε-methylated K9 residue of histone H3. Altered PHF8 activity is linked to genetic diseases and cancer; thus, it is an interesting target for epigenetic modulation. We describe the use of combined quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations to explore the mechanism of PHF8, including dioxygen activation, 2OG binding modes, and substrate demethylation steps. A PHF8 crystal structure manifests the 2OG C-1 carboxylate bound to iron in a nonproductive orientation, i.e., trans to His247. A ferryl-oxo intermediate formed by activating dioxygen bound to the vacant site in this complex would be nonproductive, i.e., "off-line" with respect to reaction with Nε-methylated K9. We show rearrangement of the "off-line" ferryl-oxo intermediate to a productive "in-line" geometry via a solvent exchange reaction (called "ferryl-flip") is energetically unfavorable. The calculations imply that movement of the 2OG C-1 carboxylate prior to dioxygen binding at a five-coordination stage in catalysis proceeds with a low barrier, suggesting that two possible 2OG C-1 carboxylate geometries can coexist at room temperature. We explored alternative mechanisms for hydrogen atom transfer and show that second sphere interactions orient the Nε-methylated lysine in a conformation where hydrogen abstraction from a methyl C-H bond is energetically more favorable than hydrogen abstraction from the N-H bond of the protonated Nε-methyl group. Using multiple HAT reaction path calculations, we demonstrate the crucial role of conformational flexibility in effective hydrogen transfer. Subsequent hydroxylation occurs through a rebound mechanism, which is energetically preferred compared to desaturation, due to second sphere interactions. The overall mechanistic insights reveal the crucial role of iron-center rearrangement, second sphere interactions, and conformational flexibility in PHF8 catalysis and provide knowledge useful for the design of mechanism-based PHF8 inhibitors.
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Affiliation(s)
- Shobhit
S. Chaturvedi
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Rajeev Ramanan
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Nicolai Lehnert
- Department
of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | - Christo Z. Christov
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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14
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Seelan RS, Pisano M, Greene RM. Nucleic acid methylation and orofacial morphogenesis. Birth Defects Res 2019; 111:1593-1610. [PMID: 31385455 DOI: 10.1002/bdr2.1564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 12/19/2022]
Abstract
In this review, we highlight the current state of knowledge of the diverse roles nucleic acid methylation plays in the embryonic development of the orofacial region and how aberrant methylation may contribute to orofacial clefts. We also consider the role of methylation in the regulation of neural crest cell function as it pertains to orofacial ontogeny. Changes in DNA methylation, as a consequence of environmental effects, have been observed in the regulatory regions of several genes, potentially identifying new candidate genes for orofacial clefting and opening promising new avenues for further research. While the focus of this review is primarily on the nonsyndromic forms of orofacial clefting, syndromic forms are briefly discussed in the context of aberrant nucleic acid methylation.
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Affiliation(s)
- Ratnam S Seelan
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
| | - Michele Pisano
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
| | - Robert M Greene
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
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15
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Islam MS, McDonough MA, Chowdhury R, Gault J, Khan A, Pires E, Schofield CJ. Biochemical and structural investigations clarify the substrate selectivity of the 2-oxoglutarate oxygenase JMJD6. J Biol Chem 2019; 294:11637-11652. [PMID: 31147442 PMCID: PMC6663879 DOI: 10.1074/jbc.ra119.008693] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/21/2019] [Indexed: 12/22/2022] Open
Abstract
JmjC domain-containing protein 6 (JMJD6) is a 2-oxoglutarate (2OG)-dependent oxygenase linked to various cellular processes, including splicing regulation, histone modification, transcriptional pause release, hypoxia sensing, and cancer. JMJD6 is reported to catalyze hydroxylation of lysine residue(s) of histones, the tumor-suppressor protein p53, and splicing regulatory proteins, including u2 small nuclear ribonucleoprotein auxiliary factor 65-kDa subunit (U2AF65). JMJD6 is also reported to catalyze N-demethylation of N-methylated (both mono- and di-methylated) arginine residues of histones and other proteins, including HSP70 (heat-shock protein 70), estrogen receptor α, and RNA helicase A. Here, we report MS- and NMR-based kinetic assays employing purified JMJD6 and multiple substrate fragment sequences, the results of which support the assignment of purified JMJD6 as a lysyl hydroxylase. By contrast, we did not observe N-methyl arginyl N-demethylation with purified JMJD6. Biophysical analyses, including crystallographic analyses of JMJD6Δ344-403 in complex with iron and 2OG, supported its assignment as a lysyl hydroxylase rather than an N-methyl arginyl-demethylase. The screening results supported some, but not all, of the assigned JMJD6 substrates and identified other potential JMJD6 substrates. We envision these results will be useful in cellular and biological work on the substrates and functions of JMJD6 and in the development of selective inhibitors of human 2OG oxygenases.
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Affiliation(s)
- Md Saiful Islam
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael A McDonough
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Rasheduzzaman Chowdhury
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Joseph Gault
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Amjad Khan
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Elisabete Pires
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
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16
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Zhou W, Gong L, Wu Q, Xing C, Wei B, Chen T, Zhou Y, Yin S, Jiang B, Xie H, Zhou L, Zheng S. PHF8 upregulation contributes to autophagic degradation of E-cadherin, epithelial-mesenchymal transition and metastasis in hepatocellular carcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:215. [PMID: 30180906 PMCID: PMC6122561 DOI: 10.1186/s13046-018-0890-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/21/2018] [Indexed: 12/12/2022]
Abstract
Background Plant homeodomain finger protein 8 (PHF8) serves an activator of epithelial-mesenchymal transition (EMT) and is implicated in various tumors. However, little is known about PHF8 roles in hepatocellular carcinoma (HCC) and regulating E-cadherin expression. Methods PHF8 expression pattern was investigated by informatic analysis and verified by RT-qPCR and immunochemistry in HCC tissues and cell lines. CCK8, xenograft tumor model, transwell assay, and tandem mCherry-GFP-LC3 fusion protein assay were utilized to assess the effects of PHF8 on proliferation, metastasis and autophagy of HCC cells in vitro and in vivo. ChIP, immunoblot analysis, rescue experiments and inhibitor treatment were used to clarify the mechanism by which PHF8 facilitated EMT, metastasis and autophagy. Results PHF8 upregulation was quite prevalent in HCC tissues and closely correlated with worse overall survival and disease-relapse free survival. Furthermore, PHF8-knockdown dramatically suppressed cell growth, migration, invasion and autophagy, and the expression of SNAI1, VIM, N-cadherin and FIP200, and increased E-cadherin level, while PHF8-overexpression led to the opposite results. Additionally, FIP200 augmentation reversed the inhibited effects of PHF8-siliencing on tumor migration, invasion and autophagy. Mechanistically, PHF8 was involved in transcriptionally regulating the expression of SNAI1, VIM and FIP200, rather than N-cadherin and E-cadherin. Noticeably, E-cadherin degradation could be accelerated by PHF8-mediated FIP200-dependent autophagy, a crucial pathway complementary to transcriptional repression of E-cadherin by SNAI1 activation. Conclusion These findings suggested that PHF8 played an oncogenic role in facilitating FIP200-dependent autophagic degradation of E-cadherin, EMT and metastasis in HCC. PHF8 might be a promising target for prevention, treatment and prognostic prediction of HCC. Electronic supplementary material The online version of this article (10.1186/s13046-018-0890-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wuhua Zhou
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHFPC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Collaborative Innovation Center for Diagnosis Treatment of Infectious Disease, Zhejiang University, Hangzhou, China
| | - Li Gong
- Department of Endocrinology, Taihe Hospital, Shiyan, China
| | - Qinchuan Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHFPC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Collaborative Innovation Center for Diagnosis Treatment of Infectious Disease, Zhejiang University, Hangzhou, China
| | - Chunyang Xing
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Bajin Wei
- NHFPC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China
| | - Tianchi Chen
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHFPC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Collaborative Innovation Center for Diagnosis Treatment of Infectious Disease, Zhejiang University, Hangzhou, China
| | - Yuan Zhou
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,NHFPC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Collaborative Innovation Center for Diagnosis Treatment of Infectious Disease, Zhejiang University, Hangzhou, China
| | - Shengyong Yin
- NHFPC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China
| | - Bin Jiang
- Department of Hepatobiliary and Pancreatic Surgery, Taihe Hospital, Shiyan, China
| | - Haiyang Xie
- NHFPC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China.,Key Laboratory of the Diagnosis and Treatment of Organ transplantation, CAMS, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Collaborative Innovation Center for Diagnosis Treatment of Infectious Disease, Zhejiang University, Hangzhou, China
| | - Lin Zhou
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China. .,NHFPC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China. .,Key Laboratory of the Diagnosis and Treatment of Organ transplantation, CAMS, Hangzhou, China. .,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China. .,Collaborative Innovation Center for Diagnosis Treatment of Infectious Disease, Zhejiang University, Hangzhou, China.
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China. .,NHFPC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China. .,Key Laboratory of the Diagnosis and Treatment of Organ transplantation, CAMS, Hangzhou, China. .,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China. .,Collaborative Innovation Center for Diagnosis Treatment of Infectious Disease, Zhejiang University, Hangzhou, China.
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17
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Ruggero K, Farran-Matas S, Martinez-Tebar A, Aytes A. Epigenetic Regulation in Prostate Cancer Progression. ACTA ACUST UNITED AC 2018; 4:101-115. [PMID: 29888169 PMCID: PMC5976687 DOI: 10.1007/s40610-018-0095-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Purpose of Review An important number of newly identified molecular alterations in prostate cancer affect gene encoding master regulators of chromatin biology epigenetic regulation. This review will provide an updated view of the key epigenetic mechanisms underlying prostate cancer progression, therapy resistance, and potential actionable mechanisms and biomarkers. Recent Findings Key players in chromatin biology and epigenetic master regulators has been recently described to be crucially altered in metastatic CRPC and tumors that progress to AR independency. As such, epigenetic dysregulation represents a driving mechanism in the reprograming of prostate cancer cells as they lose AR-imposed identity. Summary Chromatin integrity and accessibility for transcriptional regulation are key features altered in cancer progression, and particularly relevant in nuclear hormone receptor-driven tumors like prostate cancer. Understanding how chromatin remodeling dictates prostate development and how its deregulation contributes to prostate cancer onset and progression may improve risk stratification and treatment selection for prostate cancer patients.
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Affiliation(s)
- Katia Ruggero
- Programs of Molecular Mechanisms and Experimental Therapeutics in Oncology (ONCOBell), Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, Granvia de l'Hopitalet, 199 08908, L'Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Sonia Farran-Matas
- Programs of Molecular Mechanisms and Experimental Therapeutics in Oncology (ONCOBell), Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, Granvia de l'Hopitalet, 199 08908, L'Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Adrian Martinez-Tebar
- Programs of Molecular Mechanisms and Experimental Therapeutics in Oncology (ONCOBell), Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, Granvia de l'Hopitalet, 199 08908, L'Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Alvaro Aytes
- Programs of Molecular Mechanisms and Experimental Therapeutics in Oncology (ONCOBell), Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, Granvia de l'Hopitalet, 199 08908, L'Hospitalet de Llobregat, 08907 Barcelona, Spain.,Programs of Cancer Therapeutics Resistance (ProCURE), Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, L'Hospitalet de Llobregat, 08907 Barcelona, Spain
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18
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Daskalaki MG, Tsatsanis C, Kampranis SC. Histone methylation and acetylation in macrophages as a mechanism for regulation of inflammatory responses. J Cell Physiol 2018; 233:6495-6507. [PMID: 29574768 DOI: 10.1002/jcp.26497] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/22/2018] [Indexed: 12/25/2022]
Abstract
Macrophages respond to noxious stimuli and contribute to inflammatory responses by eliminating pathogens or damaged tissue and maintaining homeostasis. Response to activation signals and maintenance of homeostasis require tight regulation of genes involved in macrophage activation and inactivation processes, as well as genes involved in determining their polarization state. Recent evidence has revealed that such regulation occurs through histone modifications that render inflammatory or polarizing gene promoters accessible to transcriptional complexes. Thus, inflammatory and anti-inflammatory genes are regulated by histone acetylation and methylation, determining their activation state. Herein, we review the current knowledge on the role of histone modifying enzymes (acetyltransferases, deacetylases, methyltransferases, and demethylases) in determining the responsiveness and M1 or M2 polarization of macrophages. The contribution of these enzymes in the development of inflammatory diseases is also presented.
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Affiliation(s)
- Maria G Daskalaki
- Laboratory of Biochemistry, Medical School, University of Crete, Heraklion, Crete, Greece.,Laboratory of Clinical Chemistry, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Christos Tsatsanis
- Laboratory of Clinical Chemistry, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Sotirios C Kampranis
- Laboratory of Biochemistry, Medical School, University of Crete, Heraklion, Crete, Greece
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19
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Hong S, Kim D. Computational characterization of chromatin domain boundary-associated genomic elements. Nucleic Acids Res 2017; 45:10403-10414. [PMID: 28977568 PMCID: PMC5737353 DOI: 10.1093/nar/gkx738] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 08/14/2017] [Indexed: 02/06/2023] Open
Abstract
Topologically associated domains (TADs) are 3D genomic structures with high internal interactions that play important roles in genome compaction and gene regulation. Their genomic locations and their association with CCCTC-binding factor (CTCF)-binding sites and transcription start sites (TSSs) were recently reported. However, the relationship between TADs and other genomic elements has not been systematically evaluated. This was addressed in the present study, with a focus on the enrichment of these genomic elements and their ability to predict the TAD boundary region. We found that consensus CTCF-binding sites were strongly associated with TAD boundaries as well as with the transcription factors (TFs) Zinc finger protein (ZNF)143 and Yin Yang (YY)1. TAD boundary-associated genomic elements include DNase I-hypersensitive sites, H3K36 trimethylation, TSSs, RNA polymerase II, and TFs such as Specificity protein 1, ZNF274 and SIX homeobox 5. Computational modeling with these genomic elements suggests that they have distinct roles in TAD boundary formation. We propose a structural model of TAD boundaries based on these findings that provides a basis for studying the mechanism of chromatin structure formation and gene regulation.
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Affiliation(s)
- Seungpyo Hong
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
| | - Dongsup Kim
- Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea
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20
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Abstract
![]()
Post-translational
modifications of histones by protein methyltransferases
(PMTs) and histone demethylases (KDMs) play an important role in the
regulation of gene expression and transcription and are implicated
in cancer and many other diseases. Many of these enzymes also target
various nonhistone proteins impacting numerous crucial biological
pathways. Given their key biological functions and implications in
human diseases, there has been a growing interest in assessing these
enzymes as potential therapeutic targets. Consequently, discovering
and developing inhibitors of these enzymes has become a very active
and fast-growing research area over the past decade. In this review,
we cover the discovery, characterization, and biological application
of inhibitors of PMTs and KDMs with emphasis on key advancements in
the field. We also discuss challenges, opportunities, and future directions
in this emerging, exciting research field.
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Affiliation(s)
- H Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Michael L Martini
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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21
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The HIF/PHF8/AR axis promotes prostate cancer progression. Oncogenesis 2016; 5:e283. [PMID: 27991916 PMCID: PMC5177772 DOI: 10.1038/oncsis.2016.74] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 10/17/2016] [Accepted: 10/23/2016] [Indexed: 12/27/2022] Open
Abstract
Recent studies provide strong evidence that the androgen receptor (AR) signaling pathway remains active in castration-resistant prostate cancer (CRPC). However, the underlying mechanisms are not well understood. In this study, we demonstrate that plant homeo domain finger protein 8 (PHF8 )interacts with and functions as an essential histone demethylase activity-dependent AR coactivator. Furthermore, we demonstrate that the expression of PHF8 is induced by hypoxia in various prostate cancer cell lines. Knockdown of either hypoxia-inducible factor HIF2α or HIF1α almost completely abolished hypoxia-induced PHF8 expression. Importantly, we observed that PHF8 is highly expressed in clinical androgen deprived prostate cancer samples and expression of PHF8 correlates with increased levels of HIF1α and HIF2α. Moreover, elevated PHF8 is associated with higher grade prostate cancers and unfavorable outcomes. Our findings support a working model in which hypoxia in castrated prostate cancer activates HIF transcription factors which then induces PHF8 expression. The elevated PHF8 in turn promotes the AR signaling pathway and prostate cancer progression. Therefore, the HIF/PHF8/AR axis could serve as a potential biomarker for CRPC and is also a promising therapeutic target in combating CRPC.
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Alberro N, Torrent-Sucarrat M, Arrastia I, Arrieta A, Cossío FP. Two-State Reactivity of Histone Demethylases Containing Jumonji-C Active Sites: Different Mechanisms for Different Methylation Degrees. Chemistry 2016; 23:137-148. [DOI: 10.1002/chem.201604219] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Nerea Alberro
- Department of Organic Chemistry I; Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU); Centro de Innovación en Química Avanzada (ORFEO-CINQA); Manuel Lardizabal Ibilbidea 3 20018 San Sebastián/Donostia Spain
| | - Miquel Torrent-Sucarrat
- Department of Organic Chemistry I; Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU); Centro de Innovación en Química Avanzada (ORFEO-CINQA); Manuel Lardizabal Ibilbidea 3 20018 San Sebastián/Donostia Spain
- Donostia International Physics Center (DIPC); Manuel Lardizabal Ibilbidea 4 20018 San Sebastián/Donostia Spain
- Ikerbasque; Basque Foundation for Science; María Díaz de Haro 3, 6 floor 48013 Bilbao Spain
| | - Iosune Arrastia
- Donostia International Physics Center (DIPC); Manuel Lardizabal Ibilbidea 4 20018 San Sebastián/Donostia Spain
| | - Ana Arrieta
- Department of Organic Chemistry I; Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU); Centro de Innovación en Química Avanzada (ORFEO-CINQA); Manuel Lardizabal Ibilbidea 3 20018 San Sebastián/Donostia Spain
| | - Fernando P. Cossío
- Department of Organic Chemistry I; Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU); Centro de Innovación en Química Avanzada (ORFEO-CINQA); Manuel Lardizabal Ibilbidea 3 20018 San Sebastián/Donostia Spain
- Donostia International Physics Center (DIPC); Manuel Lardizabal Ibilbidea 4 20018 San Sebastián/Donostia Spain
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Thaler F, Mercurio C. Compounds and methods for inhibiting histone demethylases: a patent evaluation of US20160102096A1. Expert Opin Ther Pat 2016; 26:1367-1370. [PMID: 27730846 DOI: 10.1080/13543776.2016.1246539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The Jumonji C (JmjC) domain containing histone lysine demethylases have a clear role both in the development and in some diseases including inflammation and cancer. The histone lysine demethylases represent an attractive target for the identification of therapeutic agents and the pyridine derivatives are a scaffolds largely investigated for the identification and development of inhibitors of enzymes of the Jumonji family. This commentary is a scientific evaluation of a patent application US20160102096A1 that describes novel pyridine derivatives in which the introduction of specific substituents is used to modulate the selectivity profile of the inhibitors.
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Affiliation(s)
- Florian Thaler
- a Experimental Therapeutics Unit , IFOM - The FIRC Institute of Molecular Oncology , Milan , Italy
| | - Ciro Mercurio
- a Experimental Therapeutics Unit , IFOM - The FIRC Institute of Molecular Oncology , Milan , Italy
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Epigenetic Mechanisms in Developmental Alcohol-Induced Neurobehavioral Deficits. Brain Sci 2016; 6:brainsci6020012. [PMID: 27070644 PMCID: PMC4931489 DOI: 10.3390/brainsci6020012] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/17/2016] [Accepted: 04/05/2016] [Indexed: 12/22/2022] Open
Abstract
Alcohol consumption during pregnancy and its damaging consequences on the developing infant brain are significant public health, social, and economic issues. The major distinctive features of prenatal alcohol exposure in humans are cognitive and behavioral dysfunction due to damage to the central nervous system (CNS), which results in a continuum of disarray that is collectively called fetal alcohol spectrum disorder (FASD). Many rodent models have been developed to understand the mechanisms of and to reproduce the human FASD phenotypes. These animal FASD studies have provided several molecular pathways that are likely responsible for the neurobehavioral abnormalities that are associated with prenatal alcohol exposure of the developing CNS. Recently, many laboratories have identified several immediate, as well as long-lasting, epigenetic modifications of DNA methylation, DNA-associated histone proteins and microRNA (miRNA) biogenesis by using a variety of epigenetic approaches in rodent FASD models. Because DNA methylation patterns, DNA-associated histone protein modifications and miRNA-regulated gene expression are crucial for synaptic plasticity and learning and memory, they can therefore offer an answer to many of the neurobehavioral abnormalities that are found in FASD. In this review, we briefly discuss the current literature of DNA methylation, DNA-associated histone proteins modification and miRNA and review recent developments concerning epigenetic changes in FASD.
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Dimitrova E, Turberfield AH, Klose RJ. Histone demethylases in chromatin biology and beyond. EMBO Rep 2015; 16:1620-39. [PMID: 26564907 PMCID: PMC4687429 DOI: 10.15252/embr.201541113] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/06/2015] [Indexed: 01/05/2023] Open
Abstract
Histone methylation plays fundamental roles in regulating chromatin‐based processes. With the discovery of histone demethylases over a decade ago, it is now clear that histone methylation is dynamically regulated to shape the epigenome and regulate important nuclear processes including transcription, cell cycle control and DNA repair. In addition, recent observations suggest that these enzymes could also have functions beyond their originally proposed role as histone demethylases. In this review, we focus on recent advances in our understanding of the molecular mechanisms that underpin the role of histone demethylases in a wide variety of normal cellular processes.
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Affiliation(s)
| | | | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK
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26
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A Neuronal Activity-Dependent Dual Function Chromatin-Modifying Complex Regulates Arc Expression. eNeuro 2015; 2:eN-NWR-0020-14. [PMID: 26464965 PMCID: PMC4586916 DOI: 10.1523/eneuro.0020-14.2015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 01/18/2015] [Accepted: 01/22/2015] [Indexed: 11/21/2022] Open
Abstract
Chromatin modification is an important epigenetic mechanism underlying neuroplasticity. Histone methylation and acetylation have both been shown to modulate gene expression, but the machinery responsible for mediating these changes in neurons has remained elusive. Here we identify a chromatin-modifying complex containing the histone demethylase PHF8 and the acetyltransferase TIP60 as a key regulator of the activity-induced expression of Arc, an important mediator of synaptic plasticity. Clinically, mutations in PHF8 cause X-linked mental retardation while TIP60 has been implicated in the pathogenesis of Alzheimer's disease. Within minutes of increased synaptic activity, this dual function complex is rapidly recruited to the Arc promoter, where it specifically counteracts the transcriptionally repressive histone mark H3K9me2 to facilitate the formation of the transcriptionally permissive H3K9acS10P, thereby favoring transcriptional activation. Consequently, gain-of-function of the PHF8-TIP60 complex in primary rat hippocampal neurons has a positive effect on early activity-induced Arc gene expression, whereas interfering with the function of this complex abrogates it. A global proteomics screen revealed that the majority of common interactors of PHF8 and TIP60 were involved in mRNA processing, including PSF, an important molecule involved in neuronal gene regulation. Finally, we proceeded to show, using super-resolution microscopy, that PHF8 and TIP60 interact at the single molecule level with PSF, thereby situating this chromatin modifying complex at the crossroads of transcriptional activation. These findings point toward a mechanism by which an epigenetic pathway can regulate neuronal activity-dependent gene transcription, which has implications in the development of novel therapeutics for disorders of learning and memory.
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27
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Accari SL, Fisher PR. Emerging Roles of JmjC Domain-Containing Proteins. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 319:165-220. [DOI: 10.1016/bs.ircmb.2015.07.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Zhu G, Liu L, She L, Tan H, Wei M, Chen C, Su Z, Huang D, Tian Y, Qiu Y, Liu Y, Zhang X. Elevated expression of histone demethylase PHF8 associates with adverse prognosis in patients of laryngeal and hypopharyngeal squamous cell carcinoma. Epigenomics 2014; 7:143-53. [PMID: 25496457 DOI: 10.2217/epi.14.82] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
AIM Overexpression of histone demethylase PHF8 has been reported to function as an oncoprotein in many cancers; however, the implications of PHF8 involvement in laryngeal and hypopharyngeal squamous cell carcinoma (LHSCC) remain unclear. This study aims to explore the expression of PHF8 and its clinical significance in LHSCC. MATERIALS & METHODS Western blotting and immunohistochemistry were performed to evaluate PHF8 protein expression in fresh and archived LHSCC samples. Global expressions of H3K27 and H3K9 methylation were analyzed in a cell line with PHF8 siRNA treatment. RESULTS & CONCLUSION In our study, PHF8 was upregulated in fresh LHSCC tissues. Immunohistochemical staining revealed that the expression of PHF8 was positively associated with T classification, clinical stage, primary tumor position and tumor relapse. Survival analysis demonstrated that high PHF8 expression was significantly associated with shorter overall survival and disease-free survival. Moreover, PHF8 regulates the levels of H3K9me2 and H3K27me2 in LHSCC. Taken together, PHF8 might be a novel prognostic marker for this disease.
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Affiliation(s)
- Gangcai Zhu
- Department of Otolaryngology Head & Neck Surgery, Xiangya Hospital, Central South University, Xiangya Road 87, Changsha 410008, Hunan, China
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29
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Shpargel KB, Starmer J, Yee D, Pohlers M, Magnuson T. KDM6 demethylase independent loss of histone H3 lysine 27 trimethylation during early embryonic development. PLoS Genet 2014; 10:e1004507. [PMID: 25101834 PMCID: PMC4125042 DOI: 10.1371/journal.pgen.1004507] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 05/29/2014] [Indexed: 02/06/2023] Open
Abstract
The early mammalian embryo utilizes histone H3 lysine 27 trimethylation (H3K27me3) to maintain essential developmental genes in a repressive chromatin state. As differentiation progresses, H3K27me3 is removed in a distinct fashion to activate lineage specific patterns of developmental gene expression. These rapid changes in early embryonic chromatin environment are thought to be dependent on H3K27 demethylases. We have taken a mouse genetics approach to remove activity of both H3K27 demethylases of the Kdm6 gene family, Utx (Kdm6a, X-linked gene) and Jmjd3 (Kdm6b, autosomal gene). Male embryos null for active H3K27 demethylation by the Kdm6 gene family survive to term. At mid-gestation, embryos demonstrate proper patterning and activation of Hox genes. These male embryos retain the Y-chromosome UTX homolog, UTY, which cannot demethylate H3K27me3 due to mutations in catalytic site of the Jumonji-C domain. Embryonic stem (ES) cells lacking all enzymatic KDM6 demethylation exhibit a typical decrease in global H3K27me3 levels with differentiation. Retinoic acid differentiations of these ES cells demonstrate loss of H3K27me3 and gain of H3K4me3 to Hox promoters and other transcription factors, and induce expression similar to control cells. A small subset of genes exhibit decreased expression associated with reduction of promoter H3K4me3 and some low-level accumulation of H3K27me3. Finally, Utx and Jmjd3 mutant mouse embryonic fibroblasts (MEFs) demonstrate dramatic loss of H3K27me3 from promoters of several Hox genes and transcription factors. Our results indicate that early embryonic H3K27me3 repression can be alleviated in the absence of active demethylation by the Kdm6 gene family.
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Affiliation(s)
- Karl B. Shpargel
- Department of Genetics, Carolina Center for Genome Sciences, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Joshua Starmer
- Department of Genetics, Carolina Center for Genome Sciences, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Della Yee
- Department of Genetics, Carolina Center for Genome Sciences, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Michael Pohlers
- Department of Genetics, Carolina Center for Genome Sciences, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Terry Magnuson
- Department of Genetics, Carolina Center for Genome Sciences, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
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30
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Fueyo R, García MA, Martínez-Balbás MA. Jumonji family histone demethylases in neural development. Cell Tissue Res 2014; 359:87-98. [PMID: 24950624 DOI: 10.1007/s00441-014-1924-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 05/15/2014] [Indexed: 10/25/2022]
Abstract
Central nervous system (CNS) development is driven by coordinated actions of developmental signals and chromatin regulators that precisely regulate gene expression patterns. Histone methylation is a regulatory mechanism that controls transcriptional programs. In the last 10 years, several histone demethylases (HDM) have been identified as important players in neural development, and their implication in cell fate decisions is beginning to be recognized. Identification of the physiological roles of these enzymes and their molecular mechanisms of action will be necessary for completely understanding the process that ultimately generates different neural cells in the CNS. In this review, we provide an overview of the Jumonji family of HDMs involved in neurodevelopment, and we discuss their roles during neural fate establishment and neuronal differentiation.
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Affiliation(s)
- Raquel Fueyo
- Department of Molecular Genomics, Instituto de Biología Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Parc Científic de Barcelona (PCB), Barcelona, 08028, Spain
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31
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Kupershmit I, Khoury-Haddad H, Awwad SW, Guttmann-Raviv N, Ayoub N. KDM4C (GASC1) lysine demethylase is associated with mitotic chromatin and regulates chromosome segregation during mitosis. Nucleic Acids Res 2014; 42:6168-82. [PMID: 24728997 PMCID: PMC4041427 DOI: 10.1093/nar/gku253] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 03/11/2014] [Accepted: 03/15/2014] [Indexed: 12/11/2022] Open
Abstract
Various types of human cancers exhibit amplification or deletion of KDM4A-D members, which selectively demethylate H3K9 and H3K36, thus implicating their activity in promoting carcinogenesis. On this basis, it was hypothesized that dysregulated expression of KDM4A-D family promotes chromosomal instabilities by largely unknown mechanisms. Here, we show that unlike KDM4A-B, KDM4C is associated with chromatin during mitosis. This association is accompanied by a decrease in the mitotic levels of H3K9me3. We also show that the C-terminal region, containing the Tudor domains of KDM4C, is essential for its association with mitotic chromatin. More specifically, we show that R919 residue on the proximal Tudor domain of KDM4C is critical for its association with chromatin during mitosis. Interestingly, we demonstrate that depletion or overexpression of KDM4C, but not KDM4B, leads to over 3-fold increase in the frequency of abnormal mitotic cells showing either misaligned chromosomes at metaphase, anaphase-telophase lagging chromosomes or anaphase-telophase bridges. Furthermore, overexpression of KDM4C demethylase-dead mutant has no detectable effect on mitotic chromosome segregation. Altogether, our findings implicate KDM4C demethylase activity in regulating the fidelity of mitotic chromosome segregation by a yet unknown mechanism.
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Affiliation(s)
- Ilana Kupershmit
- Department of Biology, Technion, Israel Institute of Technology, Haifa 3200003, Israel
| | - Hanan Khoury-Haddad
- Department of Biology, Technion, Israel Institute of Technology, Haifa 3200003, Israel
| | - Samah W Awwad
- Department of Biology, Technion, Israel Institute of Technology, Haifa 3200003, Israel
| | - Noga Guttmann-Raviv
- Department of Biology, Technion, Israel Institute of Technology, Haifa 3200003, Israel
| | - Nabieh Ayoub
- Department of Biology, Technion, Israel Institute of Technology, Haifa 3200003, Israel
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32
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Uberto R, Moomaw EW. Protein similarity networks reveal relationships among sequence, structure, and function within the Cupin superfamily. PLoS One 2013; 8:e74477. [PMID: 24040257 PMCID: PMC3765361 DOI: 10.1371/journal.pone.0074477] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/01/2013] [Indexed: 12/11/2022] Open
Abstract
The cupin superfamily is extremely diverse and includes catalytically inactive seed storage proteins, sugar-binding metal-independent epimerases, and metal-dependent enzymes possessing dioxygenase, decarboxylase, and other activities. Although numerous proteins of this superfamily have been structurally characterized, the functions of many of them have not been experimentally determined. We report the first use of protein similarity networks (PSNs) to visualize trends of sequence and structure in order to make functional inferences in this remarkably diverse superfamily. PSNs provide a way to visualize relatedness of structure and sequence among a given set of proteins. Structure- and sequence-based clustering of cupin members reflects functional clustering. Networks based only on cupin domains and networks based on the whole proteins provide complementary information. Domain-clustering supports phylogenetic conclusions that the N- and C-terminal domains of bicupin proteins evolved independently. Interestingly, although many functionally similar enzymatic cupin members bind the same active site metal ion, the structure and sequence clustering does not correlate with the identity of the bound metal. It is anticipated that the application of PSNs to this superfamily will inform experimental work and influence the functional annotation of databases.
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Affiliation(s)
- Richard Uberto
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Ellen W. Moomaw
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
- * E-mail:
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33
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Breathing-in epigenetic change with vitamin C. EMBO Rep 2013; 14:337-46. [PMID: 23492828 PMCID: PMC3615655 DOI: 10.1038/embor.2013.29] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 02/19/2013] [Indexed: 01/01/2023] Open
Abstract
Vitamin C is an antioxidant that maintains the activity of iron and α-ketoglutarate-dependent dioxygenases. Despite these enzymes being implicated in a wide range of biological pathways, vitamin C is rarely included in common cell culture media. Recent studies show that reprogramming of pluripotent stem cells is enhanced when vitamin C is present, thereby illustrating previous limitations in reprogramming cultures. Here, we summarize understanding of dioxygenase function in reprogramming and epigenetic regulation. The available data suggest a link between dioxygenase function and stem cell differentiation, which is exposed to environmental influence and is relevant for human disease.
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Structure-function analysis reveals a novel mechanism for regulation of histone demethylase LSD2/AOF1/KDM1b. Cell Res 2013; 23:225-41. [PMID: 23266887 PMCID: PMC3567814 DOI: 10.1038/cr.2012.177] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
LSD2/AOF1/KDM1b catalyzes demethylation of mono- and di-methylated H3K4 and plays an important role in transcriptional regulation and genomic imprinting. Here, we report the high-resolution crystal structures of apo-LSD2 and LSD2 in complex with a peptide that mimics H3K4me2. Three structural domains of LSD2, namely, the novel N-terminal zinc finger, the centrally located SWIRM domain, and the C-terminal oxidase domain, closely pack together to form a boot-shaped structure. The active site cavity in the oxidase domain is large enough to accommodate several residues of the histone H3 tail and cannot discriminate between the different states of H3K4 methylation. The N-terminal zinc-finger domain, composed of a novel C4H2C2-type zinc finger and a specific CW-type zinc finger, is required for demethylase activity and, surprisingly, the binding of cofactor flavin adenine dinucleotide (FAD). In fact, a relay of extensive interactions through the zinc finger-SWIRM-oxidase domains is required for LSD2 demethylase activity and the binding of FAD. These results reveal a novel mechanism for the zinc finger and SWIRM domains in controlling LSD2 demethylase activity and provide a framework for elucidating the regulation and function of LSD2.
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35
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Berdasco M, Esteller M. Genetic syndromes caused by mutations in epigenetic genes. Hum Genet 2013; 132:359-83. [PMID: 23370504 DOI: 10.1007/s00439-013-1271-x] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 01/18/2013] [Indexed: 12/21/2022]
Abstract
The orchestrated organization of epigenetic factors that control chromatin dynamism, including DNA methylation, histone marks, non-coding RNAs (ncRNAs) and chromatin-remodeling proteins, is essential for the proper function of tissue homeostasis, cell identity and development. Indeed, deregulation of epigenetic profiles has been described in several human pathologies, including complex diseases (such as cancer, cardiovascular and neurological diseases), metabolic pathologies (type 2 diabetes and obesity) and imprinting disorders. Over the last decade it has become increasingly clear that mutations of genes involved in epigenetic mechanism, such as DNA methyltransferases, methyl-binding domain proteins, histone deacetylases, histone methylases and members of the SWI/SNF family of chromatin remodelers are linked to human disorders, including Immunodeficiency Centromeric instability Facial syndrome 1, Rett syndrome, Rubinstein-Taybi syndrome, Sotos syndrome or alpha-thalassemia/mental retardation X-linked syndrome, among others. As new members of the epigenetic machinery are described, the number of human syndromes associated with epigenetic alterations increases. As recent examples, mutations of histone demethylases and members of the non-coding RNA machinery have recently been associated with Kabuki syndrome, Claes-Jensen X-linked mental retardation syndrome and Goiter syndrome. In this review, we describe the variety of germline mutations of epigenetic modifiers that are known to be associated with human disorders, and discuss the therapeutic potential of epigenetic drugs as palliative care strategies in the treatment of such disorders.
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Affiliation(s)
- María Berdasco
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 3rd Floor, Hospital Duran i Reynals, Av. Gran Via 199-203, 08908 L'Hospitalet de LLobregat, Barcelona, Catalonia, Spain
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36
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Zhang X, Zhang Q, Xin Q, Yu L, Wang Z, Wu W, Jiang L, Wang G, Tian W, Deng Z, Wang Y, Liu Z, Long J, Gong Z, Chen Z. Complex Structures of the Abscisic Acid Receptor PYL3/RCAR13 Reveal a Unique Regulatory Mechanism. Structure 2012; 20:780-90. [DOI: 10.1016/j.str.2012.02.019] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 02/20/2012] [Accepted: 02/21/2012] [Indexed: 10/28/2022]
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37
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Kooistra SM, Helin K. Molecular mechanisms and potential functions of histone demethylases. Nat Rev Mol Cell Biol 2012; 13:297-311. [PMID: 22473470 DOI: 10.1038/nrm3327] [Citation(s) in RCA: 612] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Histone modifications are thought to regulate chromatin structure, transcription and other nuclear processes. Histone methylation was originally believed to be an irreversible modification that could only be removed by histone eviction or by dilution during DNA replication. However, the isolation of two families of enzymes that can demethylate histones has changed this notion. The biochemical activities of these histone demethylases towards specific Lys residues on histones, and in some cases non-histone substrates, have highlighted their importance in developmental control, cell-fate decisions and disease. Their ability to be regulated through protein-targeting complexes and post-translational modifications is also beginning to shed light on how they provide dynamic control during transcription.
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Affiliation(s)
- Susanne Marije Kooistra
- Biotech Research and Innovation Centre and Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
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38
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Abstract
Posttranslational modifications (PTMs) of histone proteins, such as acetylation, methylation, phosphorylation, and ubiquitylation, play essential roles in regulating chromatin dynamics. Combinations of different modifications on the histone proteins, termed 'histone code' in many cases, extend the information potential of the genetic code by regulating DNA at the epigenetic level. Many PTMs occur on non-histone proteins as well as histones, regulating protein-protein interactions, stability, localization, and/or enzymatic activities of proteins involved in diverse cellular processes. Although protein phosphorylation, ubiquitylation, and acetylation have been extensively studied, only a few proteins other than histones have been reported that can be modified by lysine methylation. This review summarizes the current progress on lysine methylation of non-histone proteins, and we propose that lysine methylation, like phosphorylation and acetylation, is a common PTM that regulates proteins in diverse cellular processes.
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Affiliation(s)
- Xi Zhang
- Department of Biochemistry & Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, 77030, USA
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39
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Hillringhaus L, Yue WW, Rose NR, Ng SS, Gileadi C, Loenarz C, Bello SH, Bray JE, Schofield CJ, Oppermann U. Structural and evolutionary basis for the dual substrate selectivity of human KDM4 histone demethylase family. J Biol Chem 2011; 286:41616-41625. [PMID: 21914792 PMCID: PMC3308871 DOI: 10.1074/jbc.m111.283689] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 09/09/2011] [Indexed: 12/13/2022] Open
Abstract
N(ε)-Methylations of histone lysine residues play critical roles in cell biology by "marking" chromatin for transcriptional activation or repression. Lysine demethylases reverse N(ε)-methylation in a sequence- and methylation-selective manner. The determinants of sequence selectivity for histone demethylases have been unclear. The human JMJD2 (KDM4) H3K9 and H3K36 demethylases can be divided into members that act on both H3K9 and H3K36 and H3K9 alone. Kinetic, crystallographic, and mutagenetic studies in vitro and in cells on KDM4A-E reveal that selectivity is determined by multiple interactions within the catalytic domain but outside the active site. Structurally informed phylogenetic analyses reveal that KDM4A-C orthologues exist in all genome-sequenced vertebrates with earlier animals containing only a single KDM4 enzyme. KDM4D orthologues only exist in eutherians (placental mammals) where they are conserved, including proposed substrate sequence-determining residues. The results will be useful for the identification of inhibitors for specific histone demethylases.
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Affiliation(s)
- Lars Hillringhaus
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Wyatt W Yue
- Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington, OX3 7DQ, United Kingdom
| | - Nathan R Rose
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Stanley S Ng
- Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington, OX3 7DQ, United Kingdom
| | - Carina Gileadi
- Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington, OX3 7DQ, United Kingdom
| | - Christoph Loenarz
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Simon H Bello
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - James E Bray
- Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington, OX3 7DQ, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom.
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington, OX3 7DQ, United Kingdom; Botnar Research Centre, National Institute for Health Research Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology, and Musculoskeletal Sciences, Oxford, OX3 7LD, United Kingdom.
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40
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S phase-dependent interaction with DNMT1 dictates the role of UHRF1 but not UHRF2 in DNA methylation maintenance. Cell Res 2011; 21:1723-39. [PMID: 22064703 DOI: 10.1038/cr.2011.176] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recent studies demonstrate that UHRF1 is required for DNA methylation maintenance by targeting DNMT1 to DNA replication foci, presumably through its unique hemi-methylated DNA-binding activity and interaction with DNMT1. UHRF2, another member of the UHRF family proteins, is highly similar to UHRF1 in both sequence and structure, raising questions about its role in DNA methylation. In this study, we demonstrate that, like UHRF1, UHRF2 also binds preferentially to methylated histone H3 lysine 9 (H3K9) through its conserved tudor domain and hemi-methylated DNA through the SET and Ring associated domain. Like UHRF1, UHRF2 is enriched in pericentric heterochromatin. The heterochromatin localization depends to large extent on its methylated H3K9-binding activity and to less extent on its methylated DNA-binding activity. Coimmunoprecipitation experiments demonstrate that both UHRF1 and UHRF2 interact with DNMT1, DNMT3a, DNMT3b and G9a. Despite all these conserved functions, we find that UHRF2 is not able to rescue the DNA methylation defect in Uhrf1 null mouse embryonic stem cells. This can be attributed to the inability for UHRF2 to recruit DNMT1 to replication foci during S phase of the cell cycle. Indeed, we find that while UHRF1 interacts with DNMT1 in an S phase-dependent manner in cells, UHRF2 does not. Thus, our study demonstrates that UHRF2 and UHRF1 are not functionally redundant in DNA methylation maintenance and reveals the cell-cycle-dependent interaction between UHRF1 and DNMT1 as a key regulatory mechanism targeting DNMT1 for DNA methylation.
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Rotili D, Altun M, Kawamura A, Wolf A, Fischer R, Leung IKH, Mackeen MM, Tian YM, Ratcliffe PJ, Mai A, Kessler BM, Schofield CJ. A photoreactive small-molecule probe for 2-oxoglutarate oxygenases. ACTA ACUST UNITED AC 2011; 18:642-654. [PMID: 21609845 DOI: 10.1016/j.chembiol.2011.03.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 03/01/2011] [Accepted: 03/02/2011] [Indexed: 11/29/2022]
Abstract
2-oxoglutarate (2-OG)-dependent oxygenases have diverse roles in human biology. The inhibition of several 2-OG oxygenases is being targeted for therapeutic intervention, including for cancer, anemia, and ischemic diseases. We report a small-molecule probe for 2-OG oxygenases that employs a hydroxyquinoline template coupled to a photoactivable crosslinking group and an affinity-purification tag. Following studies with recombinant proteins, the probe was shown to crosslink to 2-OG oxygenases in human crude cell extracts, including to proteins at endogenous levels. This approach is useful for inhibitor profiling, as demonstrated by crosslinking to the histone demethylase FBXL11 (KDM2A) in HEK293T nuclear extracts. The results also suggest that small-molecule probes may be suitable for substrate identification studies.
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Affiliation(s)
- Dante Rotili
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom.,Pasteur Institute - Cenci Bolognetti Foundation, Department of Chemistry and Technologies of Drugs, University of Rome "La Sapienza", P.le A. Moro 5, 00185 Rome, Italy
| | - Mikael Altun
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Akane Kawamura
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Alexander Wolf
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Roman Fischer
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Ivanhoe K H Leung
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Mukram M Mackeen
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Ya-Min Tian
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Peter J Ratcliffe
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Antonello Mai
- Pasteur Institute - Cenci Bolognetti Foundation, Department of Chemistry and Technologies of Drugs, University of Rome "La Sapienza", P.le A. Moro 5, 00185 Rome, Italy
| | - Benedikt M Kessler
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
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42
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The Histone Demethylase PHF8 and Neural Development*. PROG BIOCHEM BIOPHYS 2011. [DOI: 10.3724/sp.j.1206.2010.00390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Giri NC, Sun H, Chen H, Costa M, Maroney MJ. X-ray absorption spectroscopy structural investigation of early intermediates in the mechanism of DNA repair by human ABH2. Biochemistry 2011; 50:5067-76. [PMID: 21510633 PMCID: PMC3124014 DOI: 10.1021/bi101668x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human ABH2 repairs DNA lesions by using an Fe(II)- and αKG-dependent oxidative demethylation mechanism. The structure of the active site features the facial triad of protein ligands consisting of the side chains of two histidine residues and one aspartate residue that is common to many non-heme Fe(II) oxygenases. X-ray absorption spectroscopy (XAS) of metallated (Fe and Ni) samples of ABH2 was used to investigate the mechanism of ABH2 and its inhibition by Ni(II) ions. The data are consistent with a sequential mechanism that features a five-coordinate metal center in the presence and absence of the α-ketoglutarate cofactor. This aspect is not altered in the Ni(II)-substituted enzyme, and both metals are shown to bind the cofactor. When the substrate is bound to the native Fe(II) complex with α-ketoglutarate bound, a five-coordinate Fe(II) center is retained that features an open coordination position for O(2) binding. However, in the case of the Ni(II)-substituted enzyme, the complex that forms in the presence of the cofactor and substrate is six-coordinate and, therefore, features no open coordination site for oxygen activation at the metal.
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Affiliation(s)
- Nitai Charan Giri
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, phone number 413-545-4876, fax number 413-545-4490
| | - Hong Sun
- Department of Environmental Medicine, New York University School of Medicine, New York 10016
| | - Haobin Chen
- Department of Environmental Medicine, New York University School of Medicine, New York 10016
| | - Max Costa
- Department of Environmental Medicine, New York University School of Medicine, New York 10016
| | - Michael J. Maroney
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, phone number 413-545-4876, fax number 413-545-4490
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Lohse B, Kristensen JL, Kristensen LH, Agger K, Helin K, Gajhede M, Clausen RP. Inhibitors of histone demethylases. Bioorg Med Chem 2011; 19:3625-36. [DOI: 10.1016/j.bmc.2011.01.046] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2010] [Revised: 01/19/2011] [Accepted: 01/22/2011] [Indexed: 12/22/2022]
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Blair LP, Avaritt NL, Huang R, Cole PA, Taverna SD, Tackett AJ. MassSQUIRM: An assay for quantitative measurement of lysine demethylase activity. Epigenetics 2011; 6:490-9. [PMID: 21273814 DOI: 10.4161/epi.6.4.14531] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In eukaryotes, DNA is wrapped around proteins called histones and is condensed into chromatin. Post-translational modification of histones can result in changes in gene expression. One of the most well-studied histone modifications is the methylation of lysine 4 on histone H3 (H3K4). This residue can be mono-, di- or tri-methylated and these varying methylation states have been associated with different levels of gene expression. Understanding exactly what the purpose of these methylation states is, in terms of gene expression, has been a topic of much research in recent years. Enzymes that can add (methyltransferases) and remove (demethylases) these modifications are of particular interest. The first demethylase discovered, LSD1, is the most well-classified and has been implicated in contributing to human cancers and to DNA damage response pathways. Currently, there are limited methods for accurately studying the activity of demethylases in vitro or in vivo. In this work, we present MassSQUIRM (mass spectrometric quantitation using isotopic reductive methylation), a quantitative method for studying the activity of demethylases capable of removing mono- and di-methyl marks from lysine residues. We focus specifically on LSD1 due to its potential as a prime therapeutic target for human disease. This quantitative approach will enable better characterization of the activity of LSD1 and other chromatin modifying enzymes in vitro, in vivo or in response to inhibitors.
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Affiliation(s)
- Lauren P Blair
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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46
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Krishnan S, Horowitz S, Trievel RC. Structure and function of histone H3 lysine 9 methyltransferases and demethylases. Chembiochem 2011; 12:254-63. [PMID: 21243713 DOI: 10.1002/cbic.201000545] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Indexed: 12/20/2022]
Abstract
Histone lysine methylation is a dynamic chromatin modification that plays key regulatory roles in gene expression and other genomic functions. Methylation of Lys9 in histone H3 (H3K9) is a prominent modification that has been implicated in diverse processes, including transcriptional silencing, heterochromatin formation, and DNA methylation. In this review, we summarize recent advances in understanding the structure and substrate specificity of the H3K9-specific methyltransferases G9A and GLP and explore current efforts to develop inhibitors of these enzymes. In addition, we discuss the structure and specificity of the recently discovered PHF8 family of histone demethylases that target H3K9 as well as other methylation sites in histones H3 and H4. Finally, we conclude by comparing the H3K9 binding modes displayed by these enzymes and examine the relevance of these studies to their biological functions and to structure-based inhibitor design.
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Affiliation(s)
- Swathi Krishnan
- University of Michigan Medical School, Department of Biological Chemistry, Ann Arbor, MI 48109, USA
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47
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Fortschegger K, Shiekhattar R. Plant homeodomain fingers form a helping hand for transcription. Epigenetics 2011; 6:4-8. [PMID: 20818169 DOI: 10.4161/epi.6.1.13297] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Several recent publications demonstrate a co-activator function for a subgroup of plant homeodomain fingers, which in humans comprises PHF2, PHF8 and KIAA1718. Besides an N-terminal plant homeodomain (PHD) these proteins also harbor an enzymatically active Jumonji-C domain (JmjC). While they have been shown to bind via their PHDs to H3K4me3-bearing nucleosomes at active gene promoters, their JmjC-domains are able to remove mono- and dimethyl-lysine 9 or 27 on histone H3, and monomethyl-lysine 20 on histone H4, chromatin modifications which correlate with transcriptional repression. Such dual histone crosstalk insures the proper removal of repressive histone marks following transcriptional activation by RNA polymerases I and II. Mutations in the PHF8 gene lead to X-linked mental retardation (XLMR) and knockdown of KIAA1718 and PHF8 homologs in zebrafish causes brain defects. Thus, the co-activator function of this new class of chromatin modifying enzymes has important functional roles in neuronal development. To continue with the nomenclature for histone demethylases, we propose the usage of KDM7A, -B and -C for KIAA1718, PHF8 and PHF2 proteins, respectively.
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48
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McDonough MA, Loenarz C, Chowdhury R, Clifton IJ, Schofield CJ. Structural studies on human 2-oxoglutarate dependent oxygenases. Curr Opin Struct Biol 2010; 20:659-72. [PMID: 20888218 DOI: 10.1016/j.sbi.2010.08.006] [Citation(s) in RCA: 209] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 08/19/2010] [Indexed: 01/14/2023]
Abstract
2-Oxoglutarate and ferrous iron-dependent oxygenases have emerged as an important family of human enzymes that catalyse hydroxylations and related demethylation reactions. Their substrates in humans include proteins, nucleic acids, lipids and small molecules. They play roles in collagen biosynthesis, hypoxic sensing, regulation of gene expression and lipid biosynthesis/metabolism. Structural analyses, principally employing crystallography, have revealed that all of these oxygenases possess a double-stranded β-helix core fold that supports a highly conserved triad of iron binding residues and a less well conserved 2-oxoglutarate co-substrate binding site. The 2-oxoglutarate binds to the iron in a bidentate manner via its 1-carboxylate and 2-oxo groups. The primary substrate binding elements are more variable and can involve mobile elements.
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Affiliation(s)
- Michael A McDonough
- Chemistry Research Laboratory and the Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford OX1 3TA, UK
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49
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Pedersen MT, Helin K. Histone demethylases in development and disease. Trends Cell Biol 2010; 20:662-71. [PMID: 20863703 DOI: 10.1016/j.tcb.2010.08.011] [Citation(s) in RCA: 273] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 08/09/2010] [Accepted: 08/23/2010] [Indexed: 01/21/2023]
Abstract
Histone modifications serve as regulatory marks that are instrumental for the control of transcription and chromatin architecture. Strict regulation of gene expression patterns is crucial during development and differentiation, where diverse cell types evolve from common predecessors. Since the first histone lysine demethylase was discovered in 2004, a number of demethylases have been identified and implicated in the control of gene expression programmes and cell fate decisions. Histone demethylases are now emerging as important players in developmental processes and have been linked to human diseases such as neurological disorders and cancer.
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Affiliation(s)
- Marianne Terndrup Pedersen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, Denmark
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50
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Affiliation(s)
- Tamaki Suganuma
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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