1
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Damizia M, Moretta GM, De Wulf P. The RioK1 network determines p53 activity at multiple levels. Cell Death Discov 2023; 9:410. [PMID: 37935656 PMCID: PMC10630321 DOI: 10.1038/s41420-023-01704-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/09/2023] Open
Abstract
By responding to a host of adverse conditions, ranging from DNA damage to viral infection, transcription factor p53 supports genomic stability, cellular health, and survival. Not surprisingly, tumours across the cancer spectrum carry mutations in p53, misexpress the protein, or dysregulate its activity. Several signalling pathways, many of which comprise oncogenic proteins, converge upon p53 to control its stability and activity. We here present the conserved kinase/ATPase RioK1 as an upstream factor that determines p53 activity at the DNA, RNA, and protein levels. It achieves this task by integrating the regulatory events that act on p53 into a coherent response circuit. We will also discuss how RIOK1 overexpression represents an alternative mechanism for cancers to inactivate p53, and how targeting RioK1 could eradicate malignancies that are driven by a dysregulated RioK1-p53 network.
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Affiliation(s)
- Michela Damizia
- Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, 38123, Trento (TN), Italy
| | - Gian Mario Moretta
- Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, 38123, Trento (TN), Italy
| | - Peter De Wulf
- Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, 38123, Trento (TN), Italy.
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2
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Handle F, Puhr M, Gruber M, Andolfi C, Schäfer G, Klocker H, Haybaeck J, De Wulf P, Culig Z. The Oncogenic Protein Kinase/ATPase RIOK1 Is Up-Regulated via the c-myc/E2F Transcription Factor Axis in Prostate Cancer. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:1284-1297. [PMID: 37301535 DOI: 10.1016/j.ajpath.2023.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/12/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023]
Abstract
The atypical protein kinase/ATPase RIO kinase (RIOK)-1 is involved in pre-40S ribosomal subunit production, cell-cycle progression, and protein arginine N-methyltransferase 5 methylosome substrate recruitment. RIOK1 overexpression is a characteristic of several malignancies and is correlated with cancer stage, therapy resistance, poor patient survival, and other prognostic factors. However, its role in prostate cancer (PCa) is unknown. In this study, the expression, regulation, and therapeutic potential of RIOK1 in PCa were examined. RIOK1 mRNA and protein expression were elevated in PCa tissue samples and correlated with proliferative and protein homeostasis-related pathways. RIOK1 was identified as a downstream target gene of the c-myc/E2F transcription factors. Proliferation of PCa cells was significantly reduced with RIOK1 knockdown and overexpression of the dominant-negative RIOK1-D324A mutant. Biochemical inhibition of RIOK1 with toyocamycin led to strong antiproliferative effects in androgen receptor-negative and -positive PCa cell lines with EC50 values of 3.5 to 8.8 nmol/L. Rapid decreases in RIOK1 protein expression and total rRNA content, and a shift in the 28S/18S rRNA ratio, were found with toyocamycin treatment. Apoptosis was induced with toyocamycin treatment at a level similar to that with the chemotherapeutic drug docetaxel used in clinical practice. In summary, the current study indicates that RIOK1 is a part of the MYC oncogene network, and as such, could be considered for future treatment of patients with PCa.
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Affiliation(s)
- Florian Handle
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria; Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Innsbruck, Austria
| | - Martin Puhr
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Martina Gruber
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Chiara Andolfi
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Georg Schäfer
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Innsbruck, Austria
| | - Helmut Klocker
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Johannes Haybaeck
- Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck, Innsbruck, Austria; Diagnostic and Research Center for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Peter De Wulf
- Department of Cellular, Computational, and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Zoran Culig
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria.
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3
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Amgalan B, Day CP, Przytycka TM. Exploring tumor-normal cross-talk with TranNet: Role of the environment in tumor progression. PLoS Comput Biol 2023; 19:e1011472. [PMID: 37721939 PMCID: PMC10538798 DOI: 10.1371/journal.pcbi.1011472] [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: 07/11/2023] [Revised: 09/28/2023] [Accepted: 08/23/2023] [Indexed: 09/20/2023] Open
Abstract
There is a growing awareness that tumor-adjacent normal tissues used as control samples in cancer studies do not represent fully healthy tissues. Instead, they are intermediates between healthy tissues and tumors. The factors that contribute to the deviation of such control samples from healthy state include exposure to the tumor-promoting factors, tumor-related immune response, and other aspects of tumor microenvironment. Characterizing the relation between gene expression of tumor-adjacent control samples and tumors is fundamental for understanding roles of microenvironment in tumor initiation and progression, as well as for identification of diagnostic and prognostic biomarkers for cancers. To address the demand, we developed and validated TranNet, a computational approach that utilizes gene expression in matched control and tumor samples to study the relation between their gene expression profiles. TranNet infers a sparse weighted bipartite graph from gene expression profiles of matched control samples to tumors. The results allow us to identify predictors (potential regulators) of this transition. To our knowledge, TranNet is the first computational method to infer such dependencies. We applied TranNet to the data of several cancer types and their matched control samples from The Cancer Genome Atlas (TCGA). Many predictors identified by TranNet are genes associated with regulation by the tumor microenvironment as they are enriched in G-protein coupled receptor signaling, cell-to-cell communication, immune processes, and cell adhesion. Correspondingly, targets of inferred predictors are enriched in pathways related to tissue remodelling (including the epithelial-mesenchymal Transition (EMT)), immune response, and cell proliferation. This implies that the predictors are markers and potential stromal facilitators of tumor progression. Our results provide new insights into the relationships between tumor adjacent control sample, tumor and the tumor environment. Moreover, the set of predictors identified by TranNet will provide a valuable resource for future investigations.
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Affiliation(s)
- Bayarbaatar Amgalan
- National Center for Biotechnology Information/National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics/Center for Cancer Research/National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Teresa M. Przytycka
- National Center for Biotechnology Information/National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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4
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Yi J, Wang L, Du J, Wang M, Shen H, Liu Z, Qin Y, Liu J, Hu G, Xiao R, Ding J, Chen X, Wang H, Huang H, Ouyang G, Liu W. ER-localized JmjC domain-containing protein JMJD8 targets STING to promote immune evasion and tumor growth in breast cancer. Dev Cell 2023; 58:760-778.e6. [PMID: 37054705 DOI: 10.1016/j.devcel.2023.03.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 01/15/2023] [Accepted: 03/20/2023] [Indexed: 04/15/2023]
Abstract
The STING-mediated type I interferon (IFN) signaling pathway has been shown to play critical roles in antitumor immunity. Here, we demonstrate that an endoplasmic reticulum (ER)-localized JmjC domain-containing protein, JMJD8, inhibits STING-induced type I IFN responses to promote immune evasion and breast tumorigenesis. Mechanistically, JMJD8 competes with TBK1 for binding with STING, blocking STING-TBK1 complex formation and restricting type I IFN and IFN-stimulated gene (ISG) expression as well as immune cell infiltration. JMJD8 knockdown improves the efficacy of chemotherapy and immune checkpoint therapy in treating both human and mouse breast cancer cell-derived implanted tumors. The clinical relevance is highlighted in that JMJD8 is highly expressed in human breast tumor samples, and its expression is inversely correlated with that of type I IFN and ISGs as well as immune cell infiltration. Overall, our study found that JMJD8 regulates type I IFN responses, and targeting JMJD8 triggers antitumor immunity.
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Affiliation(s)
- Jia Yi
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Lei Wang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Jiao Du
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Mingyue Wang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Haifeng Shen
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Zhiying Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Yao Qin
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Jing Liu
- Xiamen University-Amogene Joint R&D Center for Genetic Diagnostics, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Guosheng Hu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Rongquan Xiao
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Jiancheng Ding
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Xiaoyan Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Hongjiao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Haihua Huang
- Department of Pathology, The Second Affiliated Hospital, Shantou University Medical College, Dongxia North Road, Shantou, Guangdong 515041, China
| | - Gaoliang Ouyang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China.
| | - Wen Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China.
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5
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Das ND, Niwa H, Umehara T. Chemical Inhibitors Targeting the Histone Lysine Demethylase Families with Potential for Drug Discovery. EPIGENOMES 2023; 7:epigenomes7010007. [PMID: 36975603 PMCID: PMC10048553 DOI: 10.3390/epigenomes7010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/21/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
The dynamic regulation of histone methylation and demethylation plays an important role in the regulation of gene expression. Aberrant expression of histone lysine demethylases has been implicated in various diseases including intractable cancers, and thus lysine demethylases serve as promising therapeutic targets. Recent studies in epigenomics and chemical biology have led to the development of a series of small-molecule demethylase inhibitors that are potent, specific, and have in vivo efficacy. In this review, we highlight emerging small-molecule inhibitors targeting the histone lysine demethylases and their progress toward drug discovery.
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6
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Türkmen VA, Hintzen JCJ, Tumber A, Moesgaard L, Salah E, Kongsted J, Schofield CJ, Mecinović J. Substrate selectivity and inhibition of histidine JmjC hydroxylases MINA53 and NO66. RSC Chem Biol 2023; 4:235-243. [PMID: 36908702 PMCID: PMC9994133 DOI: 10.1039/d2cb00182a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/12/2023] [Indexed: 01/15/2023] Open
Abstract
Non-haem Fe(ii) and 2-oxoglutarate (2OG) dependent oxygenases catalyse oxidation of multiple proteins in organisms ranging from bacteria to humans. We describe studies on the substrate selectivity and inhibition of the human ribosomal oxygenases (ROX) MINA53 and NO66, members of the JmjC 2OG oxygenase subfamily, which catalyse C-3 hydroxylation of histidine residues in Rpl27a and Rpl8, respectively. Assays with natural and unnatural histidine analogues incorporated into Rpl peptides provide evidence that MINA53 and NO66 have narrow substrate selectivities compared to some other human JmjC hydroxylases, including factor inhibiting HIF and JMJD6. Notably, the results of inhibition assays with Rpl peptides containing histidine analogues with acyclic side chains, including Asn, Gln and homoGln, suggest the activities of MINA53/NO66, and by implication related 2OG dependent protein hydroxylases/demethylases, might be regulated in vivo by competition with non-oxidised proteins/peptides. The inhibition results also provide avenues for development of inhibitors selective for MINA53 and NO66.
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Affiliation(s)
- Vildan A Türkmen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
| | - Jordi C J Hintzen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
| | - Anthony Tumber
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road OX1 3TA Oxford UK
| | - Laust Moesgaard
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
| | - Eidarus Salah
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road OX1 3TA Oxford UK
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
| | - Christopher J Schofield
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road OX1 3TA Oxford UK
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
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7
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Amgalan B, Day CP, Przytycka TM. Exploring tumor-normal cross-talk with TranNet: role of the environment in tumor progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529899. [PMID: 36945455 PMCID: PMC10028821 DOI: 10.1101/2023.02.24.529899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
There is a growing awareness that tumor-adjacent normal tissues used as control samples in cancer studies do not represent fully healthy tissues. Instead, they are intermediates between healthy tissues and tumors. The factors that contribute to the deviation of such control samples from healthy state include exposure to the tumor-promoting factors, tumor-related immune response, and other aspects of tumor microenvironment. Characterizing the relation between gene expression of tumor-adjacent control samples and tumors is fundamental for understanding roles of microenvironment in tumor initiation and progression, as well as for identification of diagnostic and prognostic biomarkers for cancers. To address the demand, we developed and validated TranNet, a computational approach that utilizes gene expression in matched control and tumor samples to study the relation between their gene expression profiles. TranNet infers a sparse weighted bipartite graph from gene expression profiles of matched control samples to tumors. The results allow us to identify predictors (potential regulators) of this transition. To our knowledge, TranNet is the first computational method to infer such regulation. We applied TranNet to the data of several cancer types and their matched control samples from The Cancer Genome Atlas (TCGA). Many predictors identified by TranNet are genes associated with regulation by the tumor microenvironment as they are enriched in G-protein coupled receptor signaling, cell-to-cell communication, immune processes, and cell adhesion. Correspondingly, targets of inferred predictors are enriched in pathways related to tissue remodelling (including the epithelial-mesenchymal Transition (EMT)), immune response, and cell proliferation. This implies that the predictors are markers and potential stromal facilitators of tumor progression. Our results provide new insights for the relationships between tumor adjacent control sample, tumor and the tumor environment. Moreover, the set of predictors identified by TranNet will provide a valuable resource for future investigations. The TranNet method was implemented in python, source codes and the data sets used for and generated during this study are available at the Github site https://github.com/ncbi/TranNet .
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Affiliation(s)
- Bayarbaatar Amgalan
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, USA
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Teresa M. Przytycka
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, Maryland, USA
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8
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Nowak R, Tumber A, Hendrix E, Ansari MS, Sabatino M, Antonini L, Andrijes R, Salah E, Mautone N, Pellegrini FR, Simelis K, Kawamura A, Johansson C, Passeri D, Pellicciari R, Ciogli A, Del Bufalo D, Ragno R, Coleman ML, Trisciuoglio D, Mai A, Oppermann U, Schofield CJ, Rotili D. First-in-Class Inhibitors of the Ribosomal Oxygenase MINA53. J Med Chem 2021; 64:17031-17050. [PMID: 34843649 PMCID: PMC8667043 DOI: 10.1021/acs.jmedchem.1c00605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Indexed: 01/05/2023]
Abstract
MINA53 is a JmjC domain 2-oxoglutarate-dependent oxygenase that catalyzes ribosomal hydroxylation and is a target of the oncogenic transcription factor c-MYC. Despite its anticancer target potential, no small-molecule MINA53 inhibitors are reported. Using ribosomal substrate fragments, we developed mass spectrometry assays for MINA53 and the related oxygenase NO66. These assays enabled the identification of 2-(aryl)alkylthio-3,4-dihydro-4-oxoypyrimidine-5-carboxylic acids as potent MINA53 inhibitors, with selectivity over NO66 and other JmjC oxygenases. Crystallographic studies with the JmjC demethylase KDM5B revealed active site binding but without direct metal chelation; however, molecular modeling investigations indicated that the inhibitors bind to MINA53 by directly interacting with the iron cofactor. The MINA53 inhibitors manifest evidence for target engagement and selectivity for MINA53 over KDM4-6. The MINA53 inhibitors show antiproliferative activity with solid cancer lines and sensitize cancer cells to conventional chemotherapy, suggesting that further work investigating their potential in combination therapies is warranted.
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Affiliation(s)
- Radosław
P. Nowak
- Botnar
Research Centre, Nuffield Orthopaedic Centre, University of Oxford, Headington OX3 7LD, U.K.
| | - Anthony Tumber
- Botnar
Research Centre, Nuffield Orthopaedic Centre, University of Oxford, Headington OX3 7LD, U.K.
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, 12, Mansfield Road, University of Oxford, Oxford OX1 3TA, U.K.
| | - Eline Hendrix
- Institute
of Cancer and Genomic Sciences, University
of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Mohammad Salik
Zeya Ansari
- Institute
of Molecular Biology and Pathology (IMBP), National Research Council
(CNR) c/o Department of Biology and Biotechnology “Charles
Darwin” Sapienza University of Rome, Via degli Apuli 4, Rome 00185, Italy
| | - Manuela Sabatino
- Rome
Center for Molecular Design, Department of Chemistry and Technology
of Drugs, ″Sapienza″ University
of Rome, Piazzale Aldo
Moro 5, Rome 00185, Italy
| | - Lorenzo Antonini
- Rome
Center for Molecular Design, Department of Chemistry and Technology
of Drugs, ″Sapienza″ University
of Rome, Piazzale Aldo
Moro 5, Rome 00185, Italy
| | - Regina Andrijes
- Institute
of Cancer and Genomic Sciences, University
of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, 12, Mansfield Road, University of Oxford, Oxford OX1 3TA, U.K.
| | - Nicola Mautone
- Department
of Chemistry and Technology of Drugs, ″Sapienza″
University of Rome, Piazzale
Aldo Moro 5, Rome 00185, Italy
| | - Francesca Romana Pellegrini
- Institute
of Molecular Biology and Pathology (IMBP), National Research Council
(CNR) c/o Department of Biology and Biotechnology “Charles
Darwin” Sapienza University of Rome, Via degli Apuli 4, Rome 00185, Italy
| | - Klemensas Simelis
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, 12, Mansfield Road, University of Oxford, Oxford OX1 3TA, U.K.
| | - Akane Kawamura
- Chemistry
- School of Natural and Environmental Sciences, Newcastle University, Newcastle
upon Tyne NE1 7RU, U.K.
| | - Catrine Johansson
- Botnar
Research Centre, Nuffield Orthopaedic Centre, University of Oxford, Headington OX3 7LD, U.K.
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, 12, Mansfield Road, University of Oxford, Oxford OX1 3TA, U.K.
| | - Daniela Passeri
- TES
Pharma S.r.l. Via P. Togliatti 20, Corciano, Perugia 06073, Italy
| | | | - Alessia Ciogli
- Department
of Chemistry and Technology of Drugs, ″Sapienza″
University of Rome, Piazzale
Aldo Moro 5, Rome 00185, Italy
| | - Donatella Del Bufalo
- Preclinical
Models and New Therapeutic Agents Unit, IRCCS-Regina Elena National Cancer Institute, Via Elio Chianesi 53, Rome 00144, Italy
| | - Rino Ragno
- Rome
Center for Molecular Design, Department of Chemistry and Technology
of Drugs, ″Sapienza″ University
of Rome, Piazzale Aldo
Moro 5, Rome 00185, Italy
| | - Mathew L. Coleman
- Institute
of Cancer and Genomic Sciences, University
of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Daniela Trisciuoglio
- Institute
of Molecular Biology and Pathology (IMBP), National Research Council
(CNR) c/o Department of Biology and Biotechnology “Charles
Darwin” Sapienza University of Rome, Via degli Apuli 4, Rome 00185, Italy
| | - Antonello Mai
- Department
of Chemistry and Technology of Drugs, ″Sapienza″
University of Rome, Piazzale
Aldo Moro 5, Rome 00185, Italy
| | - Udo Oppermann
- Botnar
Research Centre, Nuffield Orthopaedic Centre, University of Oxford, Headington OX3 7LD, U.K.
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, 12, Mansfield Road, University of Oxford, Oxford OX1 3TA, U.K.
| | - Dante Rotili
- Department
of Chemistry and Technology of Drugs, ″Sapienza″
University of Rome, Piazzale
Aldo Moro 5, Rome 00185, Italy
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9
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Ataei A, Arab SS, Zahiri J, Rajabpour A, Kletenkov K, Rizvanov A. Filtering of the Gene Signature as the Predictors of Cisplatin-Resistance in Ovarian Cancer. IRANIAN JOURNAL OF BIOTECHNOLOGY 2021; 19:e2643. [PMID: 34825010 PMCID: PMC8590720 DOI: 10.30498/ijb.2021.209370.2643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
BACKGROUND Gene expression profiling and prediction of drug responses based on the molecular signature indicate new molecular biomarkers which help to find the most effective drugs according to the tumor characteristics. OBJECTIVES In this study two independent datasets, GSE28646 and GSE15372 were subjected to meta-analysis based on Affymetrix microarrays. MATERIAL AND METHODS In-silico methods were used to determine differentially expressed genes (DEGs) in the previously reported sensitive and resistant A2780 cell lines to Cisplatin. Gene Fuzzy Scoring (GFS) and Principle Component Analysis (PCA) were then used to eliminate batch effects and reduce data dimension, respectively. Moreover, SVM method was performed to classify sensitive and resistant data samples. Furthermore, Wilcoxon Rank sum test was performed to determine DEGs. Following the selection of drug resistance markers, several networks including transcription factor-target regulatory network and miRNA-target network were constructed and Differential correlation analysis was performed on these networks. RESULTS The trained SVM successfully classified sensitive and resistant data samples. Moreover, Performing DiffCorr analysis on the sensitive and resistant samples resulted in detection of 27 and 25 significant (with correlation ≥|0.9|) pairs of genes that respectively correspond to newly constructed correlations and loss of correlations in the resistant samples. CONCLUSIONS Our results indicated the functional genes and networks in Cisplatin resistance of ovarian cancer cells and support the importance of differential expression studies in ovarian cancer chemotherapeutic agent responsiveness.
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Affiliation(s)
- Atousa Ataei
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Javad Zahiri
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Azam Rajabpour
- Department of Molecular medicine, Pasteur Institute of Iran, Tehran, Iran
| | - Konstantin Kletenkov
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Albert Rizvanov
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
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10
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Deng H, Yu B, Yu Y, Tian G, Yang L. NO66 overexpression rescues ethanol-induced cell apoptosis in human AC16 cardiomyocytes by suppressing PTEN and activating the PI3K/Akt signaling. Acta Biochim Biophys Sin (Shanghai) 2020; 52:1093-1101. [PMID: 33085743 DOI: 10.1093/abbs/gmaa100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 02/06/2023] Open
Abstract
Previously, Nucleolar protein 66 (NO66) was reported to be closely associated with alcohol exposure-induced injury. However, the role of NO66 in alcohol-induced cytotoxicity remains unclear. In this study, we explored the potential effect and mechanism of NO66 on ethanol-induced apoptosis in human AC16 cardiomyocytes. The AC16 cell lines with NO66 and phosphatase and tensin homolog (PTEN) overexpression were constructed. Cell counting kit-8 (CCK-8), lactate dehydrogenase (LDH) assay, Annexin V-FITC/PI staining, and flow cytometry were used to evaluate the cell viability, membrane damage, and apoptosis, respectively. Quantitative real-time PCR (qRT-PCR) and western blot analysis were applied to measure mRNA and protein expression. The results showed that acute ethanol exposure markedly augmented cytotoxicity and reduced NO66 level in AC16 cardiomyocytes. Overexpression of NO66 partially reversed ethanol-induced apoptosis. NO66 upregulation reversed the decrease in phosphorylation of protein kinase B (Akt) and B-cell lymphoma-2/Bcl-2-associated x (Bcl-2/Bax) ratio and the increase in PTEN, p53, and caspase-3 activity induced by ethanol treatment. Meanwhile, the application of PI3K inhibitor (LY294002) and PTEN overexpression attenuated the inhibition efficiency of NO66 on cell apoptosis. In addition, PTEN overexpression weakened the effect of NO66 on PI3K/Akt activation, without affecting the level of NO66. Our data suggested that NO66 overexpression might play an anti-apoptotic role in ethanol-induced cell injury via reducing PTEN and upregulating the PI3K/Akt pathway.
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Affiliation(s)
- Hanyu Deng
- Department of Cardiology, the First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Bo Yu
- Department of Cardiology, the First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Yang Yu
- Department of Cardiology, the First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Ge Tian
- Department of Cardiology, Jinzhou Medical University, Jinzhou 121001, China
| | - Liu Yang
- Department of Cardiology, the First Affiliated Hospital of China Medical University, Shenyang 110001, China
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11
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Nakamura M, Takano A, Thang PM, Tsevegjav B, Zhu M, Yokose T, Yamashita T, Miyagi Y, Daigo Y. Characterization of KIF20A as a prognostic biomarker and therapeutic target for different subtypes of breast cancer. Int J Oncol 2020; 57:277-288. [PMID: 32467984 DOI: 10.3892/ijo.2020.5060] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/06/2020] [Indexed: 11/05/2022] Open
Abstract
The aim of the present study was to identify novel prognostic biomarkers and therapeutic targets for breast cancer; thus, genes that are frequently overexpressed in several types of breast cancer were screened. Kinesin family member 20A (KIF20A) was identified as a candidate molecule during this process. Immunohistochemical staining performed using tissue microarrays from 257 samples of different breast cancer subtypes revealed that KIF20A was expressed in 195 (75.9%) of these samples, whereas it was seldom expressed in normal breast tissue. KIF20A protein was expressed in all types of breast cancer observed. However, it was more frequently expressed in human epidermal growth factor receptor 2 (HER2)‑positive and triple‑negative breast cancer than in the luminal type. Moreover, KIF20A expression was significantly associated with the poor prognosis of patients with breast cancer. A multivariate analysis indicated that KIF20A expression was an independent prognostic factor for patients with breast cancer. The suppression of endogenous KIF20A expression using small interfering ribonucleic acids or via treatment with paprotrain, a selective inhibitor of KIF20A, significantly inhibited breast cancer cell growth through cell cycle arrest at the G2/M phase and subsequent mitotic cell death. These results suggest that KIF20A is a candidate prognostic biomarker and therapeutic target for different types of breast cancer.
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Affiliation(s)
- Masako Nakamura
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520‑2192, Japan
| | - Atsushi Takano
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520‑2192, Japan
| | - Phung Manh Thang
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520‑2192, Japan
| | - Bayarbat Tsevegjav
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520‑2192, Japan
| | - Ming Zhu
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520‑2192, Japan
| | - Tomoyuki Yokose
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Kanagawa 241‑8515, Japan
| | - Toshinari Yamashita
- Department of Breast and Endocrine Surgery, Kanagawa Cancer Center, Yokohama, Kanagawa 241‑8515, Japan
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Kanagawa 241‑8515, Japan
| | - Yataro Daigo
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520‑2192, Japan
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12
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Blanquart C, Linot C, Cartron PF, Tomaselli D, Mai A, Bertrand P. Epigenetic Metalloenzymes. Curr Med Chem 2019; 26:2748-2785. [PMID: 29984644 DOI: 10.2174/0929867325666180706105903] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 12/12/2022]
Abstract
Epigenetics controls the expression of genes and is responsible for cellular phenotypes. The fundamental basis of these mechanisms involves in part the post-translational modifications (PTMs) of DNA and proteins, in particular, the nuclear histones. DNA can be methylated or demethylated on cytosine. Histones are marked by several modifications including acetylation and/or methylation, and of particular importance are the covalent modifications of lysine. There exists a balance between addition and removal of these PTMs, leading to three groups of enzymes involved in these processes: the writers adding marks, the erasers removing them, and the readers able to detect these marks and participating in the recruitment of transcription factors. The stimulation or the repression in the expression of genes is thus the result of a subtle equilibrium between all the possibilities coming from the combinations of these PTMs. Indeed, these mechanisms can be deregulated and then participate in the appearance, development and maintenance of various human diseases, including cancers, neurological and metabolic disorders. Some of the key players in epigenetics are metalloenzymes, belonging mostly to the group of erasers: the zinc-dependent histone deacetylases (HDACs), the iron-dependent lysine demethylases of the Jumonji family (JMJ or KDM) and for DNA the iron-dependent ten-eleven-translocation enzymes (TET) responsible for the oxidation of methylcytosine prior to the demethylation of DNA. This review presents these metalloenzymes, their importance in human disease and their inhibitors.
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Affiliation(s)
- Christophe Blanquart
- CRCINA, INSERM, Universite d'Angers, Universite de Nantes, Nantes, France.,Réseau Epigénétique du Cancéropôle Grand Ouest, France
| | - Camille Linot
- CRCINA, INSERM, Universite d'Angers, Universite de Nantes, Nantes, France
| | - Pierre-François Cartron
- CRCINA, INSERM, Universite d'Angers, Universite de Nantes, Nantes, France.,Réseau Epigénétique du Cancéropôle Grand Ouest, France
| | - Daniela Tomaselli
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Antonello Mai
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy.,Pasteur Institute - Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Philippe Bertrand
- Réseau Epigénétique du Cancéropôle Grand Ouest, France.,Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, 4 rue Michel Brunet, TSA 51106, B27, 86073, Poitiers cedex 09, France
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13
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Iacovella MG, Bremang M, Basha O, Giacò L, Carotenuto W, Golfieri C, Szakal B, Dal Maschio M, Infantino V, Beznoussenko GV, Joseph CR, Visintin C, Mironov AA, Visintin R, Branzei D, Ferreira-Cerca S, Yeger-Lotem E, De Wulf P. Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae. Nucleic Acids Res 2019; 46:7586-7611. [PMID: 30011030 PMCID: PMC6125641 DOI: 10.1093/nar/gky618] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/28/2018] [Indexed: 12/14/2022] Open
Abstract
The Saccharomyces cerevisiae kinase/adenosine triphosphatase Rio1 regulates rDNA transcription and segregation, pre-rRNA processing and small ribosomal subunit maturation. Other roles are unknown. When overexpressed, human ortholog RIOK1 drives tumor growth and metastasis. Likewise, RIOK1 promotes 40S ribosomal subunit biogenesis and has not been characterized globally. We show that Rio1 manages directly and via a series of regulators, an essential signaling network at the protein, chromatin and RNA levels. Rio1 orchestrates growth and division depending on resource availability, in parallel to the nutrient-activated Tor1 kinase. To define the Rio1 network, we identified its physical interactors, profiled its target genes/transcripts, mapped its chromatin-binding sites and integrated our data with yeast’s protein–protein and protein–DNA interaction catalogs using network computation. We experimentally confirmed network components and localized Rio1 also to mitochondria and vacuoles. Via its network, Rio1 commands protein synthesis (ribosomal gene expression, assembly and activity) and turnover (26S proteasome expression), and impinges on metabolic, energy-production and cell-cycle programs. We find that Rio1 activity is conserved to humans and propose that pathological RIOK1 may fuel promiscuous transcription, ribosome production, chromosomal instability, unrestrained metabolism and proliferation; established contributors to cancer. Our study will advance the understanding of numerous processes, here revealed to depend on Rio1 activity.
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Affiliation(s)
- Maria G Iacovella
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Michael Bremang
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.,Current address: Proteome Sciences Plc, Hamilton House, Mabledon Place, London, United Kingdom
| | - Omer Basha
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, POB 653, Beer-Sheva 84105, Israel
| | - Luciano Giacò
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Walter Carotenuto
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Cristina Golfieri
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Barnabas Szakal
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Marianna Dal Maschio
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Valentina Infantino
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Galina V Beznoussenko
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Chinnu R Joseph
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Clara Visintin
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Alexander A Mironov
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Rosella Visintin
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Dana Branzei
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy.,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Sébastien Ferreira-Cerca
- Lehrstuhl für Biochemie III, Universität Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Esti Yeger-Lotem
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, POB 653, Beer-Sheva 84105, Israel
| | - Peter De Wulf
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.,Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
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14
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Ali A, Al-Tobasei R, Lourenco D, Leeds T, Kenney B, Salem M. Genome-Wide Association Study Identifies Genomic Loci Affecting Filet Firmness and Protein Content in Rainbow Trout. Front Genet 2019; 10:386. [PMID: 31130980 PMCID: PMC6509548 DOI: 10.3389/fgene.2019.00386] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/10/2019] [Indexed: 01/10/2023] Open
Abstract
Filet quality traits determine consumer satisfaction and affect profitability of the aquaculture industry. Soft flesh is a criterion for fish filet downgrades, resulting in loss of value. Filet firmness is influenced by many factors, including rate of protein turnover. A 50K transcribed gene SNP chip was used to genotype 789 rainbow trout, from two consecutive generations, produced in the USDA/NCCCWA selective breeding program. Weighted single-step GBLUP (WssGBLUP) was used to perform genome-wide association (GWA) analyses to identify quantitative trait loci affecting filet firmness and protein content. Applying genomic sliding windows of 50 adjacent SNPs, 212 and 225 SNPs were associated with genetic variation in filet shear force and protein content, respectively. Four common SNPs in the ryanodine receptor 3 gene (RYR3) affected the aforementioned filet traits; this association suggests common mechanisms underlying filet shear force and protein content. Genes harboring SNPs were mostly involved in calcium homeostasis, proteolytic activities, transcriptional regulation, chromatin remodeling, and apoptotic processes. RYR3 harbored the highest number of SNPs (n = 32) affecting genetic variation in shear force (2.29%) and protein content (4.97%). Additionally, based on single-marker analysis, a SNP in RYR3 ranked at the top of all SNPs associated with variation in shear force. Our data suggest a role for RYR3 in muscle firmness that may be considered for genomic- and marker-assisted selection in breeding programs of rainbow trout.
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Affiliation(s)
- Ali Ali
- Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, United States
| | - Rafet Al-Tobasei
- Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, United States.,Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Daniela Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, United States
| | - Tim Leeds
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, United States
| | - Brett Kenney
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, United States
| | - Mohamed Salem
- Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, United States.,Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, United States
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15
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Oh S, Shin S, Janknecht R. The small members of the JMJD protein family: Enzymatic jewels or jinxes? Biochim Biophys Acta Rev Cancer 2019; 1871:406-418. [PMID: 31034925 DOI: 10.1016/j.bbcan.2019.04.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/07/2019] [Accepted: 04/08/2019] [Indexed: 02/07/2023]
Abstract
Jumonji C domain-containing (JMJD) proteins are mostly epigenetic regulators that demethylate histones. However, a hitherto neglected subfamily of JMJD proteins, evolutionarily distant and characterized by their relatively small molecular weight, exerts different functions by hydroxylating proteins and RNA. Recently, unsuspected proteolytic and tyrosine kinase activities were also ascribed to some of these small JMJD proteins, further increasing their enzymatic versatility. Here, we discuss the ten human small JMJD proteins (HIF1AN, HSPBAP1, JMJD4, JMJD5, JMJD6, JMJD7, JMJD8, RIOX1, RIOX2, TYW5) and their diverse physiological functions. In particular, we focus on the roles of these small JMJD proteins in cancer and other maladies and how they are modulated in diseased cells by an altered metabolic milieu, including hypoxia, reactive oxygen species and oncometabolites. Because small JMJD proteins are enzymes, they are amenable to inhibition by small molecules and may represent novel targets in the therapy of cancer and other diseases.
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Affiliation(s)
- Sangphil Oh
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Sook Shin
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Ralf Janknecht
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
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16
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Oncogenic and osteolytic functions of histone demethylase NO66 in castration-resistant prostate cancer. Oncogene 2019; 38:5038-5049. [DOI: 10.1038/s41388-019-0774-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 12/07/2018] [Accepted: 02/16/2019] [Indexed: 02/07/2023]
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17
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Hydroxylation of protein constituents of the human translation system: structural aspects and functional assignments. Future Med Chem 2019; 11:357-369. [PMID: 30802140 DOI: 10.4155/fmc-2018-0317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
During the current decade, data on the post-translational hydroxylation of specific amino acid residues of some ribosomal proteins and translation factors in both eukaryotes and eubacteria have accumulated. The reaction is catalyzed by dedicated oxygenases (so-called ribosomal oxygenases), whose action is impaired under hypoxia conditions. The modification occurs at amino acid residues directly involved in the formation of the main functional sites of ribosomes and factors. This review summarizes currently available data on the specific hydroxylation of protein constituents of eukaryotic and eubacterial translation systems with a special emphasis on the human system, as well as on the links between hypoxia impacts on the operation of ribosomal oxygenases, the functioning of the translational apparatus and human health problems.
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18
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The Rio1 protein kinases/ATPases: conserved regulators of growth, division, and genomic stability. Curr Genet 2018; 65:457-466. [DOI: 10.1007/s00294-018-0912-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 12/31/2022]
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19
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Bundred JR, Hendrix E, Coleman ML. The emerging roles of ribosomal histidyl hydroxylases in cell biology, physiology and disease. Cell Mol Life Sci 2018; 75:4093-4105. [PMID: 30151692 PMCID: PMC6182338 DOI: 10.1007/s00018-018-2903-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/06/2018] [Accepted: 08/08/2018] [Indexed: 12/27/2022]
Abstract
Hydroxylation is a novel protein modification catalyzed by a family of oxygenases that depend on fundamental nutrients and metabolites for activity. Protein hydroxylases have been implicated in a variety of key cellular processes that play important roles in both normal homeostasis and pathogenesis. Here, in this review, we summarize the current literature on a highly conserved sub-family of oxygenases that catalyze protein histidyl hydroxylation. We discuss the evidence supporting the biochemical assignment of these emerging enzymes as ribosomal protein hydroxylases, and provide an overview of their role in immunology, bone development, and cancer.
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Affiliation(s)
- James R Bundred
- Tumour Oxygenase Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Eline Hendrix
- Tumour Oxygenase Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Mathew L Coleman
- Tumour Oxygenase Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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20
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Bräuer KE, Brockers K, Moneer J, Feuchtinger A, Wollscheid-Lengeling E, Lengeling A, Wolf A. Phylogenetic and genomic analyses of the ribosomal oxygenases Riox1 (No66) and Riox2 (Mina53) provide new insights into their evolution. BMC Evol Biol 2018; 18:96. [PMID: 29914368 PMCID: PMC6006756 DOI: 10.1186/s12862-018-1215-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 06/07/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Translation of specific mRNAs can be highly regulated in different cells, tissues or under pathological conditions. Ribosome heterogeneity can originate from variable expression or post-translational modifications of ribosomal proteins. The ribosomal oxygenases RIOX1 (NO66) and RIOX2 (MINA53) modify ribosomal proteins by histidine hydroxylation. A similar mechanism is present in prokaryotes. Thus, ribosome hydroxylation may be a well-conserved regulatory mechanism with implications in disease and development. However, little is known about the evolutionary history of Riox1 and Riox2 genes and their encoded proteins across eukaryotic taxa. RESULTS In this study, we have analysed Riox1 and Riox2 orthologous genes from 49 metazoen species and have constructed phylogenomic trees for both genes. Our genomic and phylogenetic analyses revealed that Arthropoda, Annelida, Nematoda and Mollusca lack the Riox2 gene, although in the early phylum Cnidaria both genes, Riox1 and Riox2, are present and expressed. Riox1 is an intronless single-exon-gene in several species, including humans. In contrast to Riox2, Riox1 is ubiquitously present throughout the animal kingdom suggesting that Riox1 is the phylogenetically older gene from which Riox2 has evolved. Both proteins have maintained a unique protein architecture with conservation of active sites within the JmjC domains, a dimerization domain, and a winged-helix domain. In addition, Riox1 proteins possess a unique N-terminal extension domain. Immunofluorescence analyses in Hela cells and in Hydra vulgaris identified a nucleolar localisation signal within the extended N-terminal domain of human RIOX1 and an altered subnuclear localisation for the Hydra Riox2. CONCLUSIONS Conserved active site residues and uniform protein domain architecture suggest a consistent enzymatic activity within the Riox orthologs throughout evolution. However, differences in genomic architecture, like single exon genes and alterations in subnuclear localisation, as described for Hydra, point towards adaption mechanisms that may correlate with taxa- or species-specific requirements. The diversification of Riox1/Riox2 gene structures throughout evolution suggest that functional requirements in expression of protein isoforms and/or subcellular localisation of proteins may have evolved by adaptation to lifestyle.
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Affiliation(s)
- Katharina E Bräuer
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Kevin Brockers
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Jasmin Moneer
- Department of Biology II, Ludwig Maximillians University, Munich, Großhaderner Strasse 2, 82152 Planegg-, Martinsried, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Evi Wollscheid-Lengeling
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Andreas Lengeling
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.,Present address: Max-Planck-Society, Administrative Headquarters, Hofgartenstr. 8, 80539, Munich, Germany
| | - Alexander Wolf
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
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21
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Zhang T, Ji D, Wang P, Liang D, Jin L, Shi H, Liu X, Meng Q, Yu R, Gao S. The atypical protein kinase RIOK3 contributes to glioma cell proliferation/survival, migration/invasion and the AKT/mTOR signaling pathway. Cancer Lett 2017; 415:151-163. [PMID: 29233656 DOI: 10.1016/j.canlet.2017.12.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 10/31/2017] [Accepted: 12/07/2017] [Indexed: 11/30/2022]
Abstract
The RIO (right open reading frame) protein kinases include RIOK1, RIOK2 and RIOK3. Emerging evidence has suggested an important role of RIO kinases in cancer cell proliferation, apoptosis, migration and invasion. However, the expression profile and specific roles of RIOK3 are largely unknown during glioma progression. In the current study, quantitative real-time PCR, Western blot, and immunohistochemical analysis showed that RIOK3 was upregulated in glioma tissues. Available database analysis revealed that higher levels of RIOK3 were associated with poorer survival outcome in glioma patients. Flow cytometry, CCK8 and EdU assays showed that downregulation of RIOK3 arrested cell cycle progression and inhibited glioma cell proliferation. Wound healing, transwell and gelatin zymography assays revealed that silencing RIOK3 decreased glioma cell migration and invasion. Furthermore, the downregulation of RIOK3 significantly decreased the activity of AKT/mTOR signaling and induced apoptosis in glioma cells. Overexpression of RIOK3 showed the opposite effects on glioma cell proliferation, migration, invasion and the AKT/mTOR pathway. These results indicate that high RIOK3 levels in gliomas appear to contribute to the growth and expansion of this cancer, and may thus serve as a novel therapeutic target.
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Affiliation(s)
- Tong Zhang
- Institute of Nervous System Diseases, Xuzhou Medical University, 84 West Huai-Hai Road, Xuzhou 221002, Jiangsu, China; Brain Hospital, The Affiliated Hospital of Xuzhou Medical University, 99 West Huai-Hai Road, Xuzhou 221002, Jiangsu, China
| | - Daofei Ji
- Institute of Nervous System Diseases, Xuzhou Medical University, 84 West Huai-Hai Road, Xuzhou 221002, Jiangsu, China; Department of Neurosurgery, The Second Hospital of Xuzhou Medical University, 32 Mei-Jian Road, Xuzhou 221006, Jiangsu, China
| | - Peng Wang
- Institute of Nervous System Diseases, Xuzhou Medical University, 84 West Huai-Hai Road, Xuzhou 221002, Jiangsu, China; Brain Hospital, The Affiliated Hospital of Xuzhou Medical University, 99 West Huai-Hai Road, Xuzhou 221002, Jiangsu, China
| | - Dong Liang
- Institute of Nervous System Diseases, Xuzhou Medical University, 84 West Huai-Hai Road, Xuzhou 221002, Jiangsu, China; Brain Hospital, The Affiliated Hospital of Xuzhou Medical University, 99 West Huai-Hai Road, Xuzhou 221002, Jiangsu, China
| | - Lei Jin
- Institute of Nervous System Diseases, Xuzhou Medical University, 84 West Huai-Hai Road, Xuzhou 221002, Jiangsu, China; Brain Hospital, The Affiliated Hospital of Xuzhou Medical University, 99 West Huai-Hai Road, Xuzhou 221002, Jiangsu, China
| | - Hengliang Shi
- Institute of Nervous System Diseases, Xuzhou Medical University, 84 West Huai-Hai Road, Xuzhou 221002, Jiangsu, China; Brain Hospital, The Affiliated Hospital of Xuzhou Medical University, 99 West Huai-Hai Road, Xuzhou 221002, Jiangsu, China
| | - Xuejiao Liu
- Institute of Nervous System Diseases, Xuzhou Medical University, 84 West Huai-Hai Road, Xuzhou 221002, Jiangsu, China; Brain Hospital, The Affiliated Hospital of Xuzhou Medical University, 99 West Huai-Hai Road, Xuzhou 221002, Jiangsu, China
| | - Qingming Meng
- Brain Hospital, The Affiliated Hospital of Xuzhou Medical University, 99 West Huai-Hai Road, Xuzhou 221002, Jiangsu, China
| | - Rutong Yu
- Institute of Nervous System Diseases, Xuzhou Medical University, 84 West Huai-Hai Road, Xuzhou 221002, Jiangsu, China; Brain Hospital, The Affiliated Hospital of Xuzhou Medical University, 99 West Huai-Hai Road, Xuzhou 221002, Jiangsu, China.
| | - Shangfeng Gao
- Institute of Nervous System Diseases, Xuzhou Medical University, 84 West Huai-Hai Road, Xuzhou 221002, Jiangsu, China; Brain Hospital, The Affiliated Hospital of Xuzhou Medical University, 99 West Huai-Hai Road, Xuzhou 221002, Jiangsu, China.
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22
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Daigo K, Takano A, Thang PM, Yoshitake Y, Shinohara M, Tohnai I, Murakami Y, Maegawa J, Daigo Y. Characterization of KIF11 as a novel prognostic biomarker and therapeutic target for oral cancer. Int J Oncol 2017; 52:155-165. [PMID: 29115586 PMCID: PMC5743338 DOI: 10.3892/ijo.2017.4181] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/21/2017] [Indexed: 11/16/2022] Open
Abstract
Oral cancer has a high mortality rate, and its incidence is increasing gradually worldwide. As the effectiveness of standard treatments is still limited, the development of new therapeutic strategies is eagerly awaited. Kinesin family member 11 (KIF11) is a motor protein required for establishing a bipolar spindle in cell division. The role of KIF11 in oral cancer is unclear. Therefore, the present study aimed to assess the role of KIF11 in oral cancer and evaluate its role as a prognostic biomarker and therapeutic target for treating oral cancer. Immunohistochemical analysis demonstrated that KIF11 was expressed in 64 of 99 (64.6%) oral cancer tissues but not in healthy oral epithelia. Strong KIF11 expression was significantly associated with poor prognosis among oral cancer patients (P=0.034), and multivariate analysis confirmed its independent prognostic value. In addition, inhibition of KIF11 expression by transfection of siRNAs into oral cancer cells or treatment of cells with a KIF11 inhibitor significantly suppressed cell proliferation, probably through G2/M arrest and subsequent induction of apoptosis. These results suggest that KIF11 could be a potential prognostic biomarker and therapeutic target for oral cancer.
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Affiliation(s)
- Kayo Daigo
- Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science Hospital, The University of Tokyo, Tokyo, Japan
| | - Atsushi Takano
- Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science Hospital, The University of Tokyo, Tokyo, Japan
| | - Phung Manh Thang
- Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science Hospital, The University of Tokyo, Tokyo, Japan
| | - Yoshihiro Yoshitake
- Department of Oral and Maxillofacial Surgery, Kumamoto University, Kumamoto, Japan
| | - Masanori Shinohara
- Department of Oral and Maxillofacial Surgery, Kumamoto University, Kumamoto, Japan
| | - Iwau Tohnai
- Department of Oral and Maxillofacial Surgery, Yokohama City University, Yokohama, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jiro Maegawa
- Department of Plastic and Reconstructive Surgery, Yokohama City University, Yokohama, Japan
| | - Yataro Daigo
- Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science Hospital, The University of Tokyo, Tokyo, Japan
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23
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Comiskey DF, Jacob AG, Sanford BL, Montes M, Goodwin AK, Steiner H, Matsa E, Tapia-Santos AS, Bebee TW, Grieves J, La Perle K, Boyaka P, Chandler DS. A novel mouse model of rhabdomyosarcoma underscores the dichotomy of MDM2-ALT1 function in vivo. Oncogene 2017; 37:95-106. [PMID: 28892044 PMCID: PMC5756115 DOI: 10.1038/onc.2017.282] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 05/29/2017] [Accepted: 06/19/2017] [Indexed: 12/18/2022]
Abstract
Alternative splicing of the oncogene murine double minute 2 (MDM2) is induced in response to genotoxic stress. MDM2-ALT1, the major splice variant generated, is known to activate the p53 pathway and impede full-length MDM2's negative regulation of p53. Despite this perceptible tumor-suppressive role, MDM2-ALT1 is also associated with several cancers. Furthermore, expression of MDM2-ALT1 has been observed in aggressive metastatic disease in pediatric rhabdomyosarcoma (RMS), irrespective of histological subtype. Therefore, we generated a transgenic MDM2-ALT1 mouse model that would allow us to investigate the effects of this splice variant on the progression of tumorigenesis. Here we show that when MDM2-ALT1 is ubiquitously expressed in p53 null mice it leads to increased incidence of spindle cell sarcomas, including RMS. Our data provide evidence that constitutive MDM2-ALT1 expression is itself an oncogenic lesion that aggravates the tumorigenesis induced by p53 loss. On the contrary, when MDM2-ALT1 is expressed solely in B-cells in the presence of homozygous wild-type p53 it leads to significantly increased lymphomagenesis (56%) when compared with control mice (27%). However, this phenotype is observable only at later stages in life (⩾18 months). Moreover, flow cytometric analyses for B-cell markers revealed an MDM2-ALT1-associated decrease in the B-cell population of the spleens of these animals. Our data suggest that the B-cell loss is p53 dependent and is a response mounted to persistent MDM2-ALT1 expression in a wild-type p53 background. Overall, our findings highlight the importance of an MDM2 splice variant as a critical modifier of both p53-dependent and -independent tumorigenesis, underscoring the complexity of MDM2 posttranscriptional regulation in cancer. Furthermore, MDM2-ALT1-expressing p53 null mice represent a novel mouse model of fusion-negative RMS.
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Affiliation(s)
- D F Comiskey
- Molecular, Cellular and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - A G Jacob
- Molecular, Cellular and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - B L Sanford
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - M Montes
- Molecular, Cellular and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - A K Goodwin
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - H Steiner
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - E Matsa
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - A S Tapia-Santos
- Molecular, Cellular and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - T W Bebee
- Molecular, Cellular and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - J Grieves
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA.,Takeda California, Inc., Drug Safety Research & Evaluation 10410 Science Center Drive, San Diego, CA 92121, USA
| | - K La Perle
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - P Boyaka
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - D S Chandler
- Molecular, Cellular and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
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24
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Hosseini A, Minucci S. A comprehensive review of lysine-specific demethylase 1 and its roles in cancer. Epigenomics 2017; 9:1123-1142. [PMID: 28699367 DOI: 10.2217/epi-2017-0022] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Histone methylation plays a key role in the regulation of chromatin structure, and its dynamics regulates important cellular processes. The investigation of the role of alterations in histone methylation in cancer has led to the identification of histone methyltransferases and demethylases as promising novel targets for therapy. Lysine-specific demethylase 1(LSD1, also known as KDM1A) is the first discovered histone lysine demethylase, with the ability to demethylase H3K4me1/2 and H3K9me1/2 at target loci in a context-dependent manner. LSD1 regulates the balance between self-renewal and differentiation of stem cells, and is highly expressed in various cancers, playing an important role in differentiation and self-renewal of tumor cells. In this review, we summarize recent studies about the LSD1, its role in normal and tumor cells, and the potential use of small molecule LSD1 inhibitors in therapy.
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Affiliation(s)
- Amir Hosseini
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy.,Department of Biosciences, University of Milan, Milan, Italy
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25
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Weinberg F, Reischmann N, Fauth L, Taromi S, Mastroianni J, Köhler M, Halbach S, Becker AC, Deng N, Schmitz T, Uhl FM, Herbener N, Riedel B, Beier F, Swarbrick A, Lassmann S, Dengjel J, Zeiser R, Brummer T. The Atypical Kinase RIOK1 Promotes Tumor Growth and Invasive Behavior. EBioMedicine 2017; 20:79-97. [PMID: 28499923 PMCID: PMC5478185 DOI: 10.1016/j.ebiom.2017.04.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 04/07/2017] [Accepted: 04/07/2017] [Indexed: 12/27/2022] Open
Abstract
Despite being overexpressed in different tumor entities, RIO kinases are hardly characterized in mammalian cells. We investigated the role of these atypical kinases in different cancer cells. Using isogenic colon-, breast- and lung cancer cell lines, we demonstrate that knockdown of RIOK1, but not of RIOK2 or RIOK3, strongly impairs proliferation and invasiveness in conventional and 3D culture systems. Interestingly, these effects were mainly observed in RAS mutant cancer cells. In contrast, growth of RAS wildtype Caco-2 and Bcr-Abl-driven K562 cells is not affected by RIOK1 knockdown, suggesting a specific requirement for RIOK1 in the context of oncogenic RAS signaling. Furthermore, we show that RIOK1 activates NF-κB signaling and promotes cell cycle progression. Using proteomics, we identified the pro-invasive proteins Metadherin and Stathmin1 to be regulated by RIOK1. Additionally, we demonstrate that RIOK1 promotes lung colonization in vivo and that RIOK1 is overexpressed in different subtypes of human lung- and breast cancer. Altogether, our data suggest RIOK1 as a potential therapeutic target, especially in RAS-driven cancers.
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Affiliation(s)
- Florian Weinberg
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany; Faculty of Biology, ALU, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, BIOSS, ALU, Germany
| | - Nadine Reischmann
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany; Faculty of Biology, ALU, Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), ALU, Freiburg, Germany
| | - Lisa Fauth
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine, ALU, Germany
| | - Sanaz Taromi
- Department of Hematology and Oncology, University Medical Center, ALU, Freiburg, Germany
| | - Justin Mastroianni
- Faculty of Biology, ALU, Freiburg, Germany; Department of Hematology and Oncology, University Medical Center, ALU, Freiburg, Germany
| | - Martin Köhler
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany; Faculty of Biology, ALU, Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), ALU, Freiburg, Germany
| | - Sebastian Halbach
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany; Faculty of Biology, ALU, Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), ALU, Freiburg, Germany
| | - Andrea C Becker
- Freiburg Institute for Advanced Studies (FRIAS), ALU, Freiburg, Germany; Department of Dermatology, University Medical Center - ALU, Freiburg, Germany
| | - Niantao Deng
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
| | - Tatjana Schmitz
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany
| | - Franziska Maria Uhl
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany; Faculty of Biology, ALU, Freiburg, Germany; Department of Hematology and Oncology, University Medical Center, ALU, Freiburg, Germany
| | - Nicola Herbener
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine, ALU, Germany
| | - Bianca Riedel
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine, ALU, Germany
| | - Fabian Beier
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine, ALU, Germany
| | - Alexander Swarbrick
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, Australia
| | - Silke Lassmann
- BIOSS Centre for Biological Signalling Studies, BIOSS, ALU, Germany; Institute for Surgical Pathology, Medical Center and Faculty of Medicine, ALU, Germany; German Cancer Consortium (DKTK, Freiburg) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jörn Dengjel
- BIOSS Centre for Biological Signalling Studies, BIOSS, ALU, Germany; Freiburg Institute for Advanced Studies (FRIAS), ALU, Freiburg, Germany; Department of Dermatology, University Medical Center - ALU, Freiburg, Germany; Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Robert Zeiser
- BIOSS Centre for Biological Signalling Studies, BIOSS, ALU, Germany; Department of Hematology and Oncology, University Medical Center, ALU, Freiburg, Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research (IMMZ), Faculty of Medicine, Albert-Ludwigs-University (ALU), Freiburg, Germany; Faculty of Biology, ALU, Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, BIOSS, ALU, Germany; German Cancer Consortium (DKTK, Freiburg) and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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26
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Thang PM, Takano A, Yoshitake Y, Shinohara M, Murakami Y, Daigo Y. Cell division cycle associated 1 as a novel prognostic biomarker and therapeutic target for oral cancer. Int J Oncol 2016; 49:1385-93. [PMID: 27499128 DOI: 10.3892/ijo.2016.3649] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 07/25/2016] [Indexed: 11/06/2022] Open
Abstract
Oral cavity carcinoma (OCC) is one of the most common causes of cancer-related death worldwide and has poor clinical outcome after standard therapies. Therefore, new prognostic biomarkers and therapeutic targets for OCC are urgently needed. We selected cell division cycle associated 1 (CDCA1) as a candidate OCC biomarker. Immunohistochemical analysis confirmed that CDCA1 protein was expressed in 67 of 99 OCC tissues (67.7%), but not in healthy oral epithelia. CDCA1 expression was significantly associated with poor prognosis in OCC patients (P=0.0244). Knockdown of CDCA1 by siRNAs significantly increased apoptosis of tumor cells. These data suggest that CDCA1 represents a novel prognostic biomarker and therapeutic target for OCC.
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Affiliation(s)
- Phung Manh Thang
- Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Atsushi Takano
- Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoshihiro Yoshitake
- Department of Oral and Maxillofacial Surgery, Kumamoto University, Kumamoto, Japan
| | - Masanori Shinohara
- Department of Oral and Maxillofacial Surgery, Kumamoto University, Kumamoto, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yataro Daigo
- Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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27
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Nishizawa Y, Nishida N, Konno M, Kawamoto K, Asai A, Koseki J, Takahashi H, Haraguchi N, Nishimura J, Hata T, Matsuda C, Mizushima T, Satoh T, Doki Y, Mori M, Ishii H. Clinical Significance of Histone Demethylase NO66 in Invasive Colorectal Cancer. Ann Surg Oncol 2016; 24:841-849. [DOI: 10.1245/s10434-016-5395-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Indexed: 01/06/2023]
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28
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Liu K, Chen HL, Wang S, Gu MM, Chen XM, Zhang SL, Yu KJ, You QS. High Expression of RIOK2 and NOB1 Predict Human Non-small Cell Lung Cancer Outcomes. Sci Rep 2016; 6:28666. [PMID: 27346559 PMCID: PMC4921844 DOI: 10.1038/srep28666] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/08/2016] [Indexed: 01/29/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related mortality worldwide. However, there is a shortage of suitable diagnostic markers for early stages of NSCLC, and therapeutic targets are limited. Right open reading frame (Rio) kinase 2 (RIOK2) and Nin one binding (NOB1) protein are important accessory factors in ribosome assembly and are highly expressed in malignant tumours; moreover, they interact with each other. However, the RIOK2 expression profile and its clinical significance as well as NOB1's mechanism in NSCLC remain unknown. In this study, NSCLC cell lines and 15 NSCLC tumour tissues (paired with adjacent normal lung tissues) were collected for a real-time quantitative PCR (RT-qPCR) analysis. In addition, 153 NSCLC cases and 27 normal lung tissues were used in an immunohistochemical analysis to evaluate the RIOK2 and NOB1 expression profiles, their clinicopathological factors in NSCLC and their correlations with prognoses. RIOK2 and NOB1 were highly expressed in NSCLC cells and tissues, and their expression profiles were significantly associated with the Tumour Node Metastasis (TNM) clinical stage, lymph node metastasis, and differentiation. RIOK2 expression was correlated with NOB1. The results suggested that simultaneously determining the expression of RIOK2 and NOB1 will improve the diagnostic rate in early stages of NSCLC. Moreover, RIOK2 and NOB1 might be potential targets for NSCLC therapy.
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Affiliation(s)
- Kun Liu
- Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Nantong 226001, China
| | | | - Shuo Wang
- Nantong University, Nantong, 226001, China
| | - Ming-Ming Gu
- Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Xin-Ming Chen
- Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Nantong 226001, China
| | | | | | - Qing-Sheng You
- Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Nantong 226001, China
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29
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Katz MJ, Gándara L, De Lella Ezcurra AL, Wappner P. Hydroxylation and translational adaptation to stress: some answers lie beyond the STOP codon. Cell Mol Life Sci 2016; 73:1881-93. [PMID: 26874685 PMCID: PMC11108485 DOI: 10.1007/s00018-016-2160-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 01/08/2023]
Abstract
Regulation of protein synthesis contributes to maintenance of homeostasis and adaptation to environmental changes. mRNA translation is controlled at various levels including initiation, elongation and termination, through post-transcriptional/translational modifications of components of the protein synthesis machinery. Recently, protein and RNA hydroxylation have emerged as important enzymatic modifications of tRNAs, elongation and termination factors, as well as ribosomal proteins. These modifications enable a correct STOP codon recognition, ensuring translational fidelity. Recent studies are starting to show that STOP codon read-through is related to the ability of the cell to cope with different types of stress, such as oxidative and chemical insults, while correlations between defects in hydroxylation of protein synthesis components and STOP codon read-through are beginning to emerge. In this review we will discuss our current knowledge of protein synthesis regulation through hydroxylation of components of the translation machinery, with special focus on STOP codon recognition. We speculate on the possibility that programmed STOP codon read-through, modulated by hydroxylation of components of the protein synthesis machinery, is part of a concerted cellular response to stress.
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Affiliation(s)
- M J Katz
- Instituto Leloir, Buenos Aires, Argentina
| | - L Gándara
- Instituto Leloir, Buenos Aires, Argentina
| | | | - P Wappner
- Instituto Leloir, Buenos Aires, Argentina.
- Departamento de Fisiología, Biología Molecular, y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
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30
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Park SY, Park JW, Chun YS. Jumonji histone demethylases as emerging therapeutic targets. Pharmacol Res 2016; 105:146-51. [PMID: 26816087 DOI: 10.1016/j.phrs.2016.01.026] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 01/21/2016] [Indexed: 11/28/2022]
Abstract
The methylation status of lysine residues in histones determines the transcription of surrounding genes by modulating the chromatin architecture. Jumonji domain-containing histone-lysine demethylases (Jmj-KDMs) remove the methyl moiety from lysine residues in histones by utilizing Fe(2+) and α-ketoglutarate. Since genetic alterations in Jmj-KDMs occur in various human cancers, the roles of Jmj-KDMs in cancer development and progression have been investigated, but still controversial. The KDM7 subfamily, which belongs to the Jmj-KDM family, is an emerging class of transcriptional coactivators because its members erase the repressive marks H3K9me2/1, H3K27me2/1, and H4K20 me1. Recently, KDM7C (alternatively named PHF2) was discovered as a new KDM7 member and identified to play a tumor-suppressive role through the reinforcement of p53-driven growth arrest and apoptosis. In this article, we generally reviewed the roles of Jmj-KDMs in human cancers and more discussed the molecular functions and the clinical significances of KDM7C.
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Affiliation(s)
- Sung Yeon Park
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - Jong-Wan Park
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - Yang-Sook Chun
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea; Department of Physiology, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea.
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31
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Chen Q, Sinha K, Deng JM, Yasuda H, Krahe R, Behringer RR, de Crombrugghe B. Mesenchymal Deletion of Histone Demethylase NO66 in Mice Promotes Bone Formation. J Bone Miner Res 2015; 30:1608-17. [PMID: 25736226 PMCID: PMC4780322 DOI: 10.1002/jbmr.2494] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 02/26/2015] [Accepted: 03/03/2015] [Indexed: 11/07/2022]
Abstract
Our previous studies indicated that the Jumonji C (JmjC)-domain-containing NO66 is a histone demethylase with specificity for methylated histone H3K4 and H3K36. NO66 binds to the transcription factor Osterix (Osx) and inhibits its transcriptional activity in promoter assays. However, the physiological role of NO66 in formation of mammalian bones is unknown. Here, using a genetically engineered mouse model, we show that during early skeletal development, Prx1-Cre-dependent mesenchymal deletion of NO66 promotes osteogenesis and formation of both endochondral as well as intramembranous skeletal elements, leading to a larger skeleton and a high bone mass phenotype in adult mice. The excess bone formation in mice where NO66 was deleted in cells of mesenchymal origin is associated with an increase in the number of preosteoblasts and osteoblasts. Further analysis revealed that in the embryonic limbs and adult calvaria of mice with deletion of NO66 in cells of mesenchymal origin, expression of several genes including bone morphogenetic protein 2 (Bmp2), insulin-like growth factor 1 (Igf1), and osteoclast inhibitor osteoprotegerin was increased, concurrent with an increase in expression of bone formation markers such as osterix (Osx), type I collagen, and bone sialoprotein (Bsp). Taken together, our results provide the first in vivo evidence that NO66 histone demethylase plays an important role in mammalian osteogenesis during early development as well as in adult bone homeostasis. We postulate that NO66 regulates bone formation, at least in part, via regulating the number of bone-forming cells and expression of multiple genes that are critical for these processes.
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Affiliation(s)
- Qin Chen
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Krishna Sinha
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jian Min Deng
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hideyo Yasuda
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ralf Krahe
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Richard R Behringer
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Benoit de Crombrugghe
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Abstract
Hydroxylation is an emerging modification generally catalyzed by a family of ∼70 enzymes that are dependent on oxygen, Fe(II), ascorbate, and the Kreb's cycle intermediate 2-oxoglutarate (2OG). These "2OG oxygenases" sit at the intersection of nutrient availability and metabolism where they have the potential to regulate gene expression and growth in response to changes in co-factor abundance. Characterized 2OG oxygenases regulate fundamental cellular processes by catalyzing the hydroxylation or demethylation (via hydroxylation) of DNA, RNA, or protein. As such they have been implicated in various syndromes and diseases, but particularly cancer. In this review we discuss the emerging role of 2OG oxygenases in gene expression control, examine the regulation of these unique enzymes by nutrient availability and metabolic intermediates, and describe these properties in relation to the expanding role of these enzymes in cancer.
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de Matos Simoes R, Dalleau S, Williamson KE, Emmert-Streib F. Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data. BMC SYSTEMS BIOLOGY 2015; 9:21. [PMID: 25971253 PMCID: PMC4460634 DOI: 10.1186/s12918-015-0165-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 04/22/2015] [Indexed: 12/18/2022]
Abstract
BACKGROUND Urothelial pathogenesis is a complex process driven by an underlying network of interconnected genes. The identification of novel genomic target regions and gene targets that drive urothelial carcinogenesis is crucial in order to improve our current limited understanding of urothelial cancer (UC) on the molecular level. The inference of genome-wide gene regulatory networks (GRN) from large-scale gene expression data provides a promising approach for a detailed investigation of the underlying network structure associated to urothelial carcinogenesis. METHODS In our study we inferred and compared three GRNs by the application of the BC3Net inference algorithm to large-scale transitional cell carcinoma gene expression data sets from Illumina RNAseq (179 samples), Illumina Bead arrays (165 samples) and Affymetrix Oligo microarrays (188 samples). We investigated the structural and functional properties of GRNs for the identification of molecular targets associated to urothelial cancer. RESULTS We found that the urothelial cancer (UC) GRNs show a significant enrichment of subnetworks that are associated with known cancer hallmarks including cell cycle, immune response, signaling, differentiation and translation. Interestingly, the most prominent subnetworks of co-located genes were found on chromosome regions 5q31.3 (RNAseq), 8q24.3 (Oligo) and 1q23.3 (Bead), which all represent known genomic regions frequently deregulated or aberated in urothelial cancer and other cancer types. Furthermore, the identified hub genes of the individual GRNs, e.g., HID1/DMC1 (tumor development), RNF17/TDRD4 (cancer antigen) and CYP4A11 (angiogenesis/ metastasis) are known cancer associated markers. The GRNs were highly dataset specific on the interaction level between individual genes, but showed large similarities on the biological function level represented by subnetworks. Remarkably, the RNAseq UC GRN showed twice the proportion of significant functional subnetworks. Based on our analysis of inferential and experimental networks the Bead UC GRN showed the lowest performance compared to the RNAseq and Oligo UC GRNs. CONCLUSION To our knowledge, this is the first study investigating genome-scale UC GRNs. RNAseq based gene expression data is the data platform of choice for a GRN inference. Our study offers new avenues for the identification of novel putative diagnostic targets for subsequent studies in bladder tumors.
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Affiliation(s)
- Ricardo de Matos Simoes
- Centre for Cancer Research and Cell Biology (CCRCB), Queens University Belfast, 97 Lisburn Road, Belfast, County Antrim, Northern Ireland, UK.
| | - Sabine Dalleau
- Centre for Cancer Research and Cell Biology (CCRCB), Queens University Belfast, 97 Lisburn Road, Belfast, County Antrim, Northern Ireland, UK.
| | - Kate E Williamson
- Centre for Cancer Research and Cell Biology (CCRCB), Queens University Belfast, 97 Lisburn Road, Belfast, County Antrim, Northern Ireland, UK.
| | - Frank Emmert-Streib
- Computational Medicine and Statistical Learning Laboratory, Department of Signal Processing, Tampere University of Technology, Tampere, 33720, Finland. .,Institute of Biosciences and Medical Technology, Tampere, 33520, Finland.
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Chen Q, Zhang L, de Crombrugghe B, Krahe R. Mesenchyme-specific overexpression of nucleolar protein 66 in mice inhibits skeletal growth and bone formation. FASEB J 2015; 29:2555-65. [PMID: 25746793 DOI: 10.1096/fj.14-258970] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 02/18/2015] [Indexed: 11/11/2022]
Abstract
Previous studies showed that nucleolar protein 66 (NO66), the Jumonji C-domain-containing histone demethylase for methylated histone H3K4 and H3K36 (H3K36me), negatively regulates osteoblast differentiation in vitro by inhibiting the activity of transcription factor osterix (Osx). However, whether NO66 affects mammalian skeletogenesis in vivo is not yet known. Here, we generated transgenic (TG) mice overexpressing a flag-tagged NO66 transgene driven by the Prx1 (paired related homeobox 1) promoter. We found that NO66 overexpression in Prx1-expressing mesenchymal cells inhibited skeletal growth and bone formation. The inhibitory phenotype was associated with >50% decreases in chondrocyte/osteoblast proliferation and differentiation. Moreover, we found that in bones of NO66-TG mice, expression of Igf1, Igf1 receptor (Igf1r), runt-related transcription factor 2, and Osx was significantly down-regulated (P < 0.05). Consistent with these results, we observed >50% reduction in levels of phosphorylated protein kinase B (Akt) and H3K36me3 in bones of NO66-TG mice, suggesting an inverse correlation between NO66 histone demethylase and the activity of IGF1R/Akt signaling. This correlation was further confirmed by in vitro assays of C2C12 cells with NO66 overexpression. We propose that the decrease in the IGF1R/Akt signaling pathway in mice with mesenchymal overexpression of NO66 may contribute in part to the inhibition of skeletal growth and bone formation.
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Affiliation(s)
- Qin Chen
- *Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA; and Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Liping Zhang
- *Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA; and Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Benoit de Crombrugghe
- *Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA; and Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Ralf Krahe
- *Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA; and Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
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Zhuang Q, Feng T, Coleman ML. Modifying the maker: Oxygenases target ribosome biology. ACTA ACUST UNITED AC 2015; 3:e1009331. [PMID: 26779412 PMCID: PMC4682802 DOI: 10.1080/21690731.2015.1009331] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 01/14/2014] [Accepted: 01/15/2014] [Indexed: 01/05/2023]
Abstract
The complexity of the eukaryotic protein synthesis machinery is partly driven by extensive and diverse modifications to associated proteins and RNAs. These modifications can have important roles in regulating translation factor activity and ribosome biogenesis and function. Further investigation of ‘translational modifications’ is warranted considering the growing evidence implicating protein synthesis as a critical point of gene expression control that is commonly deregulated in disease. New evidence suggests that translation is a major new target for oxidative modifications, specifically hydroxylations and demethylations, which generally are catalyzed by a family of emerging oxygenase enzymes that act at the interface of nutrient availability and metabolism. This review summarizes what is currently known about the role or these enzymes in targeting rRNA synthesis, protein translation and associated cellular processes.
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Affiliation(s)
- Qinqin Zhuang
- Tumour Oxygenase Group; School of Cancer Sciences ; University of Birmingham ; Birmingham, UK
| | - Tianshu Feng
- Centre for Cellular and Molecular Physiology; University of Oxford ; Oxford, UK
| | - Mathew L Coleman
- Tumour Oxygenase Group; School of Cancer Sciences ; University of Birmingham ; Birmingham, UK
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van Staalduinen LM, Jia Z. Post-translational hydroxylation by 2OG/Fe(II)-dependent oxygenases as a novel regulatory mechanism in bacteria. Front Microbiol 2015; 5:798. [PMID: 25642226 PMCID: PMC4295552 DOI: 10.3389/fmicb.2014.00798] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/27/2014] [Indexed: 02/03/2023] Open
Abstract
Protein hydroxylation has been well-studied in eukaryotic systems. The structural importance of hydroxylation of specific proline and lysine residues during collagen biosynthesis is well established. Recently, key roles for post-translational hydroxylation in signaling and degradation pathways have been discovered. The function of hydroxylation in signaling is highlighted by its role in the hypoxic response of eukaryotic cells, where oxygen dependent hydroxylation of the hypoxia inducible transcription factor both targets it for degradation and blocks its activation. In contrast, the role of protein hydroxylation has been largely understudied in prokaryotes. Recently, an evolutionarily conserved class of ribosomal oxygenases (ROX) that catalyze the hydroxylation of specific residues in the ribosome has been identified in bacteria. ROX activity has been linked to cell growth, and has been found to have a direct impact on bulk protein translation. This discovery of ribosomal protein hydroxylation in bacteria could lead to new therapeutic targets for regulating bacterial growth, as well as, shed light on new prokaryotic hydroxylation signaling pathways. In this review, recent structural and functional studies will be highlighted and discussed, underscoring the regulatory potential of post-translational hydroxylation in bacteria.
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Affiliation(s)
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University Kingston, ON, Canada
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Weinberg F, Schulze E, Fatouros C, Schmidt E, Baumeister R, Brummer T. Expression pattern and first functional characterization of riok-1 in Caenorhabditis elegans. Gene Expr Patterns 2014; 15:124-34. [PMID: 24929033 DOI: 10.1016/j.gep.2014.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 05/20/2014] [Accepted: 05/21/2014] [Indexed: 01/08/2023]
Abstract
Rio kinases are atypical serine/threonine kinases that emerge as potential cooperation partners in Ras-driven tumors. In the current study, we performed an RNAi screen in Caenorhabditis elegans to identify suppressors of oncogenic Ras signaling. Aberrant Ras/Raf signaling in C. elegans leads to the formation of a multi-vulva (Muv) phenotype. We found that depletion of riok-1, the C. elegans orthologue of the mammalian RioK1, suppressed the Muv phenotype. By using a promoter GFP construct, we could show that riok-1 is expressed in neuronal cells, the somatic gonad, the vulva, the uterus and the spermatheca. Furthermore, we observed developmental defects in the gonad upon riok-1 knockdown in a wildtype background. Our data suggest that riok-1 is a modulator of the Ras signaling pathway, suggesting implications for novel interventions in the context of Ras-driven tumors.
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Affiliation(s)
- Florian Weinberg
- Institute of Biology III, Faculty of Biology, University of Freiburg, Germany; Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany; IMMZ - Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Germany
| | - Ekkehard Schulze
- Institute of Biology III, Faculty of Biology, University of Freiburg, Germany; BIOSS - Centre for Biological Signalling Studies, University of Freiburg, Germany
| | - Chronis Fatouros
- Institute of Biology III, Faculty of Biology, University of Freiburg, Germany; Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany; International Max Planck Research School for Molecular and Cell Biology (IMPRS-MCB), Freiburg, Germany
| | - Enrico Schmidt
- Institute of Biology III, Faculty of Biology, University of Freiburg, Germany; Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany
| | - Ralf Baumeister
- Institute of Biology III, Faculty of Biology, University of Freiburg, Germany; Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany; IMMZ - Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Germany; BIOSS - Centre for Biological Signalling Studies, University of Freiburg, Germany
| | - Tilman Brummer
- Institute of Biology III, Faculty of Biology, University of Freiburg, Germany; Centre for Biological Systems Analysis (ZBSA), Freiburg, Germany; IMMZ - Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Germany; BIOSS - Centre for Biological Signalling Studies, University of Freiburg, Germany.
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Franci G, Ciotta A, Altucci L. The Jumonji family: past, present and future of histone demethylases in cancer. Biomol Concepts 2014; 5:209-24. [DOI: 10.1515/bmc-2014-0010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/15/2014] [Indexed: 01/04/2023] Open
Abstract
AbstractThe first Jumonji gene was cloned in 1995 by Takeuchi et al. [Takeuchi T, Yamazaki Y, Katoh-Fukui Y, Tsuchiya R, Kondo S, Motoyama J, Higashinakagawa T. Gene trap capture of a novel mouse gene, jumonji, required for neural tube formation. Genes Dev 1995; 9: 1211–22.]. Several genes sharing similar biological features have since been discovered, and are currently grouped into the JMJ family. Interestingly, their deregulation has been associated with cardiac disease, obesity, neurological disorders and cancer. One of the mechanisms underlying their function is gene expression modulation via histone post-translational modifications (PTMs). Increasing evidence of Jumonji deregulation in tumours such as colon, prostate, haematological and breast cancer is continually emerging, hence the need to acquire a better understanding. The Genesapiens.org database of patient arrays allows target expression levels to be investigated in a wide range of cancers, corroborating and extending the role of the JMJ family. Here, we provide an overview of the expression profile and regulation of JMJ family members in cancer, examining the most recent literature in the light of analyses drawn from this database.
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Affiliation(s)
- Gianluigi Franci
- 1Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Università degli Studi di Napoli, Vico L. De Crecchio 7, I-80138 Napoli, Italy
| | - Alfonso Ciotta
- 1Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Università degli Studi di Napoli, Vico L. De Crecchio 7, I-80138 Napoli, Italy
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van Staalduinen LM, Novakowski SK, Jia Z. Structure and functional analysis of YcfD, a novel 2-oxoglutarate/Fe²⁺-dependent oxygenase involved in translational regulation in Escherichia coli. J Mol Biol 2014; 426:1898-910. [PMID: 24530688 DOI: 10.1016/j.jmb.2014.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 02/02/2014] [Accepted: 02/06/2014] [Indexed: 12/14/2022]
Abstract
The 2-oxoglutarate (2OG)/Fe²⁺-dependent oxygenases (2OG oxygenases) are a large family of proteins that share a similar overall three-dimensional structure and catalyze a diverse array of oxidation reactions. The Jumonji C (JmjC)-domain-containing proteins represent an important subclass of the 2OG oxygenase family that typically catalyze protein hydroxylation; however, recently, other reactions have been identified, such as tRNA modification. The Escherichia coli gene, ycfD, was predicted to be a JmjC-domain-containing protein of unknown function based on primary sequence. Recently, YcfD was determined to act as a ribosomal oxygenase, hydroxylating an arginine residue on the 50S ribosomal protein L-16 (RL-16). We have determined the crystal structure of YcfD at 2.7 Å resolution, revealing that YcfD is structurally similar to known JmjC proteins and possesses the characteristic double-stranded β-helix fold or cupin domain. Separate from the cupin domain, an additional globular module termed α-helical arm mediates dimerization of YcfD. We further have shown that 2OG binds to YcfD using isothermal titration calorimetry and identified key binding residues using mutagenesis that, together with the iron location and structural similarity with other cupin family members, allowed identification of the active site. Structural homology to ribosomal assembly proteins combined with GST (glutathione S-transferase)-YcfD pull-down of a ribosomal protein and docking of RL-16 to the YcfD active site support the role of YcfD in regulation of bacterial ribosome assembly. Furthermore, overexpression of YcfD is shown to inhibit cell growth signifying a toxic effect on ribosome assembly.
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Affiliation(s)
- Laura M van Staalduinen
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Stefanie K Novakowski
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada.
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40
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Johansson C, Tumber A, Che K, Cain P, Nowak R, Gileadi C, Oppermann U. The roles of Jumonji-type oxygenases in human disease. Epigenomics 2014; 6:89-120. [PMID: 24579949 PMCID: PMC4233403 DOI: 10.2217/epi.13.79] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The iron- and 2-oxoglutarate-dependent oxygenases constitute a phylogenetically conserved class of enzymes that catalyze hydroxylation reactions in humans by acting on various types of substrates, including metabolic intermediates, amino acid residues in different proteins and various types of nucleic acids. The discovery of jumonji (Jmj), the founding member of a class of Jmj-type chromatin modifying enzymes and transcriptional regulators, has culminated in the discovery of several branches of histone lysine demethylases, with essential functions in regulating the epigenetic landscape of the chromatin environment. This work has now been considerably expanded into other aspects of epigenetic biology and includes the discovery of enzymatic steps required for methyl-cytosine demethylation as well as modification of RNA and ribosomal proteins. This overview aims to summarize the current knowledge on the human Jmj-type enzymes and their involvement in human pathological processes, including development, cancer, inflammation and metabolic diseases.
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Affiliation(s)
- Catrine Johansson
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - KaHing Che
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
- Botnar Research Center, NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, Oxford, OX3 7LD, UK
| | - Peter Cain
- Botnar Research Center, NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, Oxford, OX3 7LD, UK
| | - Radoslaw Nowak
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
- Botnar Research Center, NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, Oxford, OX3 7LD, UK
- Systems Approaches to Biomedical Sciences, Industrial Doctorate Center (SABS IDC) Oxford, UK
| | - Carina Gileadi
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
- Botnar Research Center, NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, Oxford, OX3 7LD, UK
- Systems Approaches to Biomedical Sciences, Industrial Doctorate Center (SABS IDC) Oxford, UK
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Abstract
It has recently been demonstrated that the genes controlling the epigenetic programmes that are required for maintaining chromatin structure and cell identity include genes that drive human cancer. This observation has led to an increased awareness of chromatin-associated proteins as potentially interesting drug targets. The successful introduction of DNA methylation and histone deacetylase (HDAC) inhibitors for the treatment of specific subtypes of cancer has paved the way for the use of epigenetic therapy. Here, we highlight key biological findings demonstrating the roles of members of the histone lysine demethylase class of enzymes in the development of cancers, discuss the potential and challenges of therapeutically targeting them, and highlight emerging small-molecule inhibitors of these enzymes.
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Oshita H, Nishino R, Takano A, Fujitomo T, Aragaki M, Kato T, Akiyama H, Tsuchiya E, Kohno N, Nakamura Y, Daigo Y. RASEF is a novel diagnostic biomarker and a therapeutic target for lung cancer. Mol Cancer Res 2013; 11:937-51. [PMID: 23686708 DOI: 10.1158/1541-7786.mcr-12-0685-t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED Genome-wide gene expression profiling revealed that the Ras and EF-hand domain containing (RASEF) transcript was significantly transactivated in the majority of lung cancers. Using lung cancer cells, transient expression of RASEF promoted cell growth, whereas RASEF knockdown not only reduced its expression but resulted in growth suppression of the cancer cells. Immunohistochemical staining using tumor tissue microarrays consisting of 341 archived non-small cell lung cancers (NSCLC) revealed the association of strong RASEF positivity with poor prognosis (P = 0.0034 by multivariate analysis). Mechanistically, RASEF interacted with extracellular signal-regulated kinase (ERK) 1/2 and enhanced ERK1/2 signaling. Importantly, inhibiting the interaction between RASEF and ERK1/2 using a cell-permeable peptide that corresponded to the ERK1/2-interacting site of RASEF, suppressed growth of lung cancer cells. This study demonstrates that elevated RASEF promoted cell growth via enhanced ERK signaling and is associated with poor prognosis of NSCLC. IMPLICATIONS RASEF may play an important role in lung carcinogenesis and could serve as a vaiable prognostic biomarker and target for the development of new molecular therapies.
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Affiliation(s)
- Hideto Oshita
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, USA
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Daigo Y, Takano A, Teramoto K, Chung S, Nakamura Y. A systematic approach to the development of novel therapeutics for lung cancer using genomic analyses. Clin Pharmacol Ther 2013; 94:218-23. [PMID: 23657161 DOI: 10.1038/clpt.2013.90] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 04/30/2013] [Indexed: 12/16/2022]
Abstract
Molecularly targeted drugs for cancer therapy represent a therapeutic advance, but the proportion of patients who receive clinical benefit is still very limited. We present here the rationale and initial results of our program to define molecules involved in lung carcinogenesis with the goal of identifying new therapeutic targets and/or predictive biomarkers for drug response. We have used gene expression analysis of 120 lung cancers followed by RNA interference, tumor-tissue microarray analysis, and functional analyses to systematically distinguish potential target molecules specifically expressed in cancer cells. Through this approach, we have identified oncoproteins that provide the starting point for the development of therapeutic antibodies, dominant negative peptides, small-molecule inhibitors, and therapeutic cancer vaccines. We believe that the approach we describe should result in new molecularly targeted therapies with minimal risk of adverse events.
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Affiliation(s)
- Y Daigo
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Japan
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Campbell MJ, Turner BM. Altered histone modifications in cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 754:81-107. [PMID: 22956497 DOI: 10.1007/978-1-4419-9967-2_4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In human health and disease the choreographed actions of a wide armory of transcription factors govern the regulated expression of coding and nonprotein coding genes. These actions are central to human health and are evidently aberrant in cancer. Central components of regulated gene expression are a variety of epigenetic mechanisms that include histone modifications. The post-translational modifications of histones are widespread and diverse, and appear to be spatial--temporally regulated in a highly intricate manner. The true functional consequences of these patterns of regulation are still emerging. Correlative evidence supports the idea that these patterns are distorted in malignancy on both a genome-wide and a discrete gene loci level. These patterns of distortion also often reflect the altered expression of the enzymes that control these histone states. Similarly gene expression patterns also appear to reflect a correlation with altered histone modifications at both the candidate loci and genome-wide level. Clarity is emerging in resolving these relationships between histone modification status and gene expression -patterns. For example, altered transcription factor interactions with the key co-activator and co-repressors, which in turn marshal many of the histone-modifying enzymes, may distort regulation of histone modifications at specific gene loci. In turn these aberrant transcriptional processes can trigger other altered epigenetic events such as DNA methylation and underline the aberrant and specific gene expression patterns in cancer. Considered in this manner, altered expression and recruitment of histone-modifying enzymes may underline the distortion to transcriptional responsiveness observed in malignancy. Insight from understanding these processes addresses the challenge of targeted epigenetic therapies in cancer.
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Affiliation(s)
- Moray J Campbell
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA.
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45
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Ge W, Wolf A, Feng T, Ho CH, Sekirnik R, Zayer A, Granatino N, Cockman ME, Loenarz C, Loik ND, Hardy AP, Claridge TD, Hamed RB, Chowdhury R, Gong L, Robinson CV, Trudgian DC, Jiang M, Mackeen MM, Mccullagh JS, Gordiyenko Y, Thalhammer A, Yamamoto A, Yang M, Liu-Yi P, Zhang Z, Schmidt-Zachmann M, Kessler BM, Ratcliffe PJ, Preston GM, Coleman ML, Schofield CJ. Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans. Nat Chem Biol 2012; 8:960-962. [PMID: 23103944 PMCID: PMC4972389 DOI: 10.1038/nchembio.1093] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 09/14/2012] [Indexed: 12/21/2022]
Abstract
The finding that oxygenase-catalyzed protein hydroxylation regulates animal transcription raises questions as to whether the translation machinery and prokaryotic proteins are analogously modified. Escherichia coli ycfD is a growth-regulating 2-oxoglutarate oxygenase catalyzing arginyl hydroxylation of the ribosomal protein Rpl16. Human ycfD homologs, Myc-induced nuclear antigen (MINA53) and NO66, are also linked to growth and catalyze histidyl hydroxylation of Rpl27a and Rpl8, respectively. This work reveals new therapeutic possibilities via oxygenase inhibition and by targeting modified over unmodified ribosomes.
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Affiliation(s)
- Wei Ge
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Alexander Wolf
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Tianshu Feng
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, OX3 7BN, UK
| | - Chia-hua Ho
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Rok Sekirnik
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Adam Zayer
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, OX3 7BN, UK
| | - Nicolas Granatino
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Matthew E. Cockman
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, OX3 7BN, UK
| | - Christoph Loenarz
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Nikita D. Loik
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Adam P. Hardy
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Timothy D.W. Claridge
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Refaat B. Hamed
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Lingzhi Gong
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | | | - David C. Trudgian
- Biochemistry Dept and Proteomics Core, UT Southwestern Medical Center at Dallas, 6001 Forest Park Rd, Dallas, TX 75390-8816, USA
| | - Miao Jiang
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Mukram M. Mackeen
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - James S. Mccullagh
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Yuliya Gordiyenko
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Armin Thalhammer
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Atsushi Yamamoto
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, OX3 7BN, UK
| | - Ming Yang
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, OX3 7BN, UK
| | - Phebee Liu-Yi
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, OX3 7BN, UK
| | - Zhihong Zhang
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Marion Schmidt-Zachmann
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Benedikt M. Kessler
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, OX3 7BN, UK
| | - Peter J. Ratcliffe
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, OX3 7BN, UK
| | - Gail M. Preston
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Mathew L. Coleman
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, OX3 7BN, UK
| | - Christopher J. Schofield
- Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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46
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Blair LP, Yan Q. Epigenetic mechanisms in commonly occurring cancers. DNA Cell Biol 2012; 31 Suppl 1:S49-61. [PMID: 22519822 PMCID: PMC3460614 DOI: 10.1089/dna.2012.1654] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 03/20/2012] [Accepted: 03/20/2012] [Indexed: 12/11/2022] Open
Abstract
Cancer is a collection of very complex diseases that share many traits while differing in many ways as well. This makes a universal cure difficult to attain, and it highlights the importance of understanding each type of cancer at a molecular level. Although many strides have been made in identifying the genetic causes for some cancers, we now understand that simple changes in the primary DNA sequence cannot explain the many steps that are necessary to turn a normal cell into a rouge cancer cell. In recent years, some research has shifted to focusing on detailing epigenetic contributions to the development and progression of cancer. These changes occur apart from primary genomic sequences and include DNA methylation, histone modifications, and miRNA expression. Since these epigenetic modifications are reversible, drugs targeting epigenetic changes are becoming more common in clinical settings. Daily discoveries elucidating these complex epigenetic processes are leading to advances in the field of cancer research. These advances, however, come at a rapid and often overwhelming pace. This review specifically summarizes the main epigenetic mechanisms currently documented in solid tumors common in the United States and Europe.
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Affiliation(s)
- Lauren P Blair
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520-8023, USA.
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47
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Nguyen MH, Ueda K, Nakamura Y, Daigo Y. Identification of a novel oncogene, MMS22L, involved in lung and esophageal carcinogenesis. Int J Oncol 2012; 41:1285-96. [PMID: 22895565 DOI: 10.3892/ijo.2012.1589] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 06/12/2012] [Indexed: 11/06/2022] Open
Abstract
Genome-wide gene expression profile analyses using a cDNA microarray containing 27,648 genes or expressed sequence tags identified MMS22L (methyl methanesulfonate-sensitivity protein 22-like) to be overexpressed in the majority of clinical lung and esophageal cancers, but not expressed in normal organs except testis. Transfection of siRNAs against MMS22L into cancer cells suppressed its expression and inhibited cell growth, while exogenous expression of MMS22L enhanced the growth of mammalian cells. MMS22L protein was translocated to the nucleus and stabilized by binding to C-terminal portion of NFKBIL2 [nuclear factor of kappa (NFKB) light polypeptide gene enhancer in B-cells inhibitor-like 2]. Expression of a C-terminal portion of NFKBIL2 protein including the MMS22L-interacting site in cancer cells could reduce the levels of MMS22L in nucleus and suppressed cancer cell growth. Interestingly, reduction of MMS22L by siRNAs in cancer cells inhibited the TNF-α-dependent activation of RelA/p65 in the NFKB pathway and expression of its downstream anti-apoptotic molecules such as Bcl-XL and TRAF1. In addition, knockdown of MMS22L expression also enhanced the apoptosis of cancer cells that were exposed to DNA-damaging agents including 5-FU and CDDP. Our data strongly suggest that targeting MMS22L as well as its interaction with NFKBIL2 could be a promising strategy for novel cancer treatments, and also improve the efficacy of DNA damaging anticancer drugs.
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Affiliation(s)
- Minh-Hue Nguyen
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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48
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Fujitomo T, Daigo Y, Matsuda K, Ueda K, Nakamura Y. Critical function for nuclear envelope protein TMEM209 in human pulmonary carcinogenesis. Cancer Res 2012; 72:4110-8. [PMID: 22719065 DOI: 10.1158/0008-5472.can-12-0159] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Therapeutic targets for more effective and less toxic treatments of lung cancer remain important. Here we report the identification of the integral nuclear envelope protein TMEM209 as a critical driver of human lung cancer growth and survival. TMEM209 expression was normally limited to testis, but we found that it was widely expressed in lung cancer, in which it localized to the nuclear envelope, Golgi apparatus, and the cytoplasm of lung cancer cells. Ectopic overexpression of TMEM209 promoted cell growth, whereas TMEM209 attenuation was sufficient to block growth. Mass spectrometric analysis identified the nucleoporin protein NUP205 as a TMEM209-interacting protein, stabilizing NUP205 and increasing the level of c-Myc in the nucleus. Taken together, our findings indicate that TMEM209 overexpression and TMEM209-NUP205 interaction are critical drivers of lung cancer proliferation, suggesting a promising new target for lung cancer therapy.
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Affiliation(s)
- Takashi Fujitomo
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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49
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Taal HR, Pourcain BS, Thiering E, Das S, Mook-Kanamori DO, Warrington NM, Kaakinen M, Kreiner-Møller E, Bradfield JP, Freathy RM, Geller F, Guxens M, Cousminer DL, Kerkhof M, Timpson NJ, Ikram MA, Beilin LJ, Bønnelykke K, Buxton JL, Charoen P, Chawes BLK, Eriksson J, Evans DM, Hofman A, Kemp JP, Kim CE, Klopp N, Lahti J, Lye SJ, McMahon G, Mentch FD, Müller M, O'Reilly PF, Prokopenko I, Rivadeneira F, Steegers EAP, Sunyer J, Tiesler C, Yaghootkar H, Breteler MMB, Debette S, Fornage M, Gudnason V, Launer LJ, van der Lugt A, Mosley TH, Seshadri S, Smith AV, Vernooij MW, Blakemore AI, Chiavacci RM, Feenstra B, Fernandez-Benet J, Grant SFA, Hartikainen AL, van der Heijden AJ, Iñiguez C, Lathrop M, McArdle WL, Mølgaard A, Newnham JP, Palmer LJ, Palotie A, Pouta A, Ring SM, Sovio U, Standl M, Uitterlinden AG, Wichmann HE, Vissing NH, DeCarli C, van Duijn CM, McCarthy MI, Koppelman GH, Estivill X, Hattersley AT, Melbye M, Bisgaard H, Pennell CE, Widen E, Hakonarson H, Smith GD, Heinrich J, Jarvelin MR, Jaddoe VWV. Common variants at 12q15 and 12q24 are associated with infant head circumference. Nat Genet 2012; 44:532-538. [PMID: 22504419 DOI: 10.1038/ng.2238] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 03/07/2012] [Indexed: 12/20/2022]
Abstract
To identify genetic variants associated with head circumference in infancy, we performed a meta-analysis of seven genome-wide association studies (GWAS) (N = 10,768 individuals of European ancestry enrolled in pregnancy and/or birth cohorts) and followed up three lead signals in six replication studies (combined N = 19,089). rs7980687 on chromosome 12q24 (P = 8.1 × 10(-9)) and rs1042725 on chromosome 12q15 (P = 2.8 × 10(-10)) were robustly associated with head circumference in infancy. Although these loci have previously been associated with adult height, their effects on infant head circumference were largely independent of height (P = 3.8 × 10(-7) for rs7980687 and P = 1.3 × 10(-7) for rs1042725 after adjustment for infant height). A third signal, rs11655470 on chromosome 17q21, showed suggestive evidence of association with head circumference (P = 3.9 × 10(-6)). SNPs correlated to the 17q21 signal have shown genome-wide association with adult intracranial volume, Parkinson's disease and other neurodegenerative diseases, indicating that a common genetic variant in this region might link early brain growth with neurological disease in later life.
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Affiliation(s)
- H Rob Taal
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Paediatrics, Erasmus Medical Center, Rotterdam, The Netherlands.,The Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Beate St Pourcain
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Elisabeth Thiering
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Shikta Das
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, UK
| | - Dennis O Mook-Kanamori
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Paediatrics, Erasmus Medical Center, Rotterdam, The Netherlands.,The Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands.,Weill Cornell Medical College - Qatar, Doha, Qatar
| | - Nicole M Warrington
- School of Women's and Infants' Health, The University of Western Australia, Perth, Australia.,Samuel Lunenfeld Research Institute, University of Toronto, Toronto, Canada
| | - Marika Kaakinen
- Institute of Health Sciences, University of Oulu, Finland.,Biocenter Oulu, University of Oulu, Finland
| | - Eskil Kreiner-Møller
- Copenhagen Prospective Studies on Asthma in Childhood, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan P Bradfield
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Rachel M Freathy
- Genetics of Complex Traits, Peninsula College of Medicine and Dentistry, University of Exeter, Exeter, UK
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Mònica Guxens
- Center for Research in Environmental Epidemiology (CREAL), Barcelona, Catalonia, Spain.,Hospital del Mar Research Institute (IMIM), Barcelona, Catalonia, Spain.,CIBER Epidemiologia y Salud Pública (CIBERESP), Barcelona, Catalonia, Spain
| | - Diana L Cousminer
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Marjan Kerkhof
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Nicholas J Timpson
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Radiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lawrence J Beilin
- School of Medicine and Pharmacology, The University of Western Australia, Perth, Australia
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, University of Copenhagen, Copenhagen, Denmark
| | - Jessica L Buxton
- Department of Genomics of Common Disease, School of Public Health, Imperial College London
| | - Pimphen Charoen
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, UK.,Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Bo Lund Krogsgaard Chawes
- Copenhagen Prospective Studies on Asthma in Childhood, University of Copenhagen, Copenhagen, Denmark
| | - Johan Eriksson
- National Institute for Health and Welfare, Helsinki, Finland.,Department of General Practice and Primary Health Care, University of Helsinki, Helsinki, Finland.,Folkhalsan Research Centre, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - David M Evans
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.,The Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands
| | - John P Kemp
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Cecilia E Kim
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Norman Klopp
- Research Unit for Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Jari Lahti
- Institute of Behavioural Sciences, University of Helsinki, Helsinki, Finland
| | - Stephen J Lye
- Samuel Lunenfeld Research Institute, University of Toronto, Toronto, Canada
| | - George McMahon
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Frank D Mentch
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Martina Müller
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany.,Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-Universität, Munich, Germany
| | - Paul F O'Reilly
- Department of Epidemiology and Biostatistics, Imperial College London, W2 1PG London, UK
| | - Inga Prokopenko
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Eric A P Steegers
- Department of Obstetrics & Gynecology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jordi Sunyer
- Center for Research in Environmental Epidemiology (CREAL), Barcelona, Catalonia, Spain.,Hospital del Mar Research Institute (IMIM), Barcelona, Catalonia, Spain.,CIBER Epidemiologia y Salud Pública (CIBERESP), Barcelona, Catalonia, Spain.,Pompeu Fabra University (UPF), Barcelona, Catalonia, Spain
| | - Carla Tiesler
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Dr Von Hauner Children's Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Hanieh Yaghootkar
- Genetics of Complex Traits, Peninsula College of Medicine and Dentistry, University of Exeter, Exeter, UK
| | | | | | - Stephanie Debette
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Myriam Fornage
- Institute of Molecular Medicine, Human Genetics Center and Division of Epidemiology, School of Public Health, University of Texas, Houston Health Sciences Center, Houston, TX, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogus, Iceland.,University of Iceland, Reykjavik, Iceland
| | - Lenore J Launer
- Laboratory of Epidemiology, Demography and Biometry, National Institute on Aging, National Institute of Health, Bethesda, MD, USA
| | - Aad van der Lugt
- Department of Radiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Thomas H Mosley
- Department of Medicine (Geriatrics), University of Mississippi Medical Center, Jackson, MS, USA
| | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Albert V Smith
- Icelandic Heart Association, Kopavogus, Iceland.,University of Iceland, Reykjavik, Iceland
| | - Meike W Vernooij
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Radiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Alexandra If Blakemore
- Department of Genomics of Common Disease, School of Public Health, Imperial College London
| | - Rosetta M Chiavacci
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Julio Fernandez-Benet
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Struan F A Grant
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Anna-Liisa Hartikainen
- Institute of Clinical Medicine/Obstetrics and Gynecology, University of Oulu, Oulu, Finland
| | | | - Carmen Iñiguez
- CIBER Epidemiologia y Salud Pública (CIBERESP), Barcelona, Catalonia, Spain.,Division of Environment and Health, Center for Public Health Research-CSISP, Valencia, Spain
| | - Mark Lathrop
- Centre National de Génotypage, Evry, France.,Foundation Jean Dausset, CEPH, Paris, France
| | - Wendy L McArdle
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Anne Mølgaard
- Copenhagen Prospective Studies on Asthma in Childhood, University of Copenhagen, Copenhagen, Denmark
| | - John P Newnham
- School of Women's and Infants' Health, The University of Western Australia, Perth, Australia
| | - Lyle J Palmer
- Samuel Lunenfeld Research Institute, University of Toronto, Toronto, Canada.,Genetic Epidemiology and Biostatistics Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Aarno Palotie
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland.,Department of Medical Genetics, University of Helsinki, Helsinki, Finland.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Annneli Pouta
- National Institute for Health and Welfare, Oulu, Finland, Biocenter Oulu, University of Oulu, Finland
| | - Susan M Ring
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Ulla Sovio
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, UK.,London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Marie Standl
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - H-Erich Wichmann
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany.,Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-Universität, Munich, Germany
| | - Nadja Hawwa Vissing
- Copenhagen Prospective Studies on Asthma in Childhood, University of Copenhagen, Copenhagen, Denmark
| | - Charles DeCarli
- Department of Neurology and Center for Neuroscience, University of California at Davis, Sacramento, CA, USA
| | | | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Xavier Estivill
- CIBER Epidemiologia y Salud Pública (CIBERESP), Barcelona, Catalonia, Spain.,Pompeu Fabra University (UPF), Barcelona, Catalonia, Spain.,Genes and Disease Program, Center for Genomic Regulation (CRG-UPF), Barcelona, Catalonia, Spain
| | - Andrew T Hattersley
- Peninsula NIHR Clinical Research Facility, Peninsula College of Medicine and Dentistry, University of Exeter, Exeter, UK
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, University of Copenhagen, Copenhagen, Denmark
| | - Craig E Pennell
- School of Women's and Infants' Health, The University of Western Australia, Perth, Australia
| | - Elisabeth Widen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, University of Pennsylvania, Philadelphia PA 19104, USA
| | - George Davey Smith
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Joachim Heinrich
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Marjo-Riitta Jarvelin
- Institute of Health Sciences, University of Oulu, Finland.,National Institute for Health and Welfare, Oulu, Finland, Biocenter Oulu, University of Oulu, Finland.,Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, MRC Health Protection Agency (HPA) Centre for Environment and Health, Imperial College London
| | | | - Vincent W V Jaddoe
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Paediatrics, Erasmus Medical Center, Rotterdam, The Netherlands.,The Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands
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50
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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: 610] [Impact Index Per Article: 50.8] [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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