101
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Wang P, Yan Y, Yu W, Zhang H. Role of ten-eleven translocation proteins and 5-hydroxymethylcytosine in hepatocellular carcinoma. Cell Prolif 2019; 52:e12626. [PMID: 31033072 PMCID: PMC6668972 DOI: 10.1111/cpr.12626] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/26/2019] [Accepted: 04/03/2019] [Indexed: 12/13/2022] Open
Abstract
In mammals, methylation of the 5th position of cytosine (5mC) seems to be a major epigenetic modification of DNA. This process can be reversed (resulting in cytosine) with high efficiency by dioxygenases of the ten‐eleven translocation (TET) family, which perform oxidation of 5mC to 5‐hydroxymethylcytosine (5hmC), 5‐formylcytosine and 5‐carboxylcytosine. It has been demonstrated that these 5mC oxidation derivatives are in a dynamic state and have pivotal regulatory functions. Here, we comprehensively summarized the recent research progress in the understanding of the physiological functions of the TET proteins and their mechanisms of regulation of DNA methylation and transcription. Among the three TET genes, TET1 and TET2 expression levels have frequently been shown to be low in hepatocellular carcinoma (HCC) tissues and received most attention. The modulation of TET1 also correlates with microRNAs in a post‐transcriptional regulatory process. Additionally, recent studies revealed that global genomic 5hmC levels are down‐regulated in HCC tissues and cell lines. Combined with the reported results, identification of 5hmC signatures in HCC tissues and in circulating cell‐free DNA will certainly contribute to early detection and should help to design therapeutic strategies against HCC. 5hmC might also be a novel prognostic biomarker of HCC. Thus, a detailed understanding of the molecular mechanisms resulting in the premalignant and aggressive transformation of TET proteins and cells with 5hmC disruption might help to develop novel epigenetic therapies for HCC.
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Affiliation(s)
- Penghui Wang
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yunmeng Yan
- Key Clinical Laboratory of Henan Province, Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Yu
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Hongyi Zhang
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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102
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Wild-Type IDH Enzymes as Actionable Targets for Cancer Therapy. Cancers (Basel) 2019; 11:cancers11040563. [PMID: 31010244 PMCID: PMC6520797 DOI: 10.3390/cancers11040563] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 12/11/2022] Open
Abstract
Isocitrate dehydrogenases (IDHs) are enzymes that catalyze the oxidative decarboxylation of isocitrate, producing α-ketoglutarate (αKG) and CO2. The discovery of IDH1 and IDH2 mutations in several malignancies has brought to the approval of drugs targeting IDH1/2 mutants in cancers. Here, we summarized findings addressing the impact of IDH mutants in rare pathologies and focused on the relevance of non-mutated IDH enzymes in tumors. Several pieces of evidence suggest that the enzymatic inhibition of IDHs may have therapeutic potentials also in wild-type IDH cancers. Moreover, IDHs inhibition could enhance the efficacy of canonical cancer therapies, such as chemotherapy, target therapy, and radiotherapy. However, further studies are required to elucidate whether IDH proteins are diagnostic/prognostic markers, instrumental for tumor initiation and maintenance, and could be exploited as targets for anticancer therapy. The development of wild-type IDH inhibitors is expected to improve our understanding of a potential non-oncogenic addition to IDH1/2 activities and to fully address their applicability in combination with other therapies.
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103
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Wagner S, Waldman M, Arora S, Wang S, Scott V, Islam K. Allele-Specific Inhibition of Histone Demethylases. Chembiochem 2019; 20:1133-1138. [PMID: 30618116 DOI: 10.1002/cbic.201800756] [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] [Received: 12/01/2018] [Indexed: 12/21/2022]
Abstract
Histone demethylases play a critical role in mammalian gene expression by removing methyl groups from lysine residues in degree- and site-specific manner. To specifically interrogate members and isoforms of this class of enzymes, we have developed demethylase variants with an expanded active site. The mutant enzymes are capable of performing lysine demethylation with wild-type proficiency, but are sensitive to inhibition by cofactor-competitive molecules embellished with a complementary steric "bump". The selected inhibitors show more than 20-fold selectivity over the wild-type demethylase, thus overcoming issues typical to pharmacological and genetic approaches. The mutant-inhibitor pairs are shown to act on a physiologically relevant full-length substrate. By engineering a conserved amino acid to achieve member-specific perturbation, this study provides a general approach for studying histone demethylases in diverse cellular processes.
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Affiliation(s)
- Shana Wagner
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Megan Waldman
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Simran Arora
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Sinan Wang
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Valerie Scott
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Kabirul Islam
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
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104
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Abstract
Mammalian sex determination is triggered by activation of the mammalian sex-determining gene, Sry, in a spatially and temporally controlled manner. Because reduced or delayed Sry expression results in male-to-female sex reversal, male development is highly dependent on the accurate transcription of Sry. SRY dysregulation is a potential cause of human disorders of sex development (DSD). In addition to changes in DNA sequences, gene expression is regulated by epigenetic mechanisms. Epigenetic regulation ensures spatial and temporal accuracy of the expression of developmentally regulated genes. Epigenetic regulation such as histone tail modification, DNA methylation, chromatin remodeling, and non-coding RNA regulation engages several biological processes in multicellular organisms. In recent years, it has been revealed that various types of epigenetic regulation are involved in accurate gonadal differentiation in mammals. In particular, histone modification plays an integral part in sex determination, which is the first step of gonadal differentiation. Here, we focus on the findings on the epigenetic modifications that regulate Sry expression. Finally, we discuss the role of metabolism that potentially alters the epigenetic state in response to environmental cues.
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Affiliation(s)
- Shingo Miyawaki
- Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan; Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Makoto Tachibana
- Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan; Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
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105
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Thinnes CC, Lohans CT, Abboud MI, Yeh T, Tumber A, Nowak RP, Attwood M, Cockman ME, Oppermann U, Loenarz C, Schofield CJ. Selective Inhibitors of a Human Prolyl Hydroxylase (OGFOD1) Involved in Ribosomal Decoding. Chemistry 2019; 25:2019-2024. [PMID: 30427558 PMCID: PMC6471485 DOI: 10.1002/chem.201804790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Indexed: 12/12/2022]
Abstract
Human prolyl hydroxylases are involved in the modification of transcription factors, procollagen, and ribosomal proteins, and are current medicinal chemistry targets. To date, there are few reports on inhibitors selective for the different types of prolyl hydroxylases. We report a structurally informed template-based strategy for the development of inhibitors selective for the human ribosomal prolyl hydroxylase OGFOD1. These inhibitors did not target the other human oxygenases tested, including the structurally similar hypoxia-inducible transcription factor prolyl hydroxylase, PHD2.
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Affiliation(s)
| | | | | | - Tzu‐Lan Yeh
- Department of ChemistryUniversity of OxfordOxfordOX1 3TAUK
| | - Anthony Tumber
- Department of ChemistryUniversity of OxfordOxfordOX1 3TAUK
- Structural Genomics ConsortiumUniversity of OxfordHeadingtonOX3 7DQUK
| | - Radosław P. Nowak
- Structural Genomics ConsortiumUniversity of OxfordHeadingtonOX3 7DQUK
- Department of Cancer BiologyDana-Farber Cancer InstituteBoston, MA02215USA
| | - Martin Attwood
- Centre for Cellular and Molecular PhysiologyUniversity of OxfordOxfordOX3 7BNUK
| | - Matthew E. Cockman
- Centre for Cellular and Molecular PhysiologyUniversity of OxfordOxfordOX3 7BNUK
| | - Udo Oppermann
- Structural Genomics ConsortiumUniversity of OxfordHeadingtonOX3 7DQUK
| | - Christoph Loenarz
- Department of ChemistryUniversity of OxfordOxfordOX1 3TAUK
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität Freiburg79104FreiburgGermany
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106
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Lamadema N, Burr S, Brewer AC. Dynamic regulation of epigenetic demethylation by oxygen availability and cellular redox. Free Radic Biol Med 2019; 131:282-298. [PMID: 30572012 DOI: 10.1016/j.freeradbiomed.2018.12.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/04/2018] [Accepted: 12/10/2018] [Indexed: 02/07/2023]
Abstract
The chromatin structure of the mammalian genome must facilitate both precisely-controlled DNA replication together with tightly-regulated gene transcription. This necessarily involves complex mechanisms and processes which remain poorly understood. It has long been recognised that the epigenetic landscape becomes established during embryonic development and acts to specify and determine cell fate. In addition, the chromatin structure is highly dynamic and allows for both cellular reprogramming and homeostatic modulation of cell function. In this respect, the functions of epigenetic "erasers", which act to remove covalently-linked epigenetic modifications from DNA and histones are critical. The enzymatic activities of the TET and JmjC protein families have been identified as demethylases which act to remove methyl groups from DNA and histones, respectively. Further, they are characterised as members of the Fe(II)- and 2-oxoglutarate-dependent dioxygenase superfamily. This provides the intriguing possibility that their enzymatic activities may be modulated by cellular metabolism, oxygen availability and redox-based mechanisms, all of which are likely to display dynamic cell- and tissue-specific patterns of flux. Here we discuss the current evidence for such [O2]- and redox-dependent regulation of the TET and Jmjc demethylases and the potential physiological and pathophysiological functional consequences of such regulation.
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Affiliation(s)
- Nermina Lamadema
- School of Cardiovascular Medicine & Sciences, King's College London BHF Centre of Research Excellence, United Kingdom
| | - Simon Burr
- School of Cardiovascular Medicine & Sciences, King's College London BHF Centre of Research Excellence, United Kingdom
| | - Alison C Brewer
- School of Cardiovascular Medicine & Sciences, King's College London BHF Centre of Research Excellence, United Kingdom.
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107
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Diverse metabolic reactions activated during 58-hr fasting are revealed by non-targeted metabolomic analysis of human blood. Sci Rep 2019; 9:854. [PMID: 30696848 PMCID: PMC6351603 DOI: 10.1038/s41598-018-36674-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/21/2018] [Indexed: 12/30/2022] Open
Abstract
During human fasting, metabolic markers, including butyrates, carnitines, and branched-chain amino acids, are upregulated for energy substitution through gluconeogenesis and use of stored lipids. We performed non-targeted, accurate semiquantitative metabolomic analysis of human whole blood, plasma, and red blood cells during 34–58 hr fasting of four volunteers. During this period, 44 of ~130 metabolites increased 1.5~60-fold. Consistently fourteen were previously reported. However, we identified another 30 elevated metabolites, implicating hitherto unrecognized metabolic mechanisms induced by fasting. Metabolites in pentose phosphate pathway are abundant, probably due to demand for antioxidants, NADPH, gluconeogenesis and anabolic metabolism. Global increases of TCA cycle-related compounds reflect enhanced mitochondrial activity in tissues during fasting. Enhanced purine/pyrimidine metabolites support RNA/protein synthesis and transcriptional reprogramming, which is promoted also by some fasting-related metabolites, possibly via epigenetic modulations. Thus diverse, pronounced metabolite increases result from greatly activated catabolism and anabolism stimulated by fasting. Anti-oxidation may be a principal response to fasting.
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108
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Demarquoy C, Demarquoy J. Autism and carnitine: A possible link. World J Biol Chem 2019; 10:7-16. [PMID: 30622681 PMCID: PMC6314880 DOI: 10.4331/wjbc.v10.i1.7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/26/2018] [Accepted: 11/26/2018] [Indexed: 02/05/2023] Open
Abstract
Patients with autism spectrum disorders (ASD) present deficits in social interactions and communication, they also show limited and stereotypical patterns of behaviors and interests. The pathophysiological bases of ASD have not been defined yet. Many factors seem to be involved in the onset of this disorder. These include genetic and environmental factors, but autism is not linked to a single origin, only. Autism onset can be connected with various factors such as metabolic disorders: including carnitine deficiency. Carnitine is a derivative of two amino acid lysine and methionine. Carnitine is a cofactor for a large family of enzymes: the carnitine acyltransferases. Through their action these enzymes (and L-carnitine) are involved in energy production and metabolic homeostasis. Some people with autism (less than 20%) seem to have L-carnitine metabolism disorders and for these patients, a dietary supplementation with L-carnitine is beneficial. This review summarizes the available information on this topic.
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Affiliation(s)
- Caroline Demarquoy
- DATSA 71 - Foyer Marie-José Marchand, 5 allée du Carrouge, Sennecey-le-Grand 71240, France
| | - Jean Demarquoy
- Université de Bourgogne-Agrosup Dijon, UMR PAM, 6 blvd Gabriel, Dijon 21000, France
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109
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The effects of 2-hydroxyglutarate on the tumorigenesis of gliomas. Contemp Oncol (Pozn) 2018; 22:215-222. [PMID: 30783384 PMCID: PMC6377424 DOI: 10.5114/wo.2018.82642] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 12/25/2018] [Indexed: 12/19/2022] Open
Abstract
Mutation of the isocitrate-dehydrogenase (IDH) enzymes is one of the central research topics regarding gliomagenesis. Indeed, 70% of gliomas are associated with a gain-of-function IDH mutation and consequently synthesize the oncometabolite, 2-hydroxyglutarate (2-HG). This review aims to elucidate the effects of 2-HG on gliomagenesis. 2-HG promotes tumorigenesis by impacting metabolism, vascularization and altering the epigenome of glioma cells. Glioma metabolism and vascularization is altered by 2-HG's effect on the stability of hypoxia-inducible factor (HIF) and inhibition of endostatin. However, 2-HG's impacts on epigenetic mechanisms are more profound to gliomagenesis. Through competitive inhibition of JHDMs and TET proteins, 2-HG orchestrates histone and DNA hypermethylation, which is associated with gene silencing and dedifferentiation of cells. The hypermethylator phenotype induced by 2-HG also results in alterations of the interaction of the immune system with the tumour. Additionally, this study reviews 2-HG promotion of tumorigenesis by inhibiting repair of DNA alkylation damage through competitive inhibition of AlkB proteins.
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110
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Devkota AK, Veloria JR, Guo HF, Kurie JM, Cho EJ, Dalby KN. Development of a High-Throughput Lysyl Hydroxylase (LH) Assay and Identification of Small-Molecule Inhibitors against LH2. SLAS DISCOVERY 2018; 24:484-491. [PMID: 30589612 DOI: 10.1177/2472555218817057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Lysyl hydroxylase-2 (LH2) catalyzes the hydroxylation of telopeptidyl lysine residues on collagen, leading to the formation of stable collagen cross-links that connect collagen molecules and stabilize the extracellular matrix. High levels of LH2 have been reported in the formation and stabilization of hydroxylysine aldehyde-derived collagen cross-links (HLCCs), leading to fibrosis and cancer metastasis in certain tissues. Identification of small-molecule inhibitors targeting LH2 activity requires a robust and suitable assay system, which is currently lacking. Thus, despite being a promising target for these diseases, small-molecule inhibitors for LH2 have yet to be reported. Therefore, we developed a luminescence-based strategy to monitor LH activity and validated its ability to identify new inhibitors in a screen of approximately 65,000 compounds against LH2. Primary hits were confirmed using the same LH assay against mimiviral L230. This newly developed LH assay is robust, suitable for high-throughput screening, and able to identify potent specific inhibitors of LH2.
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Affiliation(s)
- Ashwini K Devkota
- 1 Targeted Therapeutic Drug Discovery and Development Program, College of Pharmacy, The University of Texas at Austin, TX, USA
| | - John R Veloria
- 1 Targeted Therapeutic Drug Discovery and Development Program, College of Pharmacy, The University of Texas at Austin, TX, USA
| | - Hou-Fu Guo
- 2 Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jonathan M Kurie
- 2 Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eun Jeong Cho
- 1 Targeted Therapeutic Drug Discovery and Development Program, College of Pharmacy, The University of Texas at Austin, TX, USA
| | - Kevin N Dalby
- 1 Targeted Therapeutic Drug Discovery and Development Program, College of Pharmacy, The University of Texas at Austin, TX, USA.,3 Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, TX, USA
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111
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Islam K. The Bump-and-Hole Tactic: Expanding the Scope of Chemical Genetics. Cell Chem Biol 2018; 25:1171-1184. [PMID: 30078633 PMCID: PMC6195450 DOI: 10.1016/j.chembiol.2018.07.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/13/2018] [Accepted: 07/02/2018] [Indexed: 12/15/2022]
Abstract
Successful mapping of the human genome has sparked a widespread interest in deciphering functional information encoded in gene sequences. However, because of the high degree of conservation in sequences along with topological and biochemical similarities among members of a protein superfamily, uncovering physiological role of a particular protein has been a challenging task. Chemical genetic approaches have made significant contributions toward understanding protein function. One such effort, dubbed the bump-and-hole approach, has convincingly demonstrated that engineering at the protein-small molecule interface constitutes a powerful method for elucidating the function of a specific gene product. By manipulating the steric component of protein-ligand interactions in a complementary manner, an orthogonal system is developed to probe a specific enzyme-cofactor pair without interference from related members. This article outlines current efforts to expand the approach for diverse protein classes and their applications. Potential future innovations to address contemporary biological problems are highlighted as well.
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Affiliation(s)
- Kabirul Islam
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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112
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Kang J, Chun YS, Huh J, Park JW. FIH permits NAA10 to catalyze the oxygen-dependent lysyl-acetylation of HIF-1α. Redox Biol 2018; 19:364-374. [PMID: 30237125 PMCID: PMC6142190 DOI: 10.1016/j.redox.2018.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/29/2018] [Accepted: 09/03/2018] [Indexed: 12/15/2022] Open
Abstract
The N-terminal acetyltransferase A (NatA) complex, which is composed of NAA10 and NAA15, catalyzes N-terminal acetylation of many proteins in a co-translational manner. Structurally, the catalytic subunit NAA10 was believed to have no activity toward an internal lysine residue because the gate of its catalytic pocket is too narrow. However, several studies have demonstrated that the monomeric NAA10 can acetylate the internal lysine residues of several substrates including hypoxia-inducible factor 1α (HIF-1α). How NAA10 acetylates lysine residues has been an unsolved question. We here found that human FIH (factor inhibiting HIF) hydroxylates human NAA10 at W38 oxygen-dependently and this permits NAA10 to express the lysyl-acetyltransferase activity. The hydroxylated W38 forms a new hydrogen-bond with A67 and widens the gate at the catalytic pocket, which allows the entrance of a lysine residue to the site. Since the FIH-dependent hydroxylation of NAA10 occurs oxygen-dependently, NAA10 acetylates HIF-1α under normoxia but does not under hypoxia. Consequently, the acetylation promotes the pVHL binding to HIF-1α, and in turn HIF-1α is destructed via the ubiquitin-proteasome system. This study provides a novel oxygen-sensing process that determines the substrate specificity of NAA10 depending on an ambient oxygen tension.
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Affiliation(s)
- Jengmin Kang
- Department of Biomedical Science, BK21-plus education program, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Department of Pharmacology, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Yang-Sook Chun
- Department of Biomedical Science, BK21-plus education program, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - June Huh
- Department of Chemical and Biological Engineering, Korea University, Anam-dong, Seongbuk-gu, Seoul 136-713, Republic of Korea.
| | - Jong-Wan Park
- Department of Biomedical Science, BK21-plus education program, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Department of Pharmacology, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea.
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113
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Sudhamalla B, Wang S, Snyder V, Kavoosi S, Arora S, Islam K. Complementary Steric Engineering at the Protein-Ligand Interface for Analogue-Sensitive TET Oxygenases. J Am Chem Soc 2018; 140:10263-10269. [PMID: 30028600 PMCID: PMC6400064 DOI: 10.1021/jacs.8b05283] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ten-eleven translocation (TET) enzymes employ O2, earth-abundant iron, and 2-ketoglutarate (2KG) to perform iterative C-H oxidation of 5-methylcytosine in DNA to control expression of the mammalian genome. Given that more than 60 such C-H oxygenases are present in humans, determining context-dependent functions of each of these enzymes is a pivotal challenge. In an effort to tackle the problem, we developed analogue-sensitive TET enzymes to perturb the activity of a specific member. We rationally engineered the TET2-2KG interface to develop TET2 variants with an expanded active site that can be specifically inhibited by the N-oxalylglycine (NOG) derivatives carrying a complementary steric "bump". Herein, we describe the identification and engineering of a bulky gatekeeper residue for TET proteins, characterize the orthogonal mutant-inhibitor pairs, and show generality of the approach. Employing cell-permeable NOG analogues, we show that the TET2 mutant can be specifically inhibited to conditionally modulate cytosine methylation in chromosomal DNA in intact human cells. Finally, we demonstrate application of the orthogonal mutant-inhibitor pair to probe transcriptional activity of a specific TET member in cells. Our work provides a general platform for developing analogue-sensitive 2KG-dependent oxygenases to unravel their functions in diverse signaling processes.
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Affiliation(s)
- Babu Sudhamalla
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sinan Wang
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | | | | | | | - Kabirul Islam
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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114
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Gao SS, Naowarojna N, Cheng R, Liu X, Liu P. Recent examples of α-ketoglutarate-dependent mononuclear non-haem iron enzymes in natural product biosyntheses. Nat Prod Rep 2018; 35:792-837. [PMID: 29932179 PMCID: PMC6093783 DOI: 10.1039/c7np00067g] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: up to 2018 α-Ketoglutarate (αKG, also known as 2-oxoglutarate)-dependent mononuclear non-haem iron (αKG-NHFe) enzymes catalyze a wide range of biochemical reactions, including hydroxylation, ring fragmentation, C-C bond cleavage, epimerization, desaturation, endoperoxidation and heterocycle formation. These enzymes utilize iron(ii) as the metallo-cofactor and αKG as the co-substrate. Herein, we summarize several novel αKG-NHFe enzymes involved in natural product biosyntheses discovered in recent years, including halogenation reactions, amino acid modifications and tailoring reactions in the biosynthesis of terpenes, lipids, fatty acids and phosphonates. We also conducted a survey of the currently available structures of αKG-NHFe enzymes, in which αKG binds to the metallo-centre bidentately through either a proximal- or distal-type binding mode. Future structure-function and structure-reactivity relationship investigations will provide crucial information regarding how activities in this large class of enzymes have been fine-tuned in nature.
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Affiliation(s)
- Shu-Shan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Ronghai Cheng
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
| | - Xueting Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA. and State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA 02215, USA.
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115
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Peng D, Ge G, Gong Y, Zhan Y, He S, Guan B, Li Y, Xu Z, Hao H, He Z, Xiong G, Zhang C, Shi Y, Zhou Y, Ci W, Li X, Zhou L. Vitamin C increases 5-hydroxymethylcytosine level and inhibits the growth of bladder cancer. Clin Epigenetics 2018; 10:94. [PMID: 30005692 PMCID: PMC6045833 DOI: 10.1186/s13148-018-0527-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 07/05/2018] [Indexed: 12/31/2022] Open
Abstract
Background 5-Hydroxymethylcytosine (5hmC) is converted from 5-methylcytosine (5mC) by a group of enzymes termed ten-eleven translocation (TET) family dioxygenases. The loss of 5hmC has been identified as a hallmark of most types of cancer and is related to tumorigenesis and progression. However, the role of 5hmC in bladder cancer is seldom investigated. Vitamin C was recently reported to induce the generation of 5hmC by acting as a cofactor for TET dioxygenases. In this study, we explored the role of 5hmC in bladder cancer and the therapeutic efficacy of vitamin C in increasing the 5hmC pattern. Results 5hmC was decreased in bladder cancer samples and was related to patient overall survival. Genome-wide mapping of 5hmC in tumor tissues and vitamin C-treated bladder cancer cells revealed that 5hmC loss was enriched in cancer-related genes and that vitamin C treatment increased 5hmC levels correspondingly. Vitamin C treatment shifted the transcriptome and inhibited the malignant phenotypes associated with bladder cancer cells in both in vitro cell lines and in vivo xenografts. Conclusions This study provided mechanistic insights regarding the 5hmC loss in bladder cancer and a rationale for exploring the therapeutic use of vitamin C as a potential epigenetic treatment for bladder cancer. Electronic supplementary material The online version of this article (10.1186/s13148-018-0527-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ding Peng
- Department of Urology, Peking University First Hospital, Beijing, 100034, China.,Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,Institute of Urology, Peking University, Beijing, 100034, China.,National Urological Cancer Center, Beijing, 100034, China.,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Beijing, 100034, China
| | - Guangzhe Ge
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, China.,National Urological Cancer Center, Beijing, 100034, China.,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Beijing, 100034, China
| | - Yonghao Zhan
- Department of Urology, Peking University First Hospital, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, China.,National Urological Cancer Center, Beijing, 100034, China.,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Beijing, 100034, China
| | - Shiming He
- Department of Urology, Peking University First Hospital, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, China.,National Urological Cancer Center, Beijing, 100034, China.,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Beijing, 100034, China
| | - Bao Guan
- Department of Urology, Peking University First Hospital, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, China.,National Urological Cancer Center, Beijing, 100034, China.,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Beijing, 100034, China
| | - Yifan Li
- Department of Urology, Peking University First Hospital, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, China.,National Urological Cancer Center, Beijing, 100034, China.,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Beijing, 100034, China
| | - Ziying Xu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Han Hao
- Department of Urology, Peking University First Hospital, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, China.,National Urological Cancer Center, Beijing, 100034, China.,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Beijing, 100034, China
| | - Zhisong He
- Department of Urology, Peking University First Hospital, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, China.,National Urological Cancer Center, Beijing, 100034, China.,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Beijing, 100034, China
| | - Gengyan Xiong
- Department of Urology, Peking University First Hospital, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, China.,National Urological Cancer Center, Beijing, 100034, China.,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Beijing, 100034, China
| | - Cuijian Zhang
- Department of Urology, Peking University First Hospital, Beijing, 100034, China.,Institute of Urology, Peking University, Beijing, 100034, China.,National Urological Cancer Center, Beijing, 100034, China.,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Beijing, 100034, China
| | - Yue Shi
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuanyuan Zhou
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Weimin Ci
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, Beijing, 100034, China. .,Institute of Urology, Peking University, Beijing, 100034, China. .,National Urological Cancer Center, Beijing, 100034, China. .,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Beijing, 100034, China.
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing, 100034, China. .,Institute of Urology, Peking University, Beijing, 100034, China. .,National Urological Cancer Center, Beijing, 100034, China. .,Urogenital Diseases (Male) Molecular Diagnosis and Treatment Center, Peking University, Beijing, 100034, China.
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Nakashima Y, Mitsuhashi T, Matsuda Y, Senda M, Sato H, Yamazaki M, Uchiyama M, Senda T, Abe I. Structural and Computational Bases for Dramatic Skeletal Rearrangement in Anditomin Biosynthesis. J Am Chem Soc 2018; 140:9743-9750. [DOI: 10.1021/jacs.8b06084] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yu Nakashima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yudai Matsuda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Miki Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Hajime Sato
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8675, Japan
- Cluster of Pioneering Research (CPR), Advanced Elements Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Science, Chiba University, 1-8-1, Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Cluster of Pioneering Research (CPR), Advanced Elements Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
- Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies (Soken-dai), 1−1 Oho, Tsukuba, Ibaraki 305−0801, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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117
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Paredes F, Suster I, Martin AS. Poldip2 takes a central role in metabolic reprograming. Oncoscience 2018; 5:130-131. [PMID: 30035163 PMCID: PMC6049324 DOI: 10.18632/oncoscience.419] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 04/21/2018] [Indexed: 02/05/2023] Open
Affiliation(s)
- Felipe Paredes
- Division of Cardiology, Department of Medicine, Emory University, 308 WMB, Atlanta, GA, 30322, USA
| | - Izabela Suster
- Division of Cardiology, Department of Medicine, Emory University, 308 WMB, Atlanta, GA, 30322, USA
| | - Alejandra San Martin
- Division of Cardiology, Department of Medicine, Emory University, 308 WMB, Atlanta, GA, 30322, USA
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118
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Bonnici J, Tumber A, Kawamura A, Schofield CJ. Inhibitors of both the N-methyl lysyl- and arginyl-demethylase activities of the JmjC oxygenases. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170071. [PMID: 29685975 PMCID: PMC5915715 DOI: 10.1098/rstb.2017.0071] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2017] [Indexed: 12/22/2022] Open
Abstract
The Jumonji C (JmjC) family of 2-oxoglutarate (2OG)-dependent oxygenases have established roles in the regulation of transcription via the catalysis of demethylation of Nε-methylated lysine residues in histone tails, especially the N-terminal tail of histone H3. Most human JmjC Nɛ -methyl lysine demethylases (KDMs) are complex enzymes, with 'reader domains' in addition to their catalytic domains. Recent biochemical evidence has shown that some, but not all, JmjC KDMs also have Nω-methyl arginyl demethylase (RDM) activity. JmjC KDM activity has been linked to multiple cancers and some JmjC proteins are therapeutic targets. It is, therefore, important to test not only whether compounds in development inhibit the KDM activity of targeted JmjC demethylases, but also whether they inhibit other activities of these proteins. Here we report biochemical studies on the potential dual inhibition of JmjC KDM and RDM activities using a model JmjC demethylase, KDM4E (JMJD2E). The results reveal that all of the tested compounds inhibit both the KDM and RDM activities, raising questions about the in vivo effects of the inhibitors.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- Joanna Bonnici
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Anthony Tumber
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Akane Kawamura
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christopher J Schofield
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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119
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Bailey PSJ, Nathan JA. Metabolic Regulation of Hypoxia-Inducible Transcription Factors: The Role of Small Molecule Metabolites and Iron. Biomedicines 2018; 6:biomedicines6020060. [PMID: 29772792 PMCID: PMC6027492 DOI: 10.3390/biomedicines6020060] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/11/2018] [Accepted: 05/15/2018] [Indexed: 02/02/2023] Open
Abstract
Hypoxia-inducible transcription factors (HIFs) facilitate cellular adaptations to low-oxygen environments. However, it is increasingly recognised that HIFs may be activated in response to metabolic stimuli, even when oxygen is present. Understanding the mechanisms for the crosstalk that exists between HIF signalling and metabolic pathways is therefore important. This review focuses on the metabolic regulation of HIFs by small molecule metabolites and iron, highlighting the latest studies that explore how tricarboxylic acid (TCA) cycle intermediates, 2-hydroxyglutarate (2-HG) and intracellular iron levels influence the HIF response through modulating the activity of prolyl hydroxylases (PHDs). We also discuss the relevance of these metabolic pathways in physiological and disease contexts. Lastly, as PHDs are members of a large family of 2-oxoglutarate (2-OG) dependent dioxygenases that can all respond to metabolic stimuli, we explore the broader role of TCA cycle metabolites and 2-HG in the regulation of 2-OG dependent dioxygenases, focusing on the enzymes involved in chromatin remodelling.
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Affiliation(s)
- Peter S J Bailey
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge CB2 0XY, UK.
| | - James A Nathan
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge CB2 0XY, UK.
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120
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Shepelin D, Hansen ASL, Lennen R, Luo H, Herrgård MJ. Selecting the Best: Evolutionary Engineering of Chemical Production in Microbes. Genes (Basel) 2018; 9:E249. [PMID: 29751691 PMCID: PMC5977189 DOI: 10.3390/genes9050249] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 05/02/2018] [Accepted: 05/02/2018] [Indexed: 01/10/2023] Open
Abstract
Microbial cell factories have proven to be an economical means of production for many bulk, specialty, and fine chemical products. However, we still lack both a holistic understanding of organism physiology and the ability to predictively tune enzyme activities in vivo, thus slowing down rational engineering of industrially relevant strains. An alternative concept to rational engineering is to use evolution as the driving force to select for desired changes, an approach often described as evolutionary engineering. In evolutionary engineering, in vivo selections for a desired phenotype are combined with either generation of spontaneous mutations or some form of targeted or random mutagenesis. Evolutionary engineering has been used to successfully engineer easily selectable phenotypes, such as utilization of a suboptimal nutrient source or tolerance to inhibitory substrates or products. In this review, we focus primarily on a more challenging problem-the use of evolutionary engineering for improving the production of chemicals in microbes directly. We describe recent developments in evolutionary engineering strategies, in general, and discuss, in detail, case studies where production of a chemical has been successfully achieved through evolutionary engineering by coupling production to cellular growth.
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Affiliation(s)
- Denis Shepelin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Anne Sofie Lærke Hansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Rebecca Lennen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Hao Luo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
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121
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Haase VH. Oxygen sensors as therapeutic targets in kidney disease. Nephrol Ther 2018; 13 Suppl 1:S29-S34. [PMID: 28577740 DOI: 10.1016/j.nephro.2017.01.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 01/20/2017] [Indexed: 01/03/2023]
Abstract
Hypoxia is a common clinical problem that has profound effects on renal homeostasis. Prolyl-4-hydroxylases PHD1, 2 and 3 function as oxygen sensors and control the activity of hypoxia-inducible factor (HIF), an oxygen-sensitive transcription factor that regulates a multitude of hypoxia responses, which help cells and tissues to adapt to low oxygen environments. This review provides an overview of the molecular mechanisms that govern these hypoxia responses and discusses clinical experience with compounds that inhibit prolyl-4-hydroxylases to harness HIF responses for therapy in nephrology.
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Affiliation(s)
- Volker H Haase
- Department of medicine, Vanderbilt university medical center, Nashville, TN, USA; Departments of cancer biology and molecular physiology and biophysics, Vanderbilt university school of medicine, Nashville, TN, USA; Medical and research services, department of veterans affairs hospital, Tennessee Valley healthcare system, Nashville, TN, USA.
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122
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Matre P, Velez J, Jacamo R, Qi Y, Su X, Cai T, Chan SM, Lodi A, Sweeney SR, Ma H, Davis RE, Baran N, Haferlach T, Su X, Flores ER, Gonzalez D, Konoplev S, Samudio I, DiNardo C, Majeti R, Schimmer AD, Li W, Wang T, Tiziani S, Konopleva M. Inhibiting glutaminase in acute myeloid leukemia: metabolic dependency of selected AML subtypes. Oncotarget 2018; 7:79722-79735. [PMID: 27806325 PMCID: PMC5340236 DOI: 10.18632/oncotarget.12944] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/13/2016] [Indexed: 02/06/2023] Open
Abstract
Metabolic reprogramming has been described as a hallmark of transformed cancer cells. In this study, we examined the role of the glutamine (Gln) utilization pathway in acute myeloid leukemia (AML) cell lines and primary AML samples. Our results indicate that a subset of AML cell lines is sensitive to Gln deprivation. Glutaminase (GLS) is a mitochondrial enzyme that catalyzes the conversion of Gln to glutamate. One of the two GLS isoenzymes, GLS1 is highly expressed in cancer and encodes two different isoforms: kidney (KGA) and glutaminase C (GAC). We analyzed mRNA expression of GLS1 splicing variants, GAC and KGA, in several large AML datasets and identified increased levels of expression in AML patients with complex cytogenetics and within specific molecular subsets. Inhibition of glutaminase by allosteric GLS inhibitor bis-2-(5-phenylacetamido-1, 2, 4-thiadiazol-2-yl) ethyl sulfide or by novel, potent, orally bioavailable GLS inhibitor CB-839 reduced intracellular glutamate levels and inhibited growth of AML cells. In cell lines and patient samples harboring IDH1/IDH2 (Isocitrate dehydrogenase 1 and 2) mutations, CB-839 reduced production of oncometabolite 2-hydroxyglutarate, inducing differentiation. These findings indicate potential utility of glutaminase inhibitors in AML therapy, which can inhibit cell growth, induce apoptosis and/or differentiation in specific leukemia subtypes.
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Affiliation(s)
- Polina Matre
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Juliana Velez
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rodrigo Jacamo
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuan Qi
- Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaoping Su
- Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tianyu Cai
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Steven M Chan
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Alessia Lodi
- Department of Nutritional Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Shannon R Sweeney
- Department of Nutritional Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Helen Ma
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Richard Eric Davis
- Lymphoma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Natalia Baran
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Xiaohua Su
- Molecular & Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elsa Renee Flores
- Molecular & Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Doriann Gonzalez
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sergej Konoplev
- Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ismael Samudio
- The Centre for Drug Research and Development Biologics, Vancouver, British Columbia, Canada
| | - Courtney DiNardo
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ravi Majeti
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Aaron D Schimmer
- Medical Biophysics, Princess Margaret Hospital / Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
| | - Weiqun Li
- Analytical Chemistry, Pharmacology, Spectroscopy, Calithera Biosciences, South San Francisco, CA, USA
| | - Taotao Wang
- Analytical Chemistry, Pharmacology, Spectroscopy, Calithera Biosciences, South San Francisco, CA, USA
| | - Stefano Tiziani
- Department of Nutritional Sciences, The University of Texas at Austin, Austin, TX, USA
| | - Marina Konopleva
- Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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123
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Gándara L, Wappner P. Metabo-Devo: A metabolic perspective of development. Mech Dev 2018; 154:12-23. [PMID: 29475040 DOI: 10.1016/j.mod.2018.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 02/19/2018] [Accepted: 02/19/2018] [Indexed: 02/07/2023]
Abstract
In the last years, several reports have established the notion that metabolism is not just a housekeeping process, but instead an active effector of physiological changes. The idea that the metabolic status may rule a wide range of phenomena in cell biology is starting to be broadly accepted. Thus, current developmental biology has begun to describe different ways by which the metabolic profile of the cell and developmental programs of the organism can crosstalk. In this review, we discuss mechanisms by which metabolism impacts on processes governing development. We review the growing body of evidence that supports the notion that aerobic glycolysis is required in cells undergoing fast growth and high proliferation, similarly to the Warburg effect described in tumor cells. Glycolytic metabolism explains not only the higher ATP synthesis rate required for cell growth, but also the uncoupling between mitochondrial activity and bioenergetics needed to provide anabolism with sufficient precursors. We also discuss some recent studies, which show that in addition to its role in providing energy and carbon chains, the metabolic status of the cell can also influence epigenetic regulation of developmental processes. Although metabolic aspects of development are just starting to be explored, there is no doubt that ongoing research in this field will shape the future landscape of Developmental Biology.
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Affiliation(s)
- Lautaro Gándara
- Instituto Leloir, Av. Patricias Argentinas 435, Ciudad de Buenos Aires C1405BWE, Argentina
| | - Pablo Wappner
- Instituto Leloir, Av. Patricias Argentinas 435, Ciudad de Buenos Aires C1405BWE, 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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124
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IDH1 mutation is associated with lower expression of VEGF but not microvessel formation in glioblastoma multiforme. Oncotarget 2018; 9:16462-16476. [PMID: 29662659 PMCID: PMC5893254 DOI: 10.18632/oncotarget.24536] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 02/10/2018] [Indexed: 12/18/2022] Open
Abstract
Introduction Glioblastoma multiforme (GBM) represents the most malignant primary brain tumor characterized by pathological vascularization. Mutations in isocitrate dehydrogenases 1 and 2 (IDH1 and IDH2) were observed in GBM. We aimed to assess the intra-tumor hypoxia, angiogenesis and microvessel formation in GBM and to find their associations with IDH1 mutation status and patients prognosis. Methods 52 patients with a diagnosis of GBM were included into the study. IDH1 R132H mutation was assessed by RT-PCR from FFPE tumor samples obtained during surgery. The expression of markers of hypoxia (HIF2α), angiogenesis (VEGF), tumor microvascularity (CD31, CD34, vWF, CD105), and proliferation (Ki-67) were assessed immunohistochemically (IHC). IDH1 mutation and IHC markers were correlated with the patient survival. Results 20 from 52 GBM tumor samples comprised IDH1 R132H mutation (38.5%). The majority of mutated tumors were classified as secondary glioblastomas (89.9%). Patients with IDH1 mutated tumors experienced better progression-free survival (P = 0.037) as well as overall survival (P = 0.035) compared with wild type tumors. The significantly lower expression of VEGF was observed in GBM with IDH1 mutation than in wild type tumors (P = 0.01). No such association was found for microvascular markers. The increased expression of newly-formed microvessels (ratio CD105/CD31) in tumor samples was associated with worse patient’s progression-free survival (P = 0.026). Summary No increase in HIF/VEGF-mediated angiogenesis was observed in IDH1-mutated GBM compared with IDH1 wild type tumors. The histological assessment of the portion of newly-formed microvessels in tumor tissue can be used for the prediction of GBM patient’s prognosis.
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125
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Song X, Lu J, Lai W. Mechanistic insights into dioxygen activation, oxygen atom exchange and substrate epoxidation by AsqJ dioxygenase from quantum mechanical/molecular mechanical calculations. Phys Chem Chem Phys 2018; 19:20188-20197. [PMID: 28726913 DOI: 10.1039/c7cp02687k] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Herein, we use in-protein quantum mechanical/molecular mechanical (QM/MM) calculations to elucidate the mechanism of dioxygen activation, oxygen atom exchange and substrate epoxidation processes by AsqJ, an FeII/α-ketoglutarate-dependent dioxygenase (α-KGD) using a 2-His-1-Asp facial triad. Our results demonstrated that the whole reaction proceeds through a quintet surface. The dioxygen activation by AsqJ leads to a quintet penta-coordinated FeIV-oxo species, which has a square pyramidal geometry with the oxo group trans to His134. This penta-coordinated FeIV-oxo species is not the reactive one in the substrate epoxidation reaction since its oxo group is pointing away from the target C[double bond, length as m-dash]C bond. Instead, it can undergo the oxo group isomerization followed by water binding or the water binding followed by oxygen atom exchange to form the reactive hexa-coordinated FeIV-oxo species with the oxo group trans to His211. The calculated parameters of Mössbauer spectra for this hexa-coordinated FeIV-oxo intermediate are in excellent agreement with the experimental values, suggesting that it is most likely the experimentally trapped species. The calculated energetics indicated that the rate-limiting step is the substrate C[double bond, length as m-dash]C bond activation. This work improves our understanding of the dioxygen activation by α-KGD and provides important structural information about the reactive FeIV-oxo species.
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Affiliation(s)
- Xudan Song
- Department of Chemistry, Renmin University of China, Beijing, 100872, China.
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126
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Xiao L, Luo G, Tang Y, Yao P. Quercetin and iron metabolism: What we know and what we need to know. Food Chem Toxicol 2018; 114:190-203. [PMID: 29432835 DOI: 10.1016/j.fct.2018.02.022] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 01/18/2018] [Accepted: 02/07/2018] [Indexed: 12/14/2022]
Abstract
Iron is a life-supporting micronutrient that is required in the human diet, and is essential for maintaining physiological homeostasis. Properly harnessing a redox-active metal such as iron is a great challenge for cells and organisms because an excess of highly reactive iron catalyzes the formation of reactive oxygen species and can lead to cell and tissue damage. Quercetin is a typical flavonoid that is commonly found in fruits and vegetables and has versatile biological effects. From a classical viewpoint, owing to its unique chemical characteristics, quercetin has long been associated with iron metabolism only in the context of its iron-chelating and ROS-scavenging activities. However, within the field of human iron biology, expanding concepts of the roles of quercetin are flourishing, and great strides are being made in understanding the interactions between quercetin and iron. This progress highlights the varied roles of quercetin in iron metabolism, which involve much more than iron chelation alone. A review of these studies provides an ideal context to summarize recent progress and discuss compelling evidence for therapeutic opportunities that could arise from a better understanding of the underlying mechanisms.
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Affiliation(s)
- Lin Xiao
- Department of Nutrition and Food Hygiene, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Ministry of Education Key Laboratory of Environment, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Gang Luo
- Department of Nutrition and Food Hygiene, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Ministry of Education Key Laboratory of Environment, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuhan Tang
- Department of Nutrition and Food Hygiene, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Ministry of Education Key Laboratory of Environment, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Ping Yao
- Department of Nutrition and Food Hygiene, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China; Ministry of Education Key Laboratory of Environment, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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127
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Pro-metastatic collagen lysyl hydroxylase dimer assemblies stabilized by Fe 2+-binding. Nat Commun 2018; 9:512. [PMID: 29410444 PMCID: PMC5802723 DOI: 10.1038/s41467-018-02859-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/04/2018] [Indexed: 11/30/2022] Open
Abstract
Collagen lysyl hydroxylases (LH1-3) are Fe2+- and 2-oxoglutarate (2-OG)-dependent oxygenases that maintain extracellular matrix homeostasis. High LH2 levels cause stable collagen cross-link accumulations that promote fibrosis and cancer progression. However, developing LH antagonists will require structural insights. Here, we report a 2 Å crystal structure and X-ray scattering on dimer assemblies for the LH domain of L230 in Acanthamoeba polyphaga mimivirus. Loop residues in the double-stranded β-helix core generate a tail-to-tail dimer. A stabilizing hydrophobic leucine locks into an aromatic tyrosine-pocket on the opposite subunit. An active site triad coordinates Fe2+. The two active sites flank a deep surface cleft that suggest dimerization creates a collagen-binding site. Loss of Fe2+-binding disrupts the dimer. Dimer disruption and charge reversal in the cleft increase Km and reduce LH activity. Ectopic L230 expression in tumors promotes collagen cross-linking and metastasis. These insights suggest inhibitor targets for fibrosis and cancer. Collagen lysyl hydroxylases promote cancer progression. Here the authors present the crystal structure of the lysyl hydroxylase domain of L230 from Acanthamoeba polyphagamimivirus, which is of interest for LH inhibitor development, and show that ectopic expression of L230 in tumors promotes collagen cross-linking and metastasis.
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128
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HIF-1-alpha links mitochondrial perturbation to the dynamic acquisition of breast cancer tumorigenicity. Oncotarget 2018; 7:34052-69. [PMID: 27058900 PMCID: PMC5085137 DOI: 10.18632/oncotarget.8570] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 03/10/2016] [Indexed: 12/20/2022] Open
Abstract
Up-regulation of hypoxia-inducible factor-1α (HIF-1α), even in normoxia, is a common feature of solid malignancies. However, the mechanisms of increased HIF-1α abundance, and its role in regulating breast cancer plasticity are not fully understood. We have previously demonstrated that dimethyl-2-ketoglutarate (DKG), a widely used cell membrane-permeable α-ketoglutarate (α-KG) analogue, transiently stabilizes HIF-1α by inhibiting prolyl hydroxylase 2. Here, we report that breast cancer tumorigenicity can be acquired through prolonged treatment with DKG. Our results indicate that, in response to prolonged DKG treatment, mitochondrial respiration becomes uncoupled, leading to the accumulation of succinate and fumarate in breast cancer cells. Further, we found that an early increase in the oxygen flux rate was accompanied by a delayed enhancement of glycolysis. Together, our results indicate that these events trigger a dynamic enrichment for cells with pluripotent/stem-like cell markers and tumorsphere-forming capacity. Moreover, DKG-mediated metabolic reprogramming results in HIF-1α induction and reductive carboxylation pathway activation. Both HIF-1α accumulation and the tumor-promoting metabolic state are required for DKG-promoted tumor repopulation capacity in vivo. Our data suggest that mitochondrial adaptation to DKG elevates the ratio of succinate or fumarate to α-KG, which in turn stabilizes HIF-1α and reprograms breast cancer cells into a stem-like state. Therefore, our results demonstrate that metabolic regulation, with succinate and/or fumarate accumulation, governs the dynamic transition of breast cancer tumorigenic states and we suggest that HIF-1α is indispensable for breast cancer tumorigenicity.
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129
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Ranchoux B, Harvey LD, Ayon RJ, Babicheva A, Bonnet S, Chan SY, Yuan JXJ, Perez VDJ. Endothelial dysfunction in pulmonary arterial hypertension: an evolving landscape (2017 Grover Conference Series). Pulm Circ 2018; 8:2045893217752912. [PMID: 29283043 PMCID: PMC5798691 DOI: 10.1177/2045893217752912] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/18/2017] [Indexed: 02/06/2023] Open
Abstract
Endothelial dysfunction is a major player in the development and progression of vascular pathology in pulmonary arterial hypertension (PAH), a disease associated with small vessel loss and obstructive vasculopathy that leads to increased pulmonary vascular resistance, subsequent right heart failure, and premature death. Over the past ten years, there has been tremendous progress in our understanding of pulmonary endothelial biology as it pertains to the genetic and molecular mechanisms that orchestrate the endothelial response to direct or indirect injury, and how their dysregulation can contribute to the pathogenesis of PAH. As one of the major topics included in the 2017 Grover Conference Series, discussion centered on recent developments in four areas of pulmonary endothelial biology: (1) angiogenesis; (2) endothelial-mesenchymal transition (EndMT); (3) epigenetics; and (4) biology of voltage-gated ion channels. The present review will summarize the content of these discussions and provide a perspective on the most promising aspects of endothelial dysfunction that may be amenable for therapeutic development.
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Affiliation(s)
| | - Lloyd D. Harvey
- University of Pittsburgh Vascular Medicine Institute Division of Cardiology, Pittsburgh, PA, USA
| | - Ramon J. Ayon
- Division of Translational and Regenerative Medicine, The University of Arizona College of Medicine, Tucson, AZ, USA
| | - Aleksandra Babicheva
- Division of Translational and Regenerative Medicine, The University of Arizona College of Medicine, Tucson, AZ, USA
| | | | - Stephen Y. Chan
- University of Pittsburgh Vascular Medicine Institute Division of Cardiology, Pittsburgh, PA, USA
| | - Jason X.-J. Yuan
- Division of Translational and Regenerative Medicine, The University of Arizona College of Medicine, Tucson, AZ, USA
| | - Vinicio de Jesus Perez
- Division of Pulmonary and Critical Care Medicine, Stanford University Medical Center, Stanford, CA, USA
- The Vera Moulton Wall Center for Pulmonary Vascular Medicine, Stanford University Medical Center, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University Medical Center, Stanford, CA, USA
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130
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Haase VH. HIF-prolyl hydroxylases as therapeutic targets in erythropoiesis and iron metabolism. Hemodial Int 2017; 21 Suppl 1:S110-S124. [PMID: 28449418 DOI: 10.1111/hdi.12567] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A classic response to systemic hypoxia is the increase in red blood cell production. This response is controlled by the prolyl hydroxylase domain/hypoxia-inducible factor (HIF) pathway, which regulates a broad spectrum of cellular functions. The discovery of this pathway as a key regulator of erythropoiesis has led to the development of small molecules that stimulate the production of endogenous erythropoietin and enhance iron metabolism. This review provides a concise overview of the cellular and molecular mechanisms that govern HIF-induced erythropoietic responses and provides an update on clinical experience with compounds that target HIF-prolyl hydroxylases for anemia therapy.
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Affiliation(s)
- Volker H Haase
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Departments of Cancer Biology and Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Department of Veterans Affairs Hospital, Medical and Research Services, Tennessee Valley Healthcare System, Nashville, Tennessee, USA
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131
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Konuma T, Yu D, Zhao C, Ju Y, Sharma R, Ren C, Zhang Q, Zhou MM, Zeng L. Structural Mechanism of the Oxygenase JMJD6 Recognition by the Extraterminal (ET) Domain of BRD4. Sci Rep 2017; 7:16272. [PMID: 29176719 PMCID: PMC5701133 DOI: 10.1038/s41598-017-16588-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 11/15/2017] [Indexed: 02/04/2023] Open
Abstract
Jumonji domain-containing protein 6 (JMJD6) is a member of the Jumonji C family of Fe(II) and 2-oxoglutarate (2OG) dependent oxygenases. It possesses unique bi-functional oxygenase activities, acting as both an arginine demethylase and a lysyl-hydroxylase. JMJD6 has been reported to be over-expressed in oral, breast, lung, and colon cancers and plays important roles in regulation of transcription through interactions with transcription regulator BRD4, histones, U2AF65, Luc7L3, and SRSF11. Here, we report a structural mechanism revealed by NMR of JMJD6 recognition by the extraterminal (ET) domain of BRD4 in that a JMJD6 peptide (Lys84-Asn96) adapts an α-helix when bound to the ET domain. This intermolecular recognition is established through JMJD6 interactions with the conserved hydrophobic core of the ET domain, and reinforced by electrostatic interactions of JMJD6 with residues in the inter-helical α1-α2 loop of the ET domain. Notably, this mode of ligand recognition is different from that of ET domain recognition of NSD3, LANA of herpesvirus, and integrase of MLV, which involves formation of an intermolecular amphipathic two- or three- strand antiparallel β sheet. Furthermore, we demonstrate that the association between the BRD4 ET domain and JMJD6 likely requires a protein conformational change induced by single-stranded RNA binding.
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Affiliation(s)
- Tsuyoshi Konuma
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Di Yu
- Bethune Institute of Epigenetic Medicine, The First Hospital, Jilin University, Changchun, Jilin, 130021, China
| | - Chengcheng Zhao
- Bethune Institute of Epigenetic Medicine, The First Hospital, Jilin University, Changchun, Jilin, 130021, China
| | - Ying Ju
- Bethune Institute of Epigenetic Medicine, The First Hospital, Jilin University, Changchun, Jilin, 130021, China
| | - Rajal Sharma
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Chunyan Ren
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Qiang Zhang
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Bethune Institute of Epigenetic Medicine, The First Hospital, Jilin University, Changchun, Jilin, 130021, China
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lei Zeng
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Bethune Institute of Epigenetic Medicine, The First Hospital, Jilin University, Changchun, Jilin, 130021, China.
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132
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Raffel S, Falcone M, Kneisel N, Hansson J, Wang W, Lutz C, Bullinger L, Poschet G, Nonnenmacher Y, Barnert A, Bahr C, Zeisberger P, Przybylla A, Sohn M, Tönjes M, Erez A, Adler L, Jensen P, Scholl C, Fröhling S, Cocciardi S, Wuchter P, Thiede C, Flörcken A, Westermann J, Ehninger G, Lichter P, Hiller K, Hell R, Herrmann C, Ho AD, Krijgsveld J, Radlwimmer B, Trumpp A. BCAT1 restricts αKG levels in AML stem cells leading to IDHmut-like DNA hypermethylation. Nature 2017; 551:384-388. [PMID: 29144447 DOI: 10.1038/nature24294] [Citation(s) in RCA: 230] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 09/19/2017] [Indexed: 12/27/2022]
Abstract
The branched-chain amino acid (BCAA) pathway and high levels of BCAA transaminase 1 (BCAT1) have recently been associated with aggressiveness in several cancer entities. However, the mechanistic role of BCAT1 in this process remains largely uncertain. Here, by performing high-resolution proteomic analysis of human acute myeloid leukaemia (AML) stem-cell and non-stem-cell populations, we find the BCAA pathway enriched and BCAT1 protein and transcripts overexpressed in leukaemia stem cells. We show that BCAT1, which transfers α-amino groups from BCAAs to α-ketoglutarate (αKG), is a critical regulator of intracellular αKG homeostasis. Further to its role in the tricarboxylic acid cycle, αKG is an essential cofactor for αKG-dependent dioxygenases such as Egl-9 family hypoxia inducible factor 1 (EGLN1) and the ten-eleven translocation (TET) family of DNA demethylases. Knockdown of BCAT1 in leukaemia cells caused accumulation of αKG, leading to EGLN1-mediated HIF1α protein degradation. This resulted in a growth and survival defect and abrogated leukaemia-initiating potential. By contrast, overexpression of BCAT1 in leukaemia cells decreased intracellular αKG levels and caused DNA hypermethylation through altered TET activity. AML with high levels of BCAT1 (BCAT1high) displayed a DNA hypermethylation phenotype similar to cases carrying a mutant isocitrate dehydrogenase (IDHmut), in which TET2 is inhibited by the oncometabolite 2-hydroxyglutarate. High levels of BCAT1 strongly correlate with shorter overall survival in IDHWTTET2WT, but not IDHmut or TET2mut AML. Gene sets characteristic for IDHmut AML were enriched in samples from patients with an IDHWTTET2WTBCAT1high status. BCAT1high AML showed robust enrichment for leukaemia stem-cell signatures, and paired sample analysis showed a significant increase in BCAT1 levels upon disease relapse. In summary, by limiting intracellular αKG, BCAT1 links BCAA catabolism to HIF1α stability and regulation of the epigenomic landscape, mimicking the effects of IDH mutations. Our results suggest the BCAA-BCAT1-αKG pathway as a therapeutic target to compromise leukaemia stem-cell function in patients with IDHWTTET2WT AML.
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Affiliation(s)
- Simon Raffel
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.,Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Mattia Falcone
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Niclas Kneisel
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jenny Hansson
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Wei Wang
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Christoph Lutz
- Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Lars Bullinger
- Department of Internal Medicine III, University Hospital Ulm, 89081 Ulm, Germany
| | - Gernot Poschet
- Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany
| | - Yannic Nonnenmacher
- Department of Bioinfomatics and Biochemistry and Braunschweig Integrated Center of Systems Biology (BRICS), Technical University Braunschweig, 38106 Braunschweig, Germany.,Luxemburg Centre for Systems Biomedicine, University of Luxemburg, L-4367 Belvaux, Luxemburg
| | - Andrea Barnert
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Carsten Bahr
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Petra Zeisberger
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Adriana Przybylla
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Markus Sohn
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Martje Tönjes
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ayelet Erez
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Lital Adler
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Patrizia Jensen
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Claudia Scholl
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), DKFZ, 69120 Heidelberg, Germany
| | - Stefan Fröhling
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Section for Personalized Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), DKFZ, 69120 Heidelberg, Germany
| | - Sibylle Cocciardi
- Department of Internal Medicine III, University Hospital Ulm, 89081 Ulm, Germany
| | - Patrick Wuchter
- Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany.,Institute of Transfusion Medicine and Immunology Mannheim, Medical Faculty Mannheim, Heidelberg University, German Red Cross Blood Service Baden-Württemberg-Hessen, 68167 Mannheim, Germany
| | - Christian Thiede
- Medical Department 1, University Hospital Carl Gustav Carus, 01307 Dresden, Germany
| | - Anne Flörcken
- Department of Hematology, Oncology and Tumor Immunology; Charité-University Medicine Berlin, Campus Virchow Klinikum, 13353 Berlin, Germany
| | - Jörg Westermann
- Department of Hematology, Oncology and Tumor Immunology; Charité-University Medicine Berlin, Campus Virchow Klinikum, 13353 Berlin, Germany
| | - Gerhard Ehninger
- Department of Hematology, Oncology and Tumor Immunology; Charité-University Medicine Berlin, Campus Virchow Klinikum, 13353 Berlin, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), DKFZ, 69120 Heidelberg, Germany
| | - Karsten Hiller
- Department of Bioinfomatics and Biochemistry and Braunschweig Integrated Center of Systems Biology (BRICS), Technical University Braunschweig, 38106 Braunschweig, Germany.,Luxemburg Centre for Systems Biomedicine, University of Luxemburg, L-4367 Belvaux, Luxemburg
| | - Rüdiger Hell
- Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany
| | - Carl Herrmann
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Institute of Pharmacy and Molecular Biotechnology, and Bioquant Center, University of Heidelberg, 69120 Heidelberg, Germany
| | - Anthony D Ho
- Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Jeroen Krijgsveld
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Bernhard Radlwimmer
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), DKFZ, 69120 Heidelberg, Germany
| | - Andreas Trumpp
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany.,Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), DKFZ, 69120 Heidelberg, Germany
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133
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Jia B, Tang K, Chun BH, Jeon CO. Large-scale examination of functional and sequence diversity of 2-oxoglutarate/Fe(II)-dependent oxygenases in Metazoa. Biochim Biophys Acta Gen Subj 2017; 1861:2922-2933. [DOI: 10.1016/j.bbagen.2017.08.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/22/2017] [Accepted: 08/23/2017] [Indexed: 12/25/2022]
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134
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Yeh TL, Leissing TM, Abboud MI, Thinnes CC, Atasoylu O, Holt-Martyn JP, Zhang D, Tumber A, Lippl K, Lohans CT, Leung IKH, Morcrette H, Clifton IJ, Claridge TDW, Kawamura A, Flashman E, Lu X, Ratcliffe PJ, Chowdhury R, Pugh CW, Schofield CJ. Molecular and cellular mechanisms of HIF prolyl hydroxylase inhibitors in clinical trials. Chem Sci 2017; 8:7651-7668. [PMID: 29435217 PMCID: PMC5802278 DOI: 10.1039/c7sc02103h] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/07/2017] [Indexed: 02/06/2023] Open
Abstract
Inhibition of the human 2-oxoglutarate (2OG) dependent hypoxia inducible factor (HIF) prolyl hydroxylases (human PHD1-3) causes upregulation of HIF, thus promoting erythropoiesis and is therefore of therapeutic interest. We describe cellular, biophysical, and biochemical studies comparing four PHD inhibitors currently in clinical trials for anaemia treatment, that describe their mechanisms of action, potency against isolated enzymes and in cells, and selectivities versus representatives of other human 2OG oxygenase subfamilies. The 'clinical' PHD inhibitors are potent inhibitors of PHD catalyzed hydroxylation of the HIF-α oxygen dependent degradation domains (ODDs), and selective against most, but not all, representatives of other human 2OG dependent dioxygenase subfamilies. Crystallographic and NMR studies provide insights into the different active site binding modes of the inhibitors. Cell-based results reveal the inhibitors have similar effects on the upregulation of HIF target genes, but differ in the kinetics of their effects and in extent of inhibition of hydroxylation of the N- and C-terminal ODDs; the latter differences correlate with the biophysical observations.
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Affiliation(s)
- Tzu-Lan Yeh
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
- Target Discovery Institute (TDI) , Nuffield Department of Medicine , University of Oxford , NDMRB Roosevelt Drive , Oxford OX3 7FZ , UK
| | - Thomas M Leissing
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
- Ludwig Institute for Cancer Research , Nuffield Department of Clinical Medicine , University of Oxford , Oxford OX3 7DQ , UK
| | - Martine I Abboud
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Cyrille C Thinnes
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Onur Atasoylu
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - James P Holt-Martyn
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Dong Zhang
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Anthony Tumber
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
- Structural Genomics Consortium (SGC) , University of Oxford , Oxford OX3 7DQ , UK
| | - Kerstin Lippl
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Christopher T Lohans
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Ivanhoe K H Leung
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Helen Morcrette
- Radcliffe Department of Medicine , Division of Cardiovascular Medicine , BHF Centre of Research Excellence , Wellcome Trust Centre for Human Genetics , Roosevelt Drive , Oxford OX3 7BN , UK
| | - Ian J Clifton
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Timothy D W Claridge
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Akane Kawamura
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
- Radcliffe Department of Medicine , Division of Cardiovascular Medicine , BHF Centre of Research Excellence , Wellcome Trust Centre for Human Genetics , Roosevelt Drive , Oxford OX3 7BN , UK
| | - Emily Flashman
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Xin Lu
- Ludwig Institute for Cancer Research , Nuffield Department of Clinical Medicine , University of Oxford , Oxford OX3 7DQ , UK
| | - Peter J Ratcliffe
- Target Discovery Institute (TDI) , Nuffield Department of Medicine , University of Oxford , NDMRB Roosevelt Drive , Oxford OX3 7FZ , UK
- The Francis Crick Institute , 1 Midland Road , London NW1 1AT , UK
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Christopher W Pugh
- Target Discovery Institute (TDI) , Nuffield Department of Medicine , University of Oxford , NDMRB Roosevelt Drive , Oxford OX3 7FZ , UK
| | - Christopher J Schofield
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
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135
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Schnicker NJ, Razzaghi M, Guha Thakurta S, Chakravarthy S, Dey M. Bacillus anthracis Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu. Biochemistry 2017; 56:5771-5785. [PMID: 28981257 DOI: 10.1021/acs.biochem.7b00601] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Prolyl hydroxylation is a very common post-translational modification and plays many roles in eukaryotes such as collagen stabilization, hypoxia sensing, and controlling protein transcription and translation. There is a growing body of evidence that suggests that prokaryotes contain prolyl 4-hydroxylases (P4Hs) homologous to the hypoxia-inducible factor (HIF) prolyl hydroxylase domain (PHD) enzymes that act on elongation factor Tu (EFTu) and are likely involved in the regulation of bacterial translation. Recent biochemical and structural studies with a PHD from Pseudomonas putida (PPHD) determined that it forms a complex with EFTu and hydroxylates a prolyl residue of EFTu. Moreover, while animal, plant, and viral P4Hs act on peptidyl proline, most prokaryotic P4Hs have been known to target free l-proline; the exceptions include PPHD and a P4H from Bacillus anthracis (BaP4H) that modifies collagen-like proline-rich peptides. Here we use biophysical and mass spectrometric methods to demonstrate that BaP4H recognizes full-length BaEFTu and a BaEFTu 9-mer peptide for site-specific proline hydroxylation. Using size-exclusion chromatography coupled small-angle X-ray scattering (SEC-SAXS) and binding studies, we determined that BaP4H forms a 1:1 heterodimeric complex with BaEFTu. The SEC-SAXS studies reveal dissociation of BaP4H dimeric subunits upon interaction with BaEFTu. While BaP4H is unusual within bacteria in that it is structurally and functionally similar to the animal PHDs and collagen P4Hs, respectively, this work provides further evidence of its promiscuous substrate recognition. It is possible that the enzyme might have evolved to hydroxylate a universally conserved protein in prokaryotes, similar to the PHDs, and implies a functional role in B. anthracis.
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Affiliation(s)
- Nicholas J Schnicker
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Mortezaali Razzaghi
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Sanjukta Guha Thakurta
- Department of Cell Biology, Harvard Medical School , 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Mishtu Dey
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
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136
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Teoh ST, Lunt SY. Metabolism in cancer metastasis: bioenergetics, biosynthesis, and beyond. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 10. [DOI: 10.1002/wsbm.1406] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/10/2017] [Accepted: 08/28/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Shao Thing Teoh
- Department of Biochemistry and Molecular Biology; Department of Chemical Engineering and Materials Science, Michigan State University; East Lansing MI USA
| | - Sophia Y. Lunt
- Department of Biochemistry and Molecular Biology; Department of Chemical Engineering and Materials Science, Michigan State University; East Lansing MI USA
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137
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Miller JJ, Shih HA, Andronesi OC, Cahill DP. Isocitrate dehydrogenase-mutant glioma: Evolving clinical and therapeutic implications. Cancer 2017; 123:4535-4546. [DOI: 10.1002/cncr.31039] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/18/2017] [Accepted: 08/29/2017] [Indexed: 02/04/2023]
Affiliation(s)
- Julie J. Miller
- Pappas Center for Neuro-Oncology, Department of Neurology, Massachusetts General Hospital, Harvard Medical School; Boston Massachusetts
| | - Helen A. Shih
- Department of Radiation Oncology; Massachusetts General Hospital, Harvard Medical School; Boston Massachusetts
| | - Ovidiu C. Andronesi
- Martinos Center for Biomedical Imaging, Department of Radiology; Massachusetts General Hospital, Harvard Medical School; Boston Massachusetts
| | - Daniel P. Cahill
- Department of Neurosurgery; Massachusetts General Hospital, Harvard Medical School; Boston Massachusetts
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138
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Sayin VI, LeBoeuf SE, Singh SX, Davidson SM, Biancur D, Guzelhan BS, Alvarez SW, Wu WL, Karakousi TR, Zavitsanou AM, Ubriaco J, Muir A, Karagiannis D, Morris PJ, Thomas CJ, Possemato R, Vander Heiden MG, Papagiannakopoulos T. Activation of the NRF2 antioxidant program generates an imbalance in central carbon metabolism in cancer. eLife 2017; 6. [PMID: 28967864 PMCID: PMC5624783 DOI: 10.7554/elife.28083] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/24/2017] [Indexed: 12/23/2022] Open
Abstract
During tumorigenesis, the high metabolic demand of cancer cells results in increased production of reactive oxygen species. To maintain oxidative homeostasis, tumor cells increase their antioxidant production through hyperactivation of the NRF2 pathway, which promotes tumor cell growth. Despite the extensive characterization of NRF2-driven metabolic rewiring, little is known about the metabolic liabilities generated by this reprogramming. Here, we show that activation of NRF2, in either mouse or human cancer cells, leads to increased dependency on exogenous glutamine through increased consumption of glutamate for glutathione synthesis and glutamate secretion by xc- antiporter system. Together, this limits glutamate availability for the tricarboxylic acid cycle and other biosynthetic reactions creating a metabolic bottleneck. Cancers with genetic or pharmacological activation of the NRF2 antioxidant pathway have a metabolic imbalance between supporting increased antioxidant capacity over central carbon metabolism, which can be therapeutically exploited.
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Affiliation(s)
- Volkan I Sayin
- Department of Pathology, New York University School of Medicine, New York, United States
| | - Sarah E LeBoeuf
- Department of Pathology, New York University School of Medicine, New York, United States
| | - Simranjit X Singh
- Department of Pathology, New York University School of Medicine, New York, United States
| | - Shawn M Davidson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Douglas Biancur
- Department of Pathology, New York University School of Medicine, New York, United States
| | - Betul S Guzelhan
- Department of Pathology, New York University School of Medicine, New York, United States
| | - Samantha W Alvarez
- Department of Pathology, New York University School of Medicine, New York, United States
| | - Warren L Wu
- Department of Pathology, New York University School of Medicine, New York, United States
| | | | | | - Julian Ubriaco
- Department of Pathology, New York University School of Medicine, New York, United States
| | - Alexander Muir
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States
| | - Dimitris Karagiannis
- Department of Pathology, New York University School of Medicine, New York, United States
| | - Patrick J Morris
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, Bethesda, United States.,Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Bethesda, United States
| | - Craig J Thomas
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, Bethesda, United States.,Division of Preclinical Innovation, National Center for Advancing Translational Sciences, Bethesda, United States
| | - Richard Possemato
- Department of Pathology, New York University School of Medicine, New York, United States
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
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139
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Kulkarni A, Mateus M, Thinnes CC, McCullagh JS, Schofield CJ, Taylor GP, Bangham CRM. Glucose Metabolism and Oxygen Availability Govern Reactivation of the Latent Human Retrovirus HTLV-1. Cell Chem Biol 2017; 24:1377-1387.e3. [PMID: 28965728 PMCID: PMC5696563 DOI: 10.1016/j.chembiol.2017.08.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/24/2017] [Accepted: 08/17/2017] [Indexed: 12/30/2022]
Abstract
The human retrovirus HTLV-1 causes a hematological malignancy or neuroinflammatory disease in ∼10% of infected individuals. HTLV-1 primarily infects CD4+ T lymphocytes and persists as a provirus integrated in their genome. HTLV-1 appears transcriptionally latent in freshly isolated cells; however, the chronically active anti-HTLV-1 cytotoxic T cell response observed in infected individuals indicates frequent proviral expression in vivo. The kinetics and regulation of HTLV-1 proviral expression in vivo are poorly understood. By using hypoxia, small-molecule hypoxia mimics, and inhibitors of specific metabolic pathways, we show that physiologically relevant levels of hypoxia, as routinely encountered by circulating T cells in the lymphoid organs and bone marrow, significantly enhance HTLV-1 reactivation from latency. Furthermore, culturing naturally infected CD4+ T cells in glucose-free medium or chemical inhibition of glycolysis or the mitochondrial electron transport chain strongly suppresses HTLV-1 plus-strand transcription. We conclude that glucose metabolism and oxygen tension regulate HTLV-1 proviral latency and reactivation in vivo. Physiological (1%) hypoxia enhances HTLV-1 plus-strand transcription HTLV-1 transcription is hypoxia regulated but HIF independent Inhibition of glycolysis or the mitochondrial ETC suppresses HTLV-1 transcription Extracellular glucose concentration regulates HTLV-1 reactivation from latency
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Affiliation(s)
- Anurag Kulkarni
- Section of Virology, Department of Medicine, Imperial College, London W2 1PG, UK
| | - Manuel Mateus
- Section of Virology, Department of Medicine, Imperial College, London W2 1PG, UK
| | - Cyrille C Thinnes
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, UK
| | - James S McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, UK
| | - Graham P Taylor
- Section of Virology, Department of Medicine, Imperial College, London W2 1PG, UK
| | - Charles R M Bangham
- Section of Virology, Department of Medicine, Imperial College, London W2 1PG, UK.
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140
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Wulansari N, Kim EH, Sulistio YA, Rhee YH, Song JJ, Lee SH. Vitamin C-Induced Epigenetic Modifications in Donor NSCs Establish Midbrain Marker Expressions Critical for Cell-Based Therapy in Parkinson's Disease. Stem Cell Reports 2017; 9:1192-1206. [PMID: 28943252 PMCID: PMC5639382 DOI: 10.1016/j.stemcr.2017.08.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 08/24/2017] [Accepted: 08/24/2017] [Indexed: 11/20/2022] Open
Abstract
Cultured neural stem/precursor cells (NSCs) are regarded as a potential systematic cell source to treat Parkinson's disease (PD). However, the therapeutic potential of these cultured NSCs is lost during culturing. Here, we show that treatment of vitamin C (VC) enhances generation of authentic midbrain-type dopamine (mDA) neurons with improved survival and functions from ventral midbrain (VM)-derived NSCs. VC acted by upregulating a series of mDA neuron-specific developmental and phenotype genes via removal of DNA methylation and repressive histone code (H3K9m3, H3K27m3) at associated gene promoter regions. Notably, the epigenetic changes induced by transient VC treatment were sustained long after VC withdrawal. Accordingly, transplantation of VC-treated NSCs resulted in improved behavioral restoration, along with enriched DA neuron engraftment, which faithfully expressed midbrain-specific markers in PD model rats. These results indicate that VC treatment to donor NSCs could be a simple, efficient, and safe therapeutic strategy for PD in the future. Vitamin C (VC) potentiates therapeutic capacity of donor NSCs to treat PD Long-lasting epigenetic activation of VM-specific genes underlies the VC effects The VC effects enhanced mDA neuron engraftment
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Affiliation(s)
- Noviana Wulansari
- Department of Biochemistry and Molecular Biology, College of Medicine, Hanyang University, 17 Haengdang-dong, Sungdong-gu, Seoul 133-791, Korea; Hanyang Biomedical Research Institute, Hanyang University, Seoul, Korea; Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, Korea
| | - Eun-Hee Kim
- Department of Biochemistry and Molecular Biology, College of Medicine, Hanyang University, 17 Haengdang-dong, Sungdong-gu, Seoul 133-791, Korea; Hanyang Biomedical Research Institute, Hanyang University, Seoul, Korea; Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, Korea
| | - Yanuar Alan Sulistio
- Department of Biochemistry and Molecular Biology, College of Medicine, Hanyang University, 17 Haengdang-dong, Sungdong-gu, Seoul 133-791, Korea; Hanyang Biomedical Research Institute, Hanyang University, Seoul, Korea; Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, Korea
| | - Yong-Hee Rhee
- Department of Biochemistry and Molecular Biology, College of Medicine, Hanyang University, 17 Haengdang-dong, Sungdong-gu, Seoul 133-791, Korea; Hanyang Biomedical Research Institute, Hanyang University, Seoul, Korea; Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, Korea
| | - Jae-Jin Song
- Department of Biochemistry and Molecular Biology, College of Medicine, Hanyang University, 17 Haengdang-dong, Sungdong-gu, Seoul 133-791, Korea; Hanyang Biomedical Research Institute, Hanyang University, Seoul, Korea; Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, Korea
| | - Sang-Hun Lee
- Department of Biochemistry and Molecular Biology, College of Medicine, Hanyang University, 17 Haengdang-dong, Sungdong-gu, Seoul 133-791, Korea; Hanyang Biomedical Research Institute, Hanyang University, Seoul, Korea; Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, Korea.
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141
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Zhou Y, Hambly BD, McLachlan CS. FTO associations with obesity and telomere length. J Biomed Sci 2017; 24:65. [PMID: 28859657 PMCID: PMC5580219 DOI: 10.1186/s12929-017-0372-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 08/23/2017] [Indexed: 12/16/2022] Open
Abstract
This review examines the biology of the Fat mass- and obesity-associated gene (FTO), and the implications of genetic association of FTO SNPs with obesity and genetic aging. Notably, we focus on the role of FTO in the regulation of methylation status as possible regulators of weight gain and genetic aging. We present a theoretical review of the FTO gene with a particular emphasis on associations with UCP2, AMPK, RBL2, IRX3, CUX1, mTORC1 and hormones involved in hunger regulation. These associations are important for dietary behavior regulation and cellular nutrient sensing via amino acids. We suggest that these pathways may also influence telomere regulation. Telomere length (TL) attrition may be influenced by obesity-related inflammation and oxidative stress, and FTO gene-involved pathways. There is additional emerging evidence to suggest that telomere length and obesity are bi-directionally associated. However, the role of obesity risk-related genotypes and associations with TL are not well understood. The FTO gene may influence pathways implicated in regulation of TL, which could help to explain some of the non-consistent relationship between weight phenotype and telomere length that is observed in population studies investigating obesity.
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Affiliation(s)
- Yuling Zhou
- Rural Clinical School, University of New South Wales, Sydney, 2052, Australia
| | - Brett D Hambly
- Discipline of Pathology and Bosch Institute, University of Sydney, Sydney, Australia
| | - Craig S McLachlan
- Rural Clinical School, University of New South Wales, Sydney, 2052, Australia.
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142
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Al-Khallaf H. Isocitrate dehydrogenases in physiology and cancer: biochemical and molecular insight. Cell Biosci 2017; 7:37. [PMID: 28785398 PMCID: PMC5543436 DOI: 10.1186/s13578-017-0165-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 08/01/2017] [Indexed: 01/31/2023] Open
Abstract
Isocitrate dehydrogenases play important roles in cellular metabolism and cancer. This review will discuss how the roles of isoforms 1 and 2 in normal cell and cancer metabolism are distinct from those of isoform 3. It will also explain why, unlike 1 and 2, mutations in isoform 3 in tumor are not likely to be driver ones. A model explaining two important features of isocitrate dehydrogenases 1 and 2 mutations, their dominant negative effect and their mutual exclusivity, will be provided. The importance of targeting these mutations and the possibility of augmenting such therapy by targeting other cancer-related pathways will also be discussed.
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Affiliation(s)
- Hamoud Al-Khallaf
- Department of Pathology and Laboratory Medicine, King Fahad Specialist Hospital, 6830 Ammar Bin Thabit St, Al Muraikabat, Dammam, 32253 Saudi Arabia
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143
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Baranek M, Belter A, Naskręt-Barciszewska MZ, Stobiecki M, Markiewicz WT, Barciszewski J. Effect of small molecules on cell reprogramming. MOLECULAR BIOSYSTEMS 2017; 13:277-313. [PMID: 27918060 DOI: 10.1039/c6mb00595k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The essential idea of regenerative medicine is to fix or replace tissues or organs with alive and patient-specific implants. Pluripotent stem cells are able to indefinitely self-renew and differentiate into all cell types of the body which makes them a potent substantial player in regenerative medicine. The easily accessible source of induced pluripotent stem cells may allow obtaining and cultivating tissues in vitro. Reprogramming refers to regression of mature cells to its initial pluripotent state. One of the approaches affecting pluripotency is the usage of low molecular mass compounds that can modulate enzymes and receptors leading to the formation of pluripotent stem cells (iPSCs). It would be great to assess the general character of such compounds and reveal their new derivatives or modifications to increase the cell reprogramming efficiency. Many improvements in the methods of pluripotency induction have been made by various groups in order to limit the immunogenicity and tumorigenesis, increase the efficiency and accelerate the kinetics. Understanding the epigenetic changes during the cellular reprogramming process will extend the comprehension of stem cell biology and lead to potential therapeutic approaches. There are compounds which have been already proven to be or for now only putative inducers of the pluripotent state that may substitute for the classic reprogramming factors (Oct3/4, Sox2, Klf4, c-Myc) in order to improve the time and efficiency of pluripotency induction. The effect of small molecules on gene expression is dosage-dependent and their application concentration needs to be strictly determined. In this review we analysed the role of small molecules in modulations leading to pluripotency induction, thereby contributing to our understanding of stem cell biology and uncovering the major mechanisms involved in that process.
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Affiliation(s)
- M Baranek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego str. 12/14, 61-704 Poznań, Poland.
| | - A Belter
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego str. 12/14, 61-704 Poznań, Poland.
| | - M Z Naskręt-Barciszewska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego str. 12/14, 61-704 Poznań, Poland.
| | - M Stobiecki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego str. 12/14, 61-704 Poznań, Poland.
| | - W T Markiewicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego str. 12/14, 61-704 Poznań, Poland.
| | - J Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego str. 12/14, 61-704 Poznań, Poland.
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144
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Colwell N, Larion M, Giles AJ, Seldomridge AN, Sizdahkhani S, Gilbert MR, Park DM. Hypoxia in the glioblastoma microenvironment: shaping the phenotype of cancer stem-like cells. Neuro Oncol 2017; 19:887-896. [PMID: 28339582 PMCID: PMC5570138 DOI: 10.1093/neuonc/now258] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Glioblastoma is the most common and aggressive malignant primary brain tumor. Cellular heterogeneity is a characteristic feature of the disease and contributes to the difficulty in formulating effective therapies. Glioma stem-like cells (GSCs) have been identified as a subpopulation of tumor cells that are thought to be largely responsible for resistance to treatment. Intratumoral hypoxia contributes to maintenance of the GSCs by supporting the critical stem cell traits of multipotency, self-renewal, and tumorigenicity. This review highlights the interaction of GSCs with the hypoxic tumor microenvironment, exploring the mechanisms underlying the contribution of GSCs to tumor vessel dynamics, immune modulation, and metabolic alteration.
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Affiliation(s)
- Nicole Colwell
- Neuro-Oncology Branch, National Cancer Institute and National Institute of Neurological Disorders and Stroke, Bethesda, Maryland ; Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland
| | - Mioara Larion
- Neuro-Oncology Branch, National Cancer Institute and National Institute of Neurological Disorders and Stroke, Bethesda, Maryland ; Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland
| | - Amber J Giles
- Neuro-Oncology Branch, National Cancer Institute and National Institute of Neurological Disorders and Stroke, Bethesda, Maryland ; Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland
| | - Ashlee N Seldomridge
- Neuro-Oncology Branch, National Cancer Institute and National Institute of Neurological Disorders and Stroke, Bethesda, Maryland ; Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland
| | - Saman Sizdahkhani
- Neuro-Oncology Branch, National Cancer Institute and National Institute of Neurological Disorders and Stroke, Bethesda, Maryland ; Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland
| | - Mark R Gilbert
- Neuro-Oncology Branch, National Cancer Institute and National Institute of Neurological Disorders and Stroke, Bethesda, Maryland ; Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland
| | - Deric M Park
- Neuro-Oncology Branch, National Cancer Institute and National Institute of Neurological Disorders and Stroke, Bethesda, Maryland ; Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland
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145
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Yin X, Xu Y. Structure and Function of TET Enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 945:275-302. [PMID: 27826843 DOI: 10.1007/978-3-319-43624-1_12] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Mammalian DNA methylation mainly occurs at the carbon-C5 position of cytosine (5mC). TET enzymes were discovered to successively oxidize 5mC to 5-hydromethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). TET enzymes and oxidized 5mC derivatives play important roles in various biological and pathological processes, including regulation of DNA demethylation, gene transcription, embryonic development, and oncogenesis. In this chapter, we will discuss the discovery of TET-mediated 5mC oxidation and the structure, function, and regulation of TET enzymes.
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Affiliation(s)
- Xiaotong Yin
- Fudan University Shanghai Cancer Center, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.
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146
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Sudhamalla B, Dey D, Breski M, Islam K. A rapid mass spectrometric method for the measurement of catalytic activity of ten-eleven translocation enzymes. Anal Biochem 2017. [PMID: 28647531 DOI: 10.1016/j.ab.2017.06.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymatic methylation at carbon five on cytosine (5mC) in DNA is a hallmark of mammalian epigenetic programming and is critical to gene regulation during early embryonic development. It has recently been shown that dynamic erasure of 5mC by three members of the ten-eleven translocation (TET) family plays a key role in cellular differentiation. TET enzymes belong to Fe (II)- and 2-ketoglutarate (2KG) dependent dioxygenases that successively oxidize 5mC to 5-hydroxymethyl cytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxycytosine (5CaC), thus providing a chemical basis for the removal of 5mC which once was thought to be a permanent mark in mammalian genome. Since then a wide range of biochemical assays have been developed to characterize TET activity. Majority of these methods require multi-step processing to detect and quantify the TET-mediated oxidized products. In this study, we have developed a MALDI mass spectrometry based method that directly measures the TET activity with high sensitivity while eliminating the need for any intermediate processing steps. We applied this method to the measurement of enzymatic activity of TET2 and 3, Michaleis-Menten parameters (KM and kcat) of TET-2KG pairs and inhibitory concentration (IC50) of known small-molecule inhibitors of TETs. We further demonstrated the suitability of the assay to analyze chemoenzymatic labeling of 5hmC by β-glucosyltransferase, highlighting the potential for broad application of our method in deconvoluting the functions of novel DNA demethylases.
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Affiliation(s)
- Babu Sudhamalla
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Debasis Dey
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Megan Breski
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Kabirul Islam
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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147
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Therapeutic targeting of the HIF oxygen-sensing pathway: Lessons learned from clinical studies. Exp Cell Res 2017; 356:160-165. [PMID: 28483447 DOI: 10.1016/j.yexcr.2017.05.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 05/03/2017] [Indexed: 12/17/2022]
Abstract
The oxygen-sensitive hypoxia-inducible factor (HIF) pathway plays a central role in the control of erythropoiesis and iron metabolism. The discovery of prolyl hydroxylase domain (PHD) proteins as key regulators of HIF activity has led to the development of inhibitory compounds that are now in phase 3 clinical development for the treatment of renal anemia, a condition that is commonly found in patients with advanced chronic kidney disease. This review provides a concise overview of clinical effects associated with pharmacologic PHD inhibition and was written in memory of Professor Lorenz Poellinger.
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148
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L2hgdh Deficiency Accumulates l-2-Hydroxyglutarate with Progressive Leukoencephalopathy and Neurodegeneration. Mol Cell Biol 2017; 37:MCB.00492-16. [PMID: 28137912 PMCID: PMC5376639 DOI: 10.1128/mcb.00492-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 01/24/2017] [Indexed: 12/30/2022] Open
Abstract
l-2-Hydroxyglutarate aciduria (L-2-HGA) is an autosomal recessive neurometabolic disorder caused by a mutation in the l-2-hydroxyglutarate dehydrogenase (L2HGDH) gene. In this study, we generated L2hgdh knockout (KO) mice and observed a robust increase of l-2-hydroxyglutarate (L-2-HG) levels in multiple tissues. The highest levels of L-2-HG were observed in the brain and testis, with a corresponding increase in histone methylation in these tissues. L2hgdh KO mice exhibit white matter abnormalities, extensive gliosis, microglia-mediated neuroinflammation, and an expansion of oligodendrocyte progenitor cells (OPCs). Moreover, L2hgdh deficiency leads to impaired adult hippocampal neurogenesis and late-onset neurodegeneration in mouse brains. Our data provide in vivo evidence that L2hgdh mutation leads to L-2-HG accumulation, leukoencephalopathy, and neurodegeneration in mice, thereby offering new insights into the pathophysiology of L-2-HGA in humans.
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Kwok J, O'Shea M, Hume DA, Lengeling A. Jmjd6, a JmjC Dioxygenase with Many Interaction Partners and Pleiotropic Functions. Front Genet 2017; 8:32. [PMID: 28360925 PMCID: PMC5352680 DOI: 10.3389/fgene.2017.00032] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/27/2017] [Indexed: 12/20/2022] Open
Abstract
Lysyl hydroxylation and arginyl demethylation are post-translational events that are important for many cellular processes. The jumonji domain containing protein 6 (JMJD6) has been reported to catalyze both lysyl hydroxylation and arginyl demethylation on diverse protein substrates. It also interacts directly with RNA. This review summarizes knowledge of JMJD6 functions that have emerged in the last 15 years and considers how a single Jumonji C (JmjC) domain-containing enzyme can target so many different substrates. New links and synergies between the three main proposed functions of Jmjd6 in histone demethylation, promoter proximal pause release of polymerase II and RNA splicing are discussed. The physiological context of the described molecular functions is considered and recently described novel roles for JMJD6 in cancer and immune biology are reviewed. The increased knowledge of JMJD6 functions has wider implications for our general understanding of the JmjC protein family of which JMJD6 is a member.
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Affiliation(s)
- Janice Kwok
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Edinburgh, UK
| | - Marie O'Shea
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Edinburgh, UK
| | - David A Hume
- 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
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TET-mediated hydroxymethylcytosine at the Pparγ locus is required for initiation of adipogenic differentiation. Int J Obes (Lond) 2017; 41:652-659. [PMID: 28100914 DOI: 10.1038/ijo.2017.8] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 12/13/2016] [Accepted: 12/17/2016] [Indexed: 12/31/2022]
Abstract
BACKGROUND/OBJECTIVES Adipose tissue is one of the main organs regulating energy homeostasis via energy storage as well as endocrine function. The adipocyte cell number is largely determined by adipogenesis. While the molecular mechanism of adipogenesis has been extensively studied, its role in dynamic DNA methylation plasticity remains unclear. Recently, it has been shown that Tet methylcytosine dioxygenase (TET) is catalytically capable of oxidizing DNA 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) toward a complete removal of the methylated cytosine. We investigate whether expression of the Tet genes and production of hydroxymethylcytosine are required for preadipocyte differentiation. SUBJECTS/METHODS Murine 3T3-L1 preadipocytes were used to evaluate the role of Tet1 and Tet2 genes during adipogenesis. Changes in adipogenic ability and in epigenetic status were analyzed, with and without interfering Tet1 and Tet2 expression using small interfering RNA (siRNA). The adipogenesis was evaluated by Oil-Red-O staining and induced expression of adipogenic genes using quantitative polymerase chain reaction (qPCR). Levels of 5-hmC and 5-mC were measured by MassARRAY, immunoprecipitation and GC mass spectrometry at specific loci as well as globally. RESULTS Both Tet1 and Tet2 genes were upregulated in a time-dependent manner, accompanied by increased expression of hallmark adipogenic genes such as Pparγ and Fabp4 (P<0.05). The TET upregulation led to reduced DNA methylation and elevated hydroxymethylcytosine, both globally and specifically at the Pparγ locus (P<0.05 and P<0.01, respectively). Knockdown of Tet1 and Tet2 blocked adipogenesis (P<0.01) by repression of Pparγ expression (P<0.05). In particular, Tet2 knockdown repressed conversion of 5-mC to 5-hmC at the Pparγ locus (P<0.01). Moreover, vitamin C treatment enhanced adipogenesis (P<0.05), while fumarate treatment inhibited it (P<0.01) by modulating TET activities. CONCLUSIONS TET proteins, particularly TET2, were required for adipogenesis by modulating DNA methylation at the Pparγ locus, subsequently by inducing Pparγ gene expression.
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