151
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Lee BH, Stallcup MR. Different chromatin and DNA sequence characteristics define glucocorticoid receptor binding sites that are blocked or not blocked by coregulator Hic-5. PLoS One 2018; 13:e0196965. [PMID: 29738565 PMCID: PMC5940187 DOI: 10.1371/journal.pone.0196965] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/24/2018] [Indexed: 11/18/2022] Open
Abstract
The glucocorticoid receptor (GR) regulates genes in many physiological pathways by binding to enhancer and silencer elements of target genes, where it recruits coregulator proteins that remodel chromatin and regulate the assembly of transcription complexes. The coregulator Hydrogen peroxide-inducible clone 5 (Hic-5) is necessary for glucocorticoid (GC) regulation of one group of GR target genes, is irrelevant for a second group, and inhibits GR binding to a third gene set, thereby blocking their regulation by GC. Gene-specific characteristics that distinguish GR binding regions (GBR) at Hic-5 blocked genes from GBR at other GC-regulated genes are unknown. Here we show genome-wide that blocked GBR generally require CHD9 and BRM for GR occupancy in contrast to GBR that are not blocked by Hic-5. Hic-5 blocked GBR are enriched near Hic-5 blocked GR target genes but not near GR target genes that are not blocked by Hic-5. Furthermore blocked GBR are in a closed conformation prior to Hic-5 depletion, and require Hic-5 depletion and glucocorticoid treatment to create an open conformation necessary for GR occupancy. A transcription factor binding motif characteristic of the ETS family was enriched near blocked GBR and blocked genes but not near non-blocked GBR or non-blocked GR target genes. Thus, we identify specific differences in chromatin conformation, chromatin remodeler requirements, and local DNA sequence motifs that contribute to gene-specific actions of transcription factors and coregulators. These findings shed light on mechanisms that contribute to binding site selection by transcription factors, which vary in a cell type-specific manner.
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Affiliation(s)
- Brian H. Lee
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Michael R. Stallcup
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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152
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Clarisse D, Van Wesemael K, Tavernier J, Offner F, Beck IM, De Bosscher K. Effect of combining glucocorticoids with Compound A on glucocorticoid receptor responsiveness in lymphoid malignancies. PLoS One 2018; 13:e0197000. [PMID: 29738549 PMCID: PMC5940183 DOI: 10.1371/journal.pone.0197000] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/24/2018] [Indexed: 11/18/2022] Open
Abstract
Glucocorticoids (GCs) are a cornerstone in the treatment of lymphoid malignancies such as multiple myeloma (MM) and acute lymphoblastic leukemia (ALL). Yet, prolonged GC use is hampered by deleterious GC-related side effects and the emergence of GC resistance. To tackle and overcome these GC-related problems, the applicability of selective glucocorticoid receptor agonists and modulators was studied, in search of fewer side-effects and at least equal therapeutic efficacy as classic GCs. Compound A (CpdA) is a prototypical example of such a selective glucocorticoid receptor modulator and does not support GR-mediated transactivation. Here, we examined whether the combination of CpdA with the classic GC dexamethasone (Dex) may improve GC responsiveness of MM and ALL cell lines. We find that the combination of Dex and CpdA does not substantially enhance GC-mediated cell killing. In line, several apoptosis hallmarks, such as caspase 3/7 activity, PARP cleavage and the levels of cleaved-caspase 3 remain unchanged upon combining Dex with CpdA. Moreover, we monitor no additional inhibition of cell proliferation and the homologous downregulation of GR is not counteracted by the combination of Dex and CpdA. In addition, CpdA is unable to modulate Dex-liganded GR transactivation and transrepression, yet, Dex-mediated transrepression is also aberrant in these lymphoid cell lines. Together, transrepression-favoring compounds, alone or combined with GCs, do not seem a valid strategy in the treatment of lymphoid malignancies.
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Affiliation(s)
- Dorien Clarisse
- Receptor Research Laboratories, Nuclear Receptor Lab (NRL) and Cytokine Receptor Lab (CRL), Department for Biomolecular Medicine, VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium
- Laboratory of Experimental Cancer Research (LECR), Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Hematology, Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - Karlien Van Wesemael
- Laboratory of Experimental Cancer Research (LECR), Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium
- Hematology, Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - Jan Tavernier
- Receptor Research Laboratories, Nuclear Receptor Lab (NRL) and Cytokine Receptor Lab (CRL), Department for Biomolecular Medicine, VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Fritz Offner
- Hematology, Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - Ilse M. Beck
- Laboratory of Experimental Cancer Research (LECR), Department of Radiation Oncology and Experimental Cancer Research, Ghent University, Ghent, Belgium
- Department of Health Sciences, Odisee University College, Ghent, Belgium
| | - Karolien De Bosscher
- Receptor Research Laboratories, Nuclear Receptor Lab (NRL) and Cytokine Receptor Lab (CRL), Department for Biomolecular Medicine, VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- * E-mail:
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153
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De Iudicibus S, Lucafò M, Vitulo N, Martelossi S, Zimbello R, De Pascale F, Forcato C, Naviglio S, Di Silvestre A, Gerdol M, Stocco G, Valle G, Ventura A, Bramuzzo M, Decorti G. High-Throughput Sequencing of microRNAs in Glucocorticoid Sensitive Paediatric Inflammatory Bowel Disease Patients. Int J Mol Sci 2018; 19:1399. [PMID: 29738455 PMCID: PMC5983624 DOI: 10.3390/ijms19051399] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/27/2018] [Accepted: 05/03/2018] [Indexed: 01/02/2023] Open
Abstract
The aim of this research was the identification of novel pharmacogenomic biomarkers for better understanding the complex gene regulation mechanisms underpinning glucocorticoid (GC) action in paediatric inflammatory bowel disease (IBD). This goal was achieved by evaluating high-throughput microRNA (miRNA) profiles during GC treatment, integrated with the assessment of expression changes in GC receptor (GR) heterocomplex genes. Furthermore, we tested the hypothesis that differentially expressed miRNAs could be directly regulated by GCs through investigating the presence of GC responsive elements (GREs) in their gene promoters. Ten IBD paediatric patients responding to GCs were enrolled. Peripheral blood was obtained at diagnosis (T0) and after four weeks of steroid treatment (T4). MicroRNA profiles were analyzed using next generation sequencing, and selected significantly differentially expressed miRNAs were validated by quantitative reverse transcription-polymerase chain reaction. In detail, 18 miRNAs were differentially expressed from T0 to T4, 16 of which were upregulated and 2 of which were downregulated. Out of these, three miRNAs (miR-144, miR-142, and miR-96) could putatively recognize the 3’UTR of the GR gene and three miRNAs (miR-363, miR-96, miR-142) contained GREs sequences, thereby potentially enabling direct regulation by the GR. In conclusion, we identified miRNAs differently expressed during GC treatment and miRNAs which could be directly regulated by GCs in blood cells of young IBD patients. These results could represent a first step towards their translation as pharmacogenomic biomarkers.
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Affiliation(s)
- Sara De Iudicibus
- Institute for Maternal and Child Health- IRCCS "Burlo Garofolo", 34127 Trieste, Italy.
| | - Marianna Lucafò
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy.
| | - Nicola Vitulo
- Department of Biotechnology, University of Verona, 37100 Verona, Italy.
| | - Stefano Martelossi
- Institute for Maternal and Child Health- IRCCS "Burlo Garofolo", 34127 Trieste, Italy.
| | - Rosanna Zimbello
- CRIBI Biotechnology Centre, University of Padua, 35100 Padua, Italy.
| | - Fabio De Pascale
- CRIBI Biotechnology Centre, University of Padua, 35100 Padua, Italy.
| | - Claudio Forcato
- CRIBI Biotechnology Centre, University of Padua, 35100 Padua, Italy.
| | - Samuele Naviglio
- PhD School in Science of Reproduction and Development, University of Trieste, 34127 Trieste, Italy.
| | - Alessia Di Silvestre
- PhD School in Science of Reproduction and Development, University of Trieste, 34127 Trieste, Italy.
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy.
| | - Gabriele Stocco
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy.
| | - Giorgio Valle
- CRIBI Biotechnology Centre, University of Padua, 35100 Padua, Italy.
| | - Alessandro Ventura
- Institute for Maternal and Child Health- IRCCS "Burlo Garofolo", 34127 Trieste, Italy.
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy.
| | - Matteo Bramuzzo
- Institute for Maternal and Child Health- IRCCS "Burlo Garofolo", 34127 Trieste, Italy.
| | - Giuliana Decorti
- Institute for Maternal and Child Health- IRCCS "Burlo Garofolo", 34127 Trieste, Italy.
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy.
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154
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Bianchetti L, Wassmer B, Defosset A, Smertina A, Tiberti ML, Stote RH, Dejaegere A. Alternative dimerization interfaces in the glucocorticoid receptor-α ligand binding domain. Biochim Biophys Acta Gen Subj 2018; 1862:1810-1825. [PMID: 29723544 DOI: 10.1016/j.bbagen.2018.04.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/19/2018] [Accepted: 04/27/2018] [Indexed: 10/17/2022]
Abstract
BACKGROUND Nuclear hormone receptors (NRs) constitute a large family of multi-domain ligand-activated transcription factors. Dimerization is essential for their regulation, and both DNA binding domain (DBD) and ligand binding domain (LBD) are implicated in dimerization. Intriguingly, the glucocorticoid receptor-α (GRα) presents a DBD dimeric architecture similar to that of the homologous estrogen receptor-α (ERα), but an atypical dimeric architecture for the LBD. The physiological relevance of the proposed GRα LBD dimer is a subject of debate. METHODS We analyzed all GRα LBD homodimers observed in crystals using an energetic analysis based on the PISA and on the MM/PBSA methods and a sequence conservation analysis, using the ERα LBD dimer as a reference point. RESULTS Several dimeric assemblies were observed for GRα LBD. The assembly generally taken to be physiologically relevant showed weak binding free energy and no significant residue conservation at the contact interface, while an alternative homodimer mediated by both helix 9 and C-terminal residues showed significant binding free energy and residue conservation. However, none of the GRα LBD assemblies found in crystals are as stable or conserved as the canonical ERα LBD dimer. GRα C-terminal sequence (F-domain) forms a steric obstacle to the canonical dimer assembly in all available structures. CONCLUSIONS Our analysis calls for a re-examination of the currently accepted GRα homodimer structure and experimental investigations of the alternative architectures. GENERAL SIGNIFICANCE This work questions the validity of the currently accepted architecture. This has implications for interpreting physiological data and for therapeutic design pertaining to glucocorticoid research.
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Affiliation(s)
- Laurent Bianchetti
- Biocomputing and Molecular Modelling Laboratory, Integrated Structural Biology Department, Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104 - Inserm U1258 - Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Bianca Wassmer
- Biocomputing and Molecular Modelling Laboratory, Integrated Structural Biology Department, Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104 - Inserm U1258 - Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Audrey Defosset
- Biocomputing and Molecular Modelling Laboratory, Integrated Structural Biology Department, Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104 - Inserm U1258 - Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Anna Smertina
- Biocomputing and Molecular Modelling Laboratory, Integrated Structural Biology Department, Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104 - Inserm U1258 - Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Marion L Tiberti
- Biocomputing and Molecular Modelling Laboratory, Integrated Structural Biology Department, Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104 - Inserm U1258 - Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Roland H Stote
- Biocomputing and Molecular Modelling Laboratory, Integrated Structural Biology Department, Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104 - Inserm U1258 - Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Annick Dejaegere
- Biocomputing and Molecular Modelling Laboratory, Integrated Structural Biology Department, Institute of Genetics and Molecular and Cellular Biology (IGBMC), CNRS UMR 7104 - Inserm U1258 - Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France.
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155
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Vitellius G, Trabado S, Bouligand J, Delemer B, Lombès M. Pathophysiology of Glucocorticoid Signaling. ANNALES D'ENDOCRINOLOGIE 2018; 79:98-106. [PMID: 29685454 DOI: 10.1016/j.ando.2018.03.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Glucocorticoids (GC), such as cortisol or dexamethasone, control various physiological functions, notably those involved in development, metabolism, inflammatory processes and stress, and exert most of their effects upon binding to the glucocorticoid receptor (GR, encoded by NR3C1 gene). GC signaling follows several consecutive steps leading to target gene transactivation, including ligand binding, nuclear translocation of ligand-activated GR complexes, DNA binding, coactivator interaction and recruitment of functional transcriptional machinery. Any step may be impaired and may account for altered GC signaling. Partial or generalized glucocorticoid resistance syndrome may result in a reduced level of functional GR, a decreased hormone affinity and binding, a defect in nuclear GR translocation, a decrease or lack of DNA binding and/or post-transcriptional GR modifications. To date, 26 loss-of-function NR3C1 mutations have been reported in the context of hypertension, hirsutism, adrenal hyperplasia or metabolic disorders. These clinical signs are generally associated with biological features including hypercortisolism without negative regulatory feedback loop on the hypothalamic-pituitary-adrenal axis. Patients had often low plasma aldosterone and renin levels despite hypertension. Only one GR gain-of-function mutation has been described associating Cushing's syndrome phenotype with normal urinary-free cortisol. Some GR polymorphisms (ER22/23EK, GR-9β) have been linked to glucocorticoid resistance and a healthier metabolic profile whereas some others seemed to be associated with GC hypersensitivity (N363S, BclI), increasing cardiovascular risk (diabetes type 2, visceral obesity). This review focuses on the earlier findings on the pathophysiology of GR signaling and presents criteria facilitating identification of novel NR3C1 mutations in selected patients.
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Affiliation(s)
- Géraldine Vitellius
- Inserm Umr_S U1185, faculté de médecine Paris-Sud, université Paris-Sud, université Paris-Saclay, 94276 Le Kremlin-Bicêtre, France; Service d'endocrinologie diabète nutrition, CHU de Reims, hôpital Robert-Debré, 51100, France
| | - Séverine Trabado
- Inserm Umr_S U1185, faculté de médecine Paris-Sud, université Paris-Sud, université Paris-Saclay, 94276 Le Kremlin-Bicêtre, France; Service de génétique moléculaire, pharmacogénétique et hormonologie, CHU de Bicêtre, hôpitaux universitaires Paris-Sud, AH-HP, 94275, France
| | - Jérôme Bouligand
- Inserm Umr_S U1185, faculté de médecine Paris-Sud, université Paris-Sud, université Paris-Saclay, 94276 Le Kremlin-Bicêtre, France; Service de génétique moléculaire, pharmacogénétique et hormonologie, CHU de Bicêtre, hôpitaux universitaires Paris-Sud, AH-HP, 94275, France
| | - Brigitte Delemer
- Service d'endocrinologie diabète nutrition, CHU de Reims, hôpital Robert-Debré, 51100, France
| | - Marc Lombès
- Inserm Umr_S U1185, faculté de médecine Paris-Sud, université Paris-Sud, université Paris-Saclay, 94276 Le Kremlin-Bicêtre, France; Service d'endocrinologie et des maladies de la reproduction, hôpitaux universitaires Paris-Sud, CHU Bicêtre, AH-HP, 94275 Le Kremlin Bicêtre, France.
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156
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Hudson WH, Vera IMSD, Nwachukwu JC, Weikum ER, Herbst AG, Yang Q, Bain DL, Nettles KW, Kojetin DJ, Ortlund EA. Cryptic glucocorticoid receptor-binding sites pervade genomic NF-κB response elements. Nat Commun 2018; 9:1337. [PMID: 29626214 PMCID: PMC5889392 DOI: 10.1038/s41467-018-03780-1] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/13/2018] [Indexed: 12/19/2022] Open
Abstract
Glucocorticoids (GCs) are potent repressors of NF-κB activity, making them a preferred choice for treatment of inflammation-driven conditions. Despite the widespread use of GCs in the clinic, current models are inadequate to explain the role of the glucocorticoid receptor (GR) within this critical signaling pathway. GR binding directly to NF-κB itself-tethering in a DNA binding-independent manner-represents the standing model of how GCs inhibit NF-κB-driven transcription. We demonstrate that direct binding of GR to genomic NF-κB response elements (κBREs) mediates GR-driven repression of inflammatory gene expression. We report five crystal structures and solution NMR data of GR DBD-κBRE complexes, which reveal that GR recognizes a cryptic response element between the binding footprints of NF-κB subunits within κBREs. These cryptic sequences exhibit high sequence and functional conservation, suggesting that GR binding to κBREs is an evolutionarily conserved mechanism of controlling the inflammatory response.
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Affiliation(s)
- William H Hudson
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, 30322, USA
- Discovery and Developmental Therapeutics, Winship Cancer Institute, Atlanta, Georgia, 30322, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, 30322, USA
| | - Ian Mitchelle S de Vera
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida, 33458, USA
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, MO, 63104, USA
| | - Jerome C Nwachukwu
- Department of Integrated Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida, 33458, USA
| | - Emily R Weikum
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, 30322, USA
- Discovery and Developmental Therapeutics, Winship Cancer Institute, Atlanta, Georgia, 30322, USA
| | - Austin G Herbst
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, 30322, USA
| | - Qin Yang
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, 80045, USA
| | - David L Bain
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, 80045, USA
| | - Kendall W Nettles
- Department of Integrated Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida, 33458, USA
| | - Douglas J Kojetin
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida, 33458, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, 30322, USA.
- Discovery and Developmental Therapeutics, Winship Cancer Institute, Atlanta, Georgia, 30322, USA.
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157
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Mesquita TR, Auguste G, Falcón D, Ruiz-Hurtado G, Salazar-Enciso R, Sabourin J, Lefebvre F, Viengchareun S, Kobeissy H, Lechène P, Nicolas V, Fernandez-Celis A, Gómez S, Lauton Santos S, Morel E, Rueda A, López-Andrés N, Gómez AM, Lombès M, Benitah JP. Specific Activation of the Alternative Cardiac Promoter of
Cacna1c
by the Mineralocorticoid Receptor. Circ Res 2018; 122:e49-e61. [DOI: 10.1161/circresaha.117.312451] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 11/16/2022]
Affiliation(s)
- Thassio R. Mesquita
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
| | - Gaëlle Auguste
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
| | - Débora Falcón
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
| | - Gema Ruiz-Hurtado
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
| | - Rogelio Salazar-Enciso
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
| | - Jessica Sabourin
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
| | - Florence Lefebvre
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
| | - Say Viengchareun
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
| | - Hussein Kobeissy
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
| | - Patrick Lechène
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
| | - Valérie Nicolas
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
| | - Amaya Fernandez-Celis
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
| | - Susana Gómez
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
| | - Sandra Lauton Santos
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
| | - Eric Morel
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
| | - Angelica Rueda
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
| | - Natalia López-Andrés
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
| | - Ana Maria Gómez
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
| | - Marc Lombès
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
| | - Jean-Pierre Benitah
- From the Signalisation et Physiopathologie Cardiovasculaire - UMR-S 1180, (T.R.M., G.A., D.F., G.R.-H., J.S., F.L., P.L., S.G., E.M., A.M.G., J.-P.B.), EA 4043 UBaPS (H.K.), and UMS-IPSIT, MIPSIT_Microscopy Facility (V.N.), Univ. Paris-Sud, INSERM, Université Paris-Saclay, 92296, Châtenay-Malabry, France; Department of Physiology, Federal University of Sergipe, Brazil (T.R.M., S.L.S.); Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, México City, D.F., México (R.S
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158
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Probing Dominant Negative Behavior of Glucocorticoid Receptor β through a Hybrid Structural and Biochemical Approach. Mol Cell Biol 2018; 38:MCB.00453-17. [PMID: 29437838 DOI: 10.1128/mcb.00453-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/30/2018] [Indexed: 11/20/2022] Open
Abstract
Glucocorticoid receptor β (GRβ) is associated with glucocorticoid resistance via dominant negative regulation of GRα. To better understand how GRβ functions as a dominant negative inhibitor of GRα at a molecular level, we determined the crystal structure of the ligand binding domain of GRβ complexed with the antagonist RU-486. The structure reveals that GRβ binds RU-486 in the same ligand binding pocket as GRα, and the unique C-terminal amino acids of GRβ are mostly disordered. Binding energy analysis suggests that these C-terminal residues of GRβ do not contribute to RU-486 binding. Intriguingly, the GRβ/RU-486 complex binds corepressor peptide with affinity similar to that of a GRα/RU-486 complex, despite the lack of helix 12. Our biophysical and biochemical analyses reveal that in the presence of RU-486, GRβ is found in a conformation that favors corepressor binding, potentially antagonizing GRα function. This study thus presents an unexpected molecular mechanism by which GRβ could repress transcription.
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159
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Abstract
The nuclear receptor family of transcription factor proteins mediates endocrine function and plays critical roles in the development, physiology and pharmacology. Malfunctioning nuclear receptors are associated with several disease states. The functional activity of nuclear receptors is regulated by small molecular hormonal and synthetic molecules. Multiple sources of evidence have identified and distinguished between the different allosteric pathways initiated by ligands, DNA and cofactors such as co-activators and co-repressors. Also, these biophysical studies are attempting to determine how these pathways that regulate co-activator and DNA recognition can control gene transcription. Thus, there is a growing interest in determining the genome-scale impact of allostery in nuclear receptors. Today, it is accepted that a detailed understanding of the allosteric regulatory pathways within the nuclear receptor molecular complex will enable the development of efficient drug therapies in the long term.
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Affiliation(s)
- Elias J Fernandez
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, USA.
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160
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Stubbs FE, Birnie MT, Biddie SC, Lightman SL, Conway-Campbell BL. SKOV3 cells containing a truncated ARID1a protein have a restricted genome-wide response to glucocorticoids. Mol Cell Endocrinol 2018; 461:226-235. [PMID: 28942102 DOI: 10.1016/j.mce.2017.09.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 08/07/2017] [Accepted: 09/13/2017] [Indexed: 12/11/2022]
Abstract
AT-rich interacting domain subunit 1a (ARID1a) is an essential SWI/SNF component frequently mutated in human cancers. ARID1a mutations have also been associated with glucocorticoid resistance, potentially related to the well-established role of the SWI/SNF complex in glucocorticoid target gene regulation. Glucocorticoids are steroid hormones important for regulating many physiological processes through the activation of the glucocorticoid receptor (GR). As GR interacts directly with ARID1a, we hypothesized that a truncating ARID mutation would interfere with GR-dependent gene regulation. Using high throughput RNA sequencing (RNA-SEQ) we show a restricted glucocorticoid response in SKOV3 cells, which contain an inactivating ARID1a mutation. We also show a lack of GR binding at the GR-dependent regulatory site in the Period 1 gene, which has previously been shown to require chromatin remodelling. Taken together, our data suggests that ARID1a may be required for regulation of a subset of glucocorticoid responsive genes. In the case of SKOV3 cells, in which ARID1a is mutated, glucocorticoid-dependent transcriptional regulation of these genes is significantly impaired.
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Affiliation(s)
- F E Stubbs
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, School of Clinical Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol BS1 3NY, UK.
| | - M T Birnie
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, School of Clinical Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol BS1 3NY, UK.
| | - S C Biddie
- West Hertfordshire NHS Trust, Watford General Hospitals, Vicarage Road, Watford, Hertfordshire WD18 0HB, UK.
| | - S L Lightman
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, School of Clinical Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol BS1 3NY, UK.
| | - B L Conway-Campbell
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, School of Clinical Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol BS1 3NY, UK.
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161
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Vandewalle J, Luypaert A, De Bosscher K, Libert C. Therapeutic Mechanisms of Glucocorticoids. Trends Endocrinol Metab 2018; 29:42-54. [PMID: 29162310 DOI: 10.1016/j.tem.2017.10.010] [Citation(s) in RCA: 346] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/26/2017] [Accepted: 10/27/2017] [Indexed: 12/20/2022]
Abstract
Glucocorticoids (GCs) have been used clinically for decades as potent anti-inflammatory and immunosuppressive agents. Nevertheless, their use is severely hampered by the risk of developing side effects and the occurrence of glucocorticoid resistance (GCR). Therefore, efforts to understand the complex mechanisms underlying GC function and GCR are ongoing. The goal is to generate new glucocorticoid receptor (GR) ligands that can dissociate anti-inflammatory from metabolic side effects and/or overcome GCR. In this review paper we discuss recent insights into GR-mediated actions in GCR and novel therapeutic strategies for acute and chronic inflammatory diseases.
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Affiliation(s)
- Jolien Vandewalle
- Center for Inflammation Research, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Astrid Luypaert
- Receptor Research Laboratories, Nuclear Receptor Lab, VIB-University of Ghent (UGent) Center for Medical Biotechnology, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Karolien De Bosscher
- Receptor Research Laboratories, Nuclear Receptor Lab, VIB-University of Ghent (UGent) Center for Medical Biotechnology, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Claude Libert
- Center for Inflammation Research, Vlaams Instituut voor Biotechnologie (VIB), Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
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162
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Lucafò M, Di Silvestre A, Romano M, Avian A, Antonelli R, Martelossi S, Naviglio S, Tommasini A, Stocco G, Ventura A, Decorti G, De Iudicibus S. Role of the Long Non-Coding RNA Growth Arrest-Specific 5 in Glucocorticoid Response in Children with Inflammatory Bowel Disease. Basic Clin Pharmacol Toxicol 2018; 122:87-93. [PMID: 28722800 DOI: 10.1111/bcpt.12851] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/06/2017] [Indexed: 12/27/2022]
Abstract
Glucocorticoids (GCs) are widely employed in inflammatory, autoimmune and neoplastic diseases, and, despite the introduction of novel therapies, remain the first-line treatment for inducing remission in inflammatory bowel disease (IBD). Given the high incidence of suboptimal response, associated with a significant number of side-effects, that are particularly severe in paediatric patients, the identification of subjects that are most likely to respond poorly to GCs is extremely important. Recent evidence suggests that the long non-coding RNA (lncRNA) GAS5 could be a potential marker of GC resistance. To address this issue, we evaluated the association between the lncRNA GAS5 and the efficacy of steroids, in terms of inhibition of proliferation, in two cell lines derived from colon and ovarian cancers, to confirm the sensitivity and specificity of these lncRNAs. These cells showed a different sensitivity to GCs and revealed differential expression of GAS5 after treatment. GAS5 was up-regulated in GC-resistant cells and accumulated more in the cytoplasm compared to the nucleus in response to the drug. The functions of GAS5 were assessed by silencing, and we found that GAS5 knock-down reduced the proliferation during GC treatment. Furthermore, for the first time, we measured GAS5 levels in 19 paediatric IBD patients at diagnosis and after the first cycle of GCs, and we demonstrated an up-regulation of the lncRNA in patients with unfavourable steroid response. Our preliminary results indicate that GAS5 could be considered a novel pharmacogenomic marker useful for the personalization of GC therapy.
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Affiliation(s)
- Marianna Lucafò
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Alessia Di Silvestre
- PhD School in Science of Reproduction and Development, University of Trieste, Trieste, Italy
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Alice Avian
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Roberta Antonelli
- Department of Neurosciences, Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
| | - Stefano Martelossi
- Institute for Maternal and Child Health - IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Samuele Naviglio
- PhD School in Science of Reproduction and Development, University of Trieste, Trieste, Italy
| | - Alberto Tommasini
- Institute for Maternal and Child Health - IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Gabriele Stocco
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Alessandro Ventura
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health - IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Giuliana Decorti
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
- Institute for Maternal and Child Health - IRCCS 'Burlo Garofolo', Trieste, Italy
| | - Sara De Iudicibus
- Institute for Maternal and Child Health - IRCCS 'Burlo Garofolo', Trieste, Italy
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163
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Álvarez LD, Presman DM, Pecci A. Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain suggest a role of the lever-arm mobility in transcriptional output. PLoS One 2017; 12:e0189588. [PMID: 29244866 PMCID: PMC5731742 DOI: 10.1371/journal.pone.0189588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/29/2017] [Indexed: 11/19/2022] Open
Abstract
One of the first and essential steps in gene expression regulation involves the recruitment of transcription factors (TFs) to specific response elements located at enhancers and/or promoters of targeted genes. These DNA elements have a certain variability in both sequence and length, which may affect the final transcriptional output. The molecular mechanisms in which TFs integrate the subtle differences within specific recognition sequences to offer different transcriptional responses is still largely unknown. Here we used molecular dynamics simulations to study the DNA binding behavior of the glucocorticoid receptor (GR), a ligand-regulated TF with pleiotropic effects in almost all cells. By comparing the behavior of the wild type receptor and a well characterized Ala477Thr substitution within the rat GR DNA binding domain, we found that the region that connects the two-zinc fingers (i.e. the lever arm) would likely play a key role in GR transcriptional output.
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Affiliation(s)
- Lautaro Damián Álvarez
- Universidad de Buenos Aires, CONICET, UMYMFOR and Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
- * E-mail:
| | - Diego Martín Presman
- Laboratory of Receptor Biology and Gene Expression, Building 41, 41 Library Drive, National Cancer Institute, National Institutes of Health, Bethesda, MD, Unitec States of America
| | - Adalí Pecci
- Universidad de Buenos Aires, CONICET, IFIBYNE and Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina
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164
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Cid‐Díaz T, Santos‐Zas I, González‐Sánchez J, Gurriarán‐Rodríguez U, Mosteiro CS, Casabiell X, García‐Caballero T, Mouly V, Pazos Y, Camiña JP. Obestatin controls the ubiquitin-proteasome and autophagy-lysosome systems in glucocorticoid-induced muscle cell atrophy. J Cachexia Sarcopenia Muscle 2017; 8:974-990. [PMID: 28675664 PMCID: PMC5700440 DOI: 10.1002/jcsm.12222] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 04/09/2017] [Accepted: 05/22/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Many pathological states characterized by muscle atrophy are associated with an increase in circulating glucocorticoids and poor patient prognosis, making it an important target for treatment. The development of treatments for glucocorticoid-induced and wasting disorder-related skeletal muscle atrophy should be designed based on how the particular transcriptional program is orchestrated and how the balance of muscle protein synthesis and degradation is deregulated. Here, we investigated whether the obestatin/GPR39 system, an autocrine/paracrine signaling system acting on myogenesis and with anabolic effects on the skeletal muscle, could protect against glucocorticoid-induced muscle cell atrophy. METHODS In the present study, we have utilized mouse C2C12 myotube cultures to examine whether the obestatin/GPR39 signaling pathways can affect the atrophy induced by the synthetic glucocorticoid dexamethasone. We have extended these findings to in vitro effects on human atrophy using human KM155C25 myotubes. RESULTS The activation of the obestatin/GPR39 system protects from glucocorticoid-induced atrophy by regulation of Akt, PKD/PKCμ, CAMKII and AMPK signaling and its downstream targets in the control of protein synthesis, ubiquitin-proteasome system and autophagy-lysosome system in mouse cells. We compared mouse and human myotube cells in their response to glucocorticoid and identified differences in both the triggering of the atrophic program and the response to obestatin stimulation. Notably, we demonstrate that specific patterns of post-translational modifications of FoxO4 and FoxO1 play a key role in directing FoxO activity in response to obestatin in human myotubes. CONCLUSIONS Our findings emphasize the function of the obestatin/GPR39 system in coordinating a variety of pathways involved in the regulation of protein degradation during catabolic conditions.
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Affiliation(s)
- Tania Cid‐Díaz
- Área de Endocrinología Molecular y Celular, Instituto de Investigación Sanitaria de Santiago (IDIS)Complejo Hospitalario Universitario de Santiago (CHUS), Servicio Gallego de Salud (SERGAS)Choupana s/n15706Santiago de CompostelaSpain
| | - Icía Santos‐Zas
- Área de Endocrinología Molecular y Celular, Instituto de Investigación Sanitaria de Santiago (IDIS)Complejo Hospitalario Universitario de Santiago (CHUS), Servicio Gallego de Salud (SERGAS)Choupana s/n15706Santiago de CompostelaSpain
| | - Jessica González‐Sánchez
- Área de Endocrinología Molecular y Celular, Instituto de Investigación Sanitaria de Santiago (IDIS)Complejo Hospitalario Universitario de Santiago (CHUS), Servicio Gallego de Salud (SERGAS)Choupana s/n15706Santiago de CompostelaSpain
| | - Uxía Gurriarán‐Rodríguez
- Sprott Center for Stem Cell ResearchOttawa Hospital Research Institute501 Smyth RoadOttawaOntarioK1H 8L6Canada
| | - Carlos S. Mosteiro
- Área de Endocrinología Molecular y Celular, Instituto de Investigación Sanitaria de Santiago (IDIS)Complejo Hospitalario Universitario de Santiago (CHUS), Servicio Gallego de Salud (SERGAS)Choupana s/n15706Santiago de CompostelaSpain
| | - Xesús Casabiell
- Departamento de FisiologíaFacultad de Veterinaria, Universidad de Santiago de Compostela (USC)Carballo Calero s/n27002LugoSpain
| | - Tomás García‐Caballero
- Departamento de Ciencias MorfológicasFacultad de Medicina, USCSan Francisco s/n15704Santiago de CompostelaSpain
| | - Vincent Mouly
- Sorbonne Universités, UPMC Université Paris 06, INSERM UMRS974, CNRS FRE3617, Center for Research in Myology47 Boulevard de l'hôpital75013ParisFrance
| | - Yolanda Pazos
- Área de Endocrinología Molecular y Celular, Instituto de Investigación Sanitaria de Santiago (IDIS)Complejo Hospitalario Universitario de Santiago (CHUS), Servicio Gallego de Salud (SERGAS)Choupana s/n15706Santiago de CompostelaSpain
| | - Jesús P. Camiña
- Área de Endocrinología Molecular y Celular, Instituto de Investigación Sanitaria de Santiago (IDIS)Complejo Hospitalario Universitario de Santiago (CHUS), Servicio Gallego de Salud (SERGAS)Choupana s/n15706Santiago de CompostelaSpain
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165
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Zhang L, Martini GD, Rube HT, Kribelbauer JF, Rastogi C, FitzPatrick VD, Houtman JC, Bussemaker HJ, Pufall MA. SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site. Genome Res 2017; 28:111-121. [PMID: 29196557 PMCID: PMC5749176 DOI: 10.1101/gr.222844.117] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 11/22/2017] [Indexed: 11/28/2022]
Abstract
The DNA-binding interfaces of the androgen (AR) and glucocorticoid (GR) receptors are virtually identical, yet these transcription factors share only about a third of their genomic binding sites and regulate similarly distinct sets of target genes. To address this paradox, we determined the intrinsic specificities of the AR and GR DNA-binding domains using a refined version of SELEX-seq. We developed an algorithm, SelexGLM, that quantifies binding specificity over a large (31-bp) binding site by iteratively fitting a feature-based generalized linear model to SELEX probe counts. This analysis revealed that the DNA-binding preferences of AR and GR homodimers differ significantly, both within and outside the 15-bp core binding site. The relative preference between the two factors can be tuned over a wide range by changing the DNA sequence, with AR more sensitive to sequence changes than GR. The specificity of AR extends to the regions flanking the core 15-bp site, where isothermal calorimetry measurements reveal that affinity is augmented by enthalpy-driven readout of poly(A) sequences associated with narrowed minor groove width. We conclude that the increased specificity of AR is correlated with more enthalpy-driven binding than GR. The binding models help explain differences in AR and GR genomic binding and provide a biophysical rationale for how promiscuous binding by GR allows functional substitution for AR in some castration-resistant prostate cancers.
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Affiliation(s)
- Liyang Zhang
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Gabriella D Martini
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA.,Department of Systems Biology, Columbia University Medical Center, New York, New York 10032, USA
| | - H Tomas Rube
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA.,Department of Systems Biology, Columbia University Medical Center, New York, New York 10032, USA
| | - Judith F Kribelbauer
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA.,Department of Systems Biology, Columbia University Medical Center, New York, New York 10032, USA
| | - Chaitanya Rastogi
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA.,Department of Systems Biology, Columbia University Medical Center, New York, New York 10032, USA
| | - Vincent D FitzPatrick
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA.,Department of Systems Biology, Columbia University Medical Center, New York, New York 10032, USA
| | - Jon C Houtman
- Department of Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA.,Department of Systems Biology, Columbia University Medical Center, New York, New York 10032, USA
| | - Miles A Pufall
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
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166
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Chirumamilla CS, Palagani A, Kamaraj B, Declerck K, Verbeek MWC, Oksana R, De Bosscher K, Bougarne N, Ruttens B, Gevaert K, Houtman R, De Vos WH, Joossens J, Van Der Veken P, Augustyns K, Van Ostade X, Bogaerts A, De Winter H, Vanden Berghe W. Selective Glucocorticoid Receptor Properties of GSK866 Analogs with Cysteine Reactive Warheads. Front Immunol 2017; 8:1324. [PMID: 29163463 PMCID: PMC5672024 DOI: 10.3389/fimmu.2017.01324] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 09/29/2017] [Indexed: 12/17/2022] Open
Abstract
Synthetic glucocorticoids (GC) are the mainstay therapy for treatment of acute and chronic inflammatory disorders. Due to the high adverse effects associated with long-term use, GC pharmacology has focused since the nineties on more selective GC ligand-binding strategies, classified as selective glucocorticoid receptor (GR) agonists (SEGRAs) or selective glucocorticoid receptor modulators (SEGRMs). In the current study, GSK866 analogs with electrophilic covalent-binding warheads were developed with potential SEGRA properties to improve their clinical safety profile for long-lasting topical skin disease applications. Since the off-rate of a covalently binding drug is negligible compared to that of a non-covalent drug, its therapeutic effects can be prolonged and typically, smaller doses of the drug are necessary to reach the same level of therapeutic efficacy, thereby potentially reducing systemic side effects. Different analogs of SEGRA GSK866 coupled to cysteine reactive warheads were characterized for GR potency and selectivity in various biochemical and cellular assays. GR- and NFκB-dependent reporter gene studies show favorable anti-inflammatory properties with reduced GR transactivation of two non-steroidal GSK866 analogs UAMC-1217 and UAMC-1218, whereas UAMC-1158 and UAMC-1159 compounds failed to modulate cellular GR activity. These results were further supported by GR immuno-localization and S211 phospho-GR western analysis, illustrating significant GR phosphoactivation and nuclear translocation upon treatment of GSK866, UAMC-1217, or UAMC-1218, but not in case of UAMC-1158 or UAMC-1159. Furthermore, mass spectrometry analysis of tryptic peptides of recombinant GR ligand-binding domain (LBD) bound to UAMC-1217 or UAMC-1218 confirmed covalent cysteine-dependent GR binding. Finally, molecular dynamics simulations, as well as glucocorticoid receptor ligand-binding domain (GR-LBD) coregulator interaction profiling of the GR-LBD bound to GSK866 or its covalently binding analogs UAMC-1217 or UAMC-1218 revealed subtle conformational differences that might underlie their SEGRA properties. Altogether, GSK866 analogs UAMC-1217 and UAMC-1218 hold promise as a novel class of covalent-binding SEGRA ligands for the treatment of topical inflammatory skin disorders.
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Affiliation(s)
- Chandra S Chirumamilla
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Ajay Palagani
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Balu Kamaraj
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Marinus W C Verbeek
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Ryabtsova Oksana
- Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Karolien De Bosscher
- Receptor Research Laboratories, Nuclear Receptor Lab (NRL) and Cytokine Receptor Lab (CRL), VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium
| | - Nadia Bougarne
- Receptor Research Laboratories, Nuclear Receptor Lab (NRL) and Cytokine Receptor Lab (CRL), VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium
| | - Bart Ruttens
- Center for Medical Biotechnology, Department of Biochemistry, VIB, Ghent University, Ghent, Belgium
| | - Kris Gevaert
- Center for Medical Biotechnology, Department of Biochemistry, VIB, Ghent University, Ghent, Belgium
| | - René Houtman
- PamGene International B.V., Den Bosch, Netherlands
| | - Winnok H De Vos
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Jurgen Joossens
- Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Pieter Van Der Veken
- Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Koen Augustyns
- Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Xaveer Van Ostade
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Annemie Bogaerts
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Hans De Winter
- Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, Belgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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167
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Gray JD, Kogan JF, Marrocco J, McEwen BS. Genomic and epigenomic mechanisms of glucocorticoids in the brain. Nat Rev Endocrinol 2017; 13:661-673. [PMID: 28862266 DOI: 10.1038/nrendo.2017.97] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Following the discovery of glucocorticoid receptors in the hippocampus and other brain regions, research has focused on understanding the effects of glucocorticoids in the brain and their role in regulating emotion and cognition. Glucocorticoids are essential for adaptation to stressors (allostasis) and in maladaptation resulting from allostatic load and overload. Allostatic overload, which can occur during chronic stress, can reshape the hypothalamic-pituitary-adrenal axis through epigenetic modification of genes in the hippocampus, hypothalamus and other stress-responsive brain regions. Glucocorticoids exert their effects on the brain through genomic mechanisms that involve both glucocorticoid receptors and mineralocorticoid receptors directly binding to DNA, as well as by non-genomic mechanisms. Furthermore, glucocorticoids synergize both genomically and non-genomically with neurotransmitters, neurotrophic factors, sex hormones and other stress mediators to shape an organism's present and future responses to a stressful environment. Here, we discuss the mechanisms of glucocorticoid action in the brain and review how glucocorticoids interact with stress mediators in the context of allostasis, allostatic load and stress-induced neuroplasticity.
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Affiliation(s)
- Jason D Gray
- Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, 1230 York Avenue, New York, NY 10065. USA
| | - Joshua F Kogan
- Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, 1230 York Avenue, New York, NY 10065. USA
| | - Jordan Marrocco
- Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, 1230 York Avenue, New York, NY 10065. USA
| | - Bruce S McEwen
- Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, The Rockefeller University, 1230 York Avenue, New York, NY 10065. USA
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168
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Weikum ER, de Vera IMS, Nwachukwu JC, Hudson WH, Nettles KW, Kojetin DJ, Ortlund EA. Tethering not required: the glucocorticoid receptor binds directly to activator protein-1 recognition motifs to repress inflammatory genes. Nucleic Acids Res 2017; 45:8596-8608. [PMID: 28591827 PMCID: PMC5737878 DOI: 10.1093/nar/gkx509] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/05/2017] [Indexed: 12/22/2022] Open
Abstract
The glucocorticoid receptor (GR) is a ligand-regulated transcription factor that controls the expression of extensive gene networks, driving both up- and down-regulation. GR utilizes multiple DNA-binding-dependent and -independent mechanisms to achieve context-specific transcriptional outcomes. The DNA-binding-independent mechanism involves tethering of GR to the pro-inflammatory transcription factor activator protein-1 (AP-1) through protein-protein interactions. This mechanism has served as the predominant model of GR-mediated transrepression of inflammatory genes. However, ChIP-seq data have consistently shown GR to occupy AP-1 response elements (TREs), even in the absence of AP-1. Therefore, the current model is insufficient to explain GR action at these sites. Here, we show that GR regulates a subset of inflammatory genes in a DNA-binding-dependent manner. Using structural biology and biochemical approaches, we show that GR binds directly to TREs via sequence-specific contacts to a GR-binding sequence (GBS) half-site found embedded within the TRE motif. Furthermore, we show that GR-mediated transrepression observed at TRE sites to be DNA-binding-dependent. This represents a paradigm shift in the field, showing that GR uses multiple mechanisms to suppress inflammatory gene expression. This work further expands our understanding of this complex multifaceted transcription factor.
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Affiliation(s)
- Emily R Weikum
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ian Mitchelle S de Vera
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jerome C Nwachukwu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - William H Hudson
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kendall W Nettles
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Douglas J Kojetin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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169
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Yoon MS. mTOR as a Key Regulator in Maintaining Skeletal Muscle Mass. Front Physiol 2017; 8:788. [PMID: 29089899 PMCID: PMC5650960 DOI: 10.3389/fphys.2017.00788] [Citation(s) in RCA: 298] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/26/2017] [Indexed: 01/02/2023] Open
Abstract
Maintenance of skeletal muscle mass is regulated by the balance between anabolic and catabolic processes. Mammalian target of rapamycin (mTOR) is an evolutionarily conserved serine/threonine kinase, and is known to play vital roles in protein synthesis. Recent findings have continued to refine our understanding of the function of mTOR in maintaining skeletal muscle mass. mTOR controls the anabolic and catabolic signaling of skeletal muscle mass, resulting in the modulation of muscle hypertrophy and muscle wastage. This review will highlight the fundamental role of mTOR in skeletal muscle growth by summarizing the phenotype of skeletal-specific mTOR deficiency. In addition, the evidence that mTOR is a dual regulator of anabolism and catabolism in skeletal muscle mass will be discussed. A full understanding of mTOR signaling in the maintenance of skeletal muscle mass could help to develop mTOR-targeted therapeutics to prevent muscle wasting.
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Affiliation(s)
- Mee-Sup Yoon
- Department of Molecular Medicine, School of Medicine, Gachon University, Incheon, South Korea
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170
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HDX reveals the conformational dynamics of DNA sequence specific VDR co-activator interactions. Nat Commun 2017; 8:923. [PMID: 29030554 PMCID: PMC5640644 DOI: 10.1038/s41467-017-00978-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/09/2017] [Indexed: 01/20/2023] Open
Abstract
The vitamin D receptor/retinoid X receptor-α heterodimer (VDRRXRα) regulates bone mineralization via transcriptional control of osteocalcin (BGLAP) gene and is the receptor for 1α,25-dihydroxyvitamin D3 (1,25D3). However, supra-physiological levels of 1,25D3 activates the calcium-regulating gene TRPV6 leading to hypercalcemia. An approach to attenuate this adverse effect is to develop selective VDR modulators (VDRMs) that differentially activate BGLAP but not TRPV6. Here we present structural insight for the action of a VDRM compared with agonists by employing hydrogen/deuterium exchange. Agonist binding directs crosstalk between co-receptors upon DNA binding, stabilizing the activation function 2 (AF2) surfaces of both receptors driving steroid receptor co-activator-1 (SRC1) interaction. In contrast, AF2 of VDR within VDRM:BGLAP bound heterodimer is more vulnerable for large stabilization upon SRC1 interaction compared with VDRM:TRPV6 bound heterodimer. These results reveal that the combination of ligand structure and DNA sequence tailor the transcriptional activity of VDR toward specific target genes. The vitamin D receptor/retinoid X receptor-α heterodimer (VDRRXRα) regulates bone mineralization. Here the authors employ hydrogen/deuterium exchange (HDX) mass spectrometry to study the conformational dynamics of VDRRXRα and give mechanistic insights into how VDRRXRα controls the transcriptional activity of specific genes.
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171
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Li J, White JT, Saavedra H, Wrabl JO, Motlagh HN, Liu K, Sowers J, Schroer TA, Thompson EB, Hilser VJ. Genetically tunable frustration controls allostery in an intrinsically disordered transcription factor. eLife 2017; 6:30688. [PMID: 29022880 PMCID: PMC5697930 DOI: 10.7554/elife.30688] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/11/2017] [Indexed: 01/08/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) present a functional paradox because they lack stable tertiary structure, but nonetheless play a central role in signaling, utilizing a process known as allostery. Historically, allostery in structured proteins has been interpreted in terms of propagated structural changes that are induced by effector binding. Thus, it is not clear how IDPs, lacking such well-defined structures, can allosterically affect function. Here, we show a mechanism by which an IDP can allosterically control function by simultaneously tuning transcriptional activation and repression, using a novel strategy that relies on the principle of ‘energetic frustration’. We demonstrate that human glucocorticoid receptor tunes this signaling in vivo by producing translational isoforms differing only in the length of the disordered region, which modulates the degree of frustration. We expect this frustration-based model of allostery will prove to be generally important in explaining signaling in other IDPs. Proteins carry out most of the key tasks inside cells. To perform these roles, proteins must fold up to form complex three-dimensional structures. Researchers used to think that the useful parts of proteins all had set structures. However, we now know that ‘disordered’ proteins with variable structures are common and disordered parts of proteins can have vital roles. In a process called allosteric regulation, regulator molecules can increase or decrease the activity of a protein by binding to it. This binding was thought to work by changing the structure of the protein, but it was not clear how this works in disordered proteins. To investigate, Li et al. studied a disordered protein called glucocorticoid receptor, and found that disordered regions can have opposing effects on other regions of the protein. This creates a ‘tug-of-war’ that Li et al. term “energetic frustration”, whereby the activity of the protein results from the combination of the opposing interactions. Further investigation revealed that the glucorticoid receptor produces different versions of itself that have different degrees of energetic frustration, which alters how effectively the proteins perform their tasks. This means that the protein can regulate its own activity even in the absence of binding to regulator molecules. The concept of energetic frustration could enhance our understanding of the many different proteins that contain disordered regions. Eventually, this knowledge could be used to develop drugs that alter the activity of these proteins and so could form part of treatments for a wide range of conditions including autoimmune diseases (such as rheumatoid arthritis and lupus), cancers, and organ rejection for transplant patients. The results presented by Li et al. suggest where more research is needed to achieve this goal. For example, we need to understand more about the stability of disordered protein regions, and to identify which surfaces of the proteins interact with each other.
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Affiliation(s)
- Jing Li
- Department of Biology, Johns Hopkins University, Baltimore, United States.,TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Jordan T White
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - Harry Saavedra
- Department of Biology, Johns Hopkins University, Baltimore, United States.,TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - James O Wrabl
- Department of Biology, Johns Hopkins University, Baltimore, United States.,TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Hesam N Motlagh
- Department of Biology, Johns Hopkins University, Baltimore, United States.,TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Kaixian Liu
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - James Sowers
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - Trina A Schroer
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - E Brad Thompson
- Department of Biology, Johns Hopkins University, Baltimore, United States.,Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, United States
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, Baltimore, United States.,TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, United States
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172
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Hintze BJ, Richardson JS, Richardson DC. Mismodeled purines: implicit alternates and hidden Hoogsteens. Acta Crystallogr D Struct Biol 2017; 73:852-859. [PMID: 28994414 PMCID: PMC5633910 DOI: 10.1107/s2059798317013729] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/25/2017] [Indexed: 12/14/2022] Open
Abstract
Hoogsteen base pairs are seen in DNA crystal structures, but only rarely. This study tests whether Hoogsteens or other syn purines are either under-modeled or over-modeled, which are known problems for rare conformations. Candidate purines needing a syn/anti 180° flip were identified by diagnostic patterns of difference electron-density peaks. Manual inspection narrowed 105 flip candidates to 20 convincing cases, all at ≤2.7 Å resolution. Rebuilding and refinement confirmed that 14 of these were authentic purine flips. Seven examples are modeled as Watson-Crick base pairs but should be Hoogsteens (commonest at duplex termini), and three had the opposite issue. Syn/anti flips were also needed for some single-stranded purines. Five of the 20 convincing cases arose from an unmodeled alternate duplex running in the opposite direction. These are in semi-palindromic DNA sequences bound by a homodimeric protein and show flipped-purine-like difference peaks at residues where the palindrome is imperfect. This study documents types of incorrect modeling which are worth avoiding. However, the primary conclusions are that such mistakes are infrequent, the bias towards fitting anti purines is very slight, and the occurrence rate of Hoogsteen base pairs in DNA crystal structures remains unchanged from earlier estimates at ∼0.3%.
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173
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Abstract
The most effective anti-inflammatory drugs used to treat patients with airways disease are topical glucocorticosteroids (GCs). These act on virtually all cells within the airway to suppress airway inflammation or prevent the recruitment of inflammatory cells into the airway. They also have profound effects on airway structural cells to reverse the effects of disease on their function. Glucorticosteroids act via specific receptors-the glucocorticosteroid receptor (GR)-which are a member of the nuclear receptor family. As such, many of the important actions of GCs are to modulate gene transcription through a number of distinct and complementary mechanisms. Targets genes include most inflammatory mediators such as chemokines, cytokines, growth factors and their receptors. GCs delivered by the inhaled route are very effective for most patients and have few systemic side effects. However, in some patients, even high doses of topical or even systemic GCs fail to control their disease. A number of mechanisms relating to inflammation have been reported to be responsible for the failure of these patients to respond correctly to GCs and these provide insight into GC actions within the airways. In these patients, the side-effect profile of GCs prevent continued use of high doses and new drugs are needed for these patients. Targeting the defective pathways associated with GC function in these patients may also reactivate GC responsiveness.
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Affiliation(s)
- Ian M Adcock
- Airway Disease Section, National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW3 6LY, UK.
| | - Sharon Mumby
- Airway Disease Section, National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW3 6LY, UK
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174
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de Vera IMS, Zheng J, Novick S, Shang J, Hughes TS, Brust R, Munoz-Tello P, Gardner WJ, Marciano DP, Kong X, Griffin PR, Kojetin DJ. Synergistic Regulation of Coregulator/Nuclear Receptor Interaction by Ligand and DNA. Structure 2017; 25:1506-1518.e4. [PMID: 28890360 DOI: 10.1016/j.str.2017.07.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/12/2017] [Accepted: 07/28/2017] [Indexed: 11/15/2022]
Abstract
Nuclear receptor (NR) transcription factors bind various coreceptors, small-molecule ligands, DNA response element sequences, and transcriptional coregulator proteins to affect gene transcription. Small-molecule ligands and DNA are known to influence receptor structure, coregulator protein interaction, and function; however, little is known on the mechanism of synergy between ligand and DNA. Using quantitative biochemical, biophysical, and solution structural methods, including 13C-detected nuclear magnetic resonance and hydrogen/deuterium exchange (HDX) mass spectrometry, we show that ligand and DNA cooperatively recruit the intrinsically disordered steroid receptor coactivator-2 (SRC-2/TIF2/GRIP1/NCoA-2) receptor interaction domain to peroxisome proliferator-activated receptor gamma-retinoid X receptor alpha (PPARγ-RXRα) heterodimer and reveal the binding determinants of the complex. Our data reveal a thermodynamic mechanism by which DNA binding propagates a conformational change in PPARγ-RXRα, stabilizes the receptor ligand binding domain dimer interface, and impacts ligand potency and cooperativity in NR coactivator recruitment.
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Affiliation(s)
- Ian Mitchelle S de Vera
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Scott Novick
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Jinsai Shang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Travis S Hughes
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Richard Brust
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Paola Munoz-Tello
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - William J Gardner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; TSRI High School Student Summer Internship Program, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - David P Marciano
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Xiangming Kong
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Douglas J Kojetin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA.
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175
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Baxley RM, Bullard JD, Klein MW, Fell AG, Morales-Rosado JA, Duan T, Geyer PK. Deciphering the DNA code for the function of the Drosophila polydactyl zinc finger protein Suppressor of Hairy-wing. Nucleic Acids Res 2017; 45:4463-4478. [PMID: 28158673 PMCID: PMC5416891 DOI: 10.1093/nar/gkx040] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/30/2017] [Indexed: 12/19/2022] Open
Abstract
Polydactyl zinc finger (ZF) proteins have prominent roles in gene regulation and often execute multiple regulatory functions. To understand how these proteins perform varied regulation, we studiedDrosophila Suppressor of Hairy-wing [Su(Hw)], an exemplar multifunctional polydactyl ZF protein. We identified separation-of-function (SOF) alleles that encode proteins disrupted in a single ZF that retain one of the Su(Hw) regulatory activities. Through extended in vitro analyses of the Su(Hw) ZF domain, we show that clusters of ZFs bind individual modules within a compound DNA consensus sequence. Through in vivo analysis of SOF mutants, we find that Su(Hw) genomic sites separate into sequence subclasses comprised of combinations of modules, with subclasses enriched for different chromatin features. These data suggest a Su(Hw) code, wherein DNA binding dictates its cofactor recruitment and regulatory output. We propose that similar DNA codes might be used to confer multiple regulatory functions of other polydactyl ZF proteins.
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Affiliation(s)
- Ryan M Baxley
- Interdisciplinary Graduate Program in Molecular and Cellular Biology, University of Iowa, Iowa City, IA 52242, USA
| | - James D Bullard
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Michael W Klein
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Ashley G Fell
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | | | - Tingting Duan
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Pamela K Geyer
- Interdisciplinary Graduate Program in Molecular and Cellular Biology, University of Iowa, Iowa City, IA 52242, USA.,Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
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176
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Changeux JP, Christopoulos A. Allosteric modulation as a unifying mechanism for receptor function and regulation. Diabetes Obes Metab 2017; 19 Suppl 1:4-21. [PMID: 28880476 DOI: 10.1111/dom.12959] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Four major receptor families enable cells to respond to chemical and physical signals from their proximal environment. The ligand- and voltage-gated ion channels, G-protein-coupled receptors, nuclear hormone receptors and receptor tyrosine kinases are all allosteric proteins that carry multiple, spatially distinct, yet conformationally linked ligand-binding sites. Recent studies point to common mechanisms governing the allosteric transitions of these receptors, including the impact of oligomerization, pre-existing and functionally distinct conformational ensembles, intrinsically disordered regions, and the occurrence of allosteric modulatory sites. Importantly, synthetic allosteric modulators are being discovered for these receptors, providing an enriched, yet challenging, landscape for novel therapeutics.
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MESH Headings
- Allosteric Regulation/drug effects
- Allosteric Site/drug effects
- Animals
- Binding Sites/drug effects
- Dimerization
- Drug Discovery/trends
- Drugs, Investigational/chemistry
- Drugs, Investigational/pharmacology
- Humans
- Ligand-Gated Ion Channels/agonists
- Ligand-Gated Ion Channels/antagonists & inhibitors
- Ligand-Gated Ion Channels/chemistry
- Ligand-Gated Ion Channels/metabolism
- Ligands
- Models, Molecular
- Protein Conformation/drug effects
- Protein Multimerization/drug effects
- Receptor Protein-Tyrosine Kinases/agonists
- Receptor Protein-Tyrosine Kinases/antagonists & inhibitors
- Receptor Protein-Tyrosine Kinases/chemistry
- Receptor Protein-Tyrosine Kinases/metabolism
- Receptors, Cytoplasmic and Nuclear/agonists
- Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/metabolism
- Receptors, G-Protein-Coupled/agonists
- Receptors, G-Protein-Coupled/antagonists & inhibitors
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/metabolism
- Voltage-Gated Sodium Channels/chemistry
- Voltage-Gated Sodium Channels/metabolism
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Affiliation(s)
| | - Arthur Christopoulos
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, VIC 3052 Parkville, Australia
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177
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A functional IL1RL1 variant regulates corticosteroid-induced sST2 expression in ulcerative colitis. Sci Rep 2017; 7:10180. [PMID: 28860510 PMCID: PMC5579262 DOI: 10.1038/s41598-017-10465-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 08/10/2017] [Indexed: 02/07/2023] Open
Abstract
The ST2/IL33 signalling pathway has been associated with ulcerative colitis (UC). ST2, encoded by the IL1RL1 gene, is expressed as both a membrane-anchored receptor (ST2L) activated by IL33 and as a soluble receptor (sST2) with anti-inflammatory properties. In UC patients, sST2 is further increased by corticosteroid treatment; however, the glucocorticoid-mediated molecular regulation remains unknown. We therefore tested whether genetic variants in the IL1RL1 distal promoter are involved in UC and affect glucocorticoid-mediated ST2 expression. Serum ST2 levels and genetic variants in the IL1RL1 distal promoter were examined by ELISA and PCR sequencing in UC patients receiving corticosteroids. Glucocorticoid-mediated ST2 production was evaluated in intestinal mucosa cultures. Molecular regulation of glucocorticoid-mediated ST2 was assessed by RT-qPCR, ChIP assay and luciferase reporter assay. Dexamethasone effect on ST2 transcript expression was analyzed in leukocytes and related to IL1RL1 variants. Sequencing of a distal IL1RL1 promoter region demonstrated that SNPs rs6543115(C) and rs6543116(A) are associated with increased sST2 in UC patients on corticosteroids. Dexamethasone up-regulated sST2 transcription through interaction with the glucocorticoid-response element (GRE) carrying rs6543115(C) variant. Our data indicate that IL1RL1 SNPs rs6543115(C) confer susceptibility to UC and is contained in the GRE, which may modulate glucocorticoid-induced sST2 expression.
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178
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Liu S, Kumari S, Hu Q, Senapati D, Venkadakrishnan VB, Wang D, DePriest AD, Schlanger SE, Ben-Salem S, Valenzuela MM, Willard B, Mudambi S, Swetzig WM, Das GM, Shourideh M, Koochekpour S, Falzarano SM, Magi-Galluzzi C, Yadav N, Chen X, Lao C, Wang J, Billaud JN, Heemers HV. A comprehensive analysis of coregulator recruitment, androgen receptor function and gene expression in prostate cancer. eLife 2017; 6:e28482. [PMID: 28826481 PMCID: PMC5608510 DOI: 10.7554/elife.28482] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/17/2017] [Indexed: 01/03/2023] Open
Abstract
Standard treatment for metastatic prostate cancer (CaP) prevents ligand-activation of androgen receptor (AR). Despite initial remission, CaP progresses while relying on AR. AR transcriptional output controls CaP behavior and is an alternative therapeutic target, but its molecular regulation is poorly understood. Here, we show that action of activated AR partitions into fractions that are controlled preferentially by different coregulators. In a 452-AR-target gene panel, each of 18 clinically relevant coregulators mediates androgen-responsiveness of 0-57% genes and acts as a coactivator or corepressor in a gene-specific manner. Selectivity in coregulator-dependent AR action is reflected in differential AR binding site composition and involvement with CaP biology and progression. Isolation of a novel transcriptional mechanism in which WDR77 unites the actions of AR and p53, the major genomic drivers of lethal CaP, to control cell cycle progression provides proof-of-principle for treatment via selective interference with AR action by exploiting AR dependence on coregulators.
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Affiliation(s)
- Song Liu
- Department of Biostatistics and BioinformaticsRoswell Park Cancer InstituteBuffaloUnited States
| | - Sangeeta Kumari
- Department of Cancer BiologyCleveland ClinicClevelandUnited States
| | - Qiang Hu
- Department of Biostatistics and BioinformaticsRoswell Park Cancer InstituteBuffaloUnited States
| | | | | | - Dan Wang
- Department of Biostatistics and BioinformaticsRoswell Park Cancer InstituteBuffaloUnited States
| | - Adam D DePriest
- Department of Cancer GeneticsRoswell Park Cancer InstituteBuffaloUnited States
| | | | - Salma Ben-Salem
- Department of Cancer BiologyCleveland ClinicClevelandUnited States
| | | | - Belinda Willard
- Department of Research Core ServicesCleveland ClinicClevelandUnited States
| | - Shaila Mudambi
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloUnited States
| | - Wendy M Swetzig
- Department of Pharmacology and TherapeuticsRoswell Park Cancer InstituteBuffaloUnited States
| | - Gokul M Das
- Department of Pharmacology and TherapeuticsRoswell Park Cancer InstituteBuffaloUnited States
| | - Mojgan Shourideh
- Department of Cancer GeneticsRoswell Park Cancer InstituteBuffaloUnited States
| | | | | | | | - Neelu Yadav
- Department of Pharmacology and TherapeuticsRoswell Park Cancer InstituteBuffaloUnited States
| | - Xiwei Chen
- Department of Biostatistics and BioinformaticsRoswell Park Cancer InstituteBuffaloUnited States
| | - Changshi Lao
- Institute for Nanosurface Science and EngineeringShenzhen UniversityShenzhenChina
| | - Jianmin Wang
- Department of Biostatistics and BioinformaticsRoswell Park Cancer InstituteBuffaloUnited States
| | | | - Hannelore V Heemers
- Department of Cancer BiologyCleveland ClinicClevelandUnited States
- Department of UrologyCleveland ClinicClevelandUnited States
- Department of Hematology/Medical OncologyCleveland ClinicClevelandUnited States
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179
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A high-throughput chemical screen identifies novel inhibitors and enhancers of anti-inflammatory functions of the glucocorticoid receptor. Sci Rep 2017; 7:7405. [PMID: 28785063 PMCID: PMC5547123 DOI: 10.1038/s41598-017-07565-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 06/28/2017] [Indexed: 02/05/2023] Open
Abstract
Glucocorticoids (GCs)—ligands of the glucocorticoid receptor (GR)—are widely used to treat inflammatory diseases, but suffer from significant side effects and poor responsiveness in certain patient populations. Identification of chemical GR modulators may provide insights into the regulatory mechanisms of anti-inflammatory functions of GR and help improve GC-based therapy. Here we report the development and application of a high-throughput screening to identify compounds that either enhance or suppress the anti-inflammatory effect of GR function. Using a cell-based GR activity assay that measures Dexamethasone (Dex)-mediated NF-κB repression, we have screened ~8,000 compounds and identified several compounds that suppressed GR activity, including multiple GSK3β inhibitors and anti-cancer agent camptothecin. Notably, we also identified two kinase IKK2 inhibitors, including TPCA-1, as GR enhancers that improve the anti-inflammatory effect of GR. In particular, TPCA-1 augmented the activity of Dex in NF-κB repression by attenuating GR down-regulation. Consistent with the observation, siRNA-mediated IKK2 knockdown decreased GR down-regulation and increased GR expression. Together, our results identified chemical compounds as novel modulators of GR and revealed an unexpected role for IKK2 in GR down-regulation. Furthermore, we have established a high-throughput screening platform for discovering GR-modulating compounds that may be repurposed to improve current GC-based therapies.
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180
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Kumari S, Senapati D, Heemers HV. Rationale for the development of alternative forms of androgen deprivation therapy. Endocr Relat Cancer 2017; 24:R275-R295. [PMID: 28566530 PMCID: PMC5886376 DOI: 10.1530/erc-17-0121] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 05/30/2017] [Indexed: 12/31/2022]
Abstract
With few exceptions, the almost 30,000 prostate cancer deaths annually in the United States are due to failure of androgen deprivation therapy. Androgen deprivation therapy prevents ligand-activation of the androgen receptor. Despite initial remission after androgen deprivation therapy, prostate cancer almost invariably progresses while continuing to rely on androgen receptor action. Androgen receptor's transcriptional output, which ultimately controls prostate cancer behavior, is an alternative therapeutic target, but its molecular regulation is poorly understood. Recent insights in the molecular mechanisms by which the androgen receptor controls transcription of its target genes are uncovering gene specificity as well as context-dependency. Heterogeneity in the androgen receptor's transcriptional output is reflected both in its recruitment to diverse cognate DNA binding motifs and in its preferential interaction with associated pioneering factors, other secondary transcription factors and coregulators at those sites. This variability suggests that multiple, distinct modes of androgen receptor action that regulate diverse aspects of prostate cancer biology and contribute differentially to prostate cancer's clinical progression are active simultaneously in prostate cancer cells. Recent progress in the development of peptidomimetics and small molecules, and application of Chem-Seq approaches indicate the feasibility for selective disruption of critical protein-protein and protein-DNA interactions in transcriptional complexes. Here, we review the recent literature on the different molecular mechanisms by which the androgen receptor transcriptionally controls prostate cancer progression, and we explore the potential to translate these insights into novel, more selective forms of therapies that may bypass prostate cancer's resistance to conventional androgen deprivation therapy.
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Affiliation(s)
- Sangeeta Kumari
- Department of Cancer BiologyCleveland Clinic, Cleveland, Ohio, USA
| | | | - Hannelore V Heemers
- Department of Cancer BiologyCleveland Clinic, Cleveland, Ohio, USA
- Department of UrologyCleveland Clinic, Cleveland, Ohio, USA
- Department of Hematology/Medical OncologyCleveland Clinic, Cleveland, Ohio, USA
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181
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Birth P, Schöne S, Stelzl U, Meijsing SH. Identification and characterization of BATF3 as a context-specific coactivator of the glucocorticoid receptor. PLoS One 2017; 12:e0181219. [PMID: 28708849 PMCID: PMC5510845 DOI: 10.1371/journal.pone.0181219] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/28/2017] [Indexed: 11/18/2022] Open
Abstract
The ability of the glucocorticoid receptor (GR) to regulate the transcriptional output of genes relies on its interactions with transcriptional coregulators. However, which coregulators are required for GR-dependent activation is context-dependent and can be influenced by the sequence of the DNA bound by GR and by the nature of the GR isoform responsible for the regulation of a gene. Here, we screened for GR-interacting proteins for which the interaction signal differed between two GR isoforms GRα and GRγ. These isoforms diverge by a single amino acid insertion in a domain, the lever arm, which adopts DNA sequence-specific conformations. We identify Basic Leucine Zipper ATF-Like Transcription Factor 3 (BATF3), an AP-1 family transcription factor, as a GR coregulator whose interaction with GR is modulated by the lever arm. Further, a combination of experiments uncovered that BATF3 acts as a gene-specific coactivator of GR whose coactivator potency is influenced by the sequence of the GR binding site. Together, our findings suggest that GR isoform and the sequence of GR binding site influence the interaction of GR with BATF3, which might direct the assembly of gene-specific regulatory complexes to fine-tune the expression of individual GR target genes.
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Affiliation(s)
- Petra Birth
- Max Planck Institute for Molecular Genetics, Ihnestraße 63–73, Berlin, Germany
| | - Stefanie Schöne
- Max Planck Institute for Molecular Genetics, Ihnestraße 63–73, Berlin, Germany
| | - Ulrich Stelzl
- Max Planck Institute for Molecular Genetics, Ihnestraße 63–73, Berlin, Germany
- Department of Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, University of Graz and BioTechMed-Graz, Universitätsplatz 1, Graz, Austria
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182
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The nature of the GRE influences the screening for GR-activity enhancing modulators. PLoS One 2017; 12:e0181101. [PMID: 28686666 PMCID: PMC5501670 DOI: 10.1371/journal.pone.0181101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/25/2017] [Indexed: 12/17/2022] Open
Abstract
Glucocorticoid resistance (GCR), i.e. unresponsiveness to the beneficial anti-inflammatory activities of the glucocorticoid receptor (GR), poses a serious problem in the treatment of inflammatory diseases. One possible solution to try and overcome GCR, is to identify molecules that prevent or revert GCR by hyper-stimulating the biological activity of the GR. To this purpose, we screened for compounds that potentiate the dexamethasone (Dex)-induced transcriptional activity of GR. To monitor GR transcriptional activity, the screen was performed using the lung epithelial cell line A549 in which a glucocorticoid responsive element (GRE) coupled to a luciferase reporter gene construct was stably integrated. Histone deacetylase inhibitors (HDACi) such as Vorinostat and Belinostat are two broad-spectrum HDACi that strongly increased the Dex-induced luciferase expression in our screening system. In sharp contrast herewith, results from a genome-wide transcriptome analysis of Dex-induced transcripts using RNAseq, revealed that Belinostat impairs the ability of GR to transactivate target genes. The stimulatory effect of Belinostat in the luciferase screen further depends on the nature of the reporter construct. In conclusion, a profound discrepancy was observed between HDACi effects on two different synthetic promoter-luciferase reporter systems. The favorable effect of HDACi on gene expression should be evaluated with care, when considering them as potential therapeutic agents. GEO accession number GSE96649.
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183
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Aikawa K, Asano M, Ono K, Habuka N, Yano J, Wilson K, Fujita H, Kandori H, Hara T, Morimoto M, Santou T, Yamaoka M, Nakayama M, Hasuoka A. Synthesis and biological evaluation of novel selective androgen receptor modulators (SARMs) Part III: Discovery of 4-(5-oxopyrrolidine-1-yl)benzonitrile derivative 2f as a clinical candidate. Bioorg Med Chem 2017; 25:3330-3349. [DOI: 10.1016/j.bmc.2017.04.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/11/2017] [Accepted: 04/12/2017] [Indexed: 12/23/2022]
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184
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Cohen DM, Steger DJ. Nuclear Receptor Function through Genomics: Lessons from the Glucocorticoid Receptor. Trends Endocrinol Metab 2017; 28:531-540. [PMID: 28495406 PMCID: PMC5505657 DOI: 10.1016/j.tem.2017.04.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/14/2017] [Accepted: 04/18/2017] [Indexed: 12/20/2022]
Abstract
Unlocking the therapeutic potential of the glucocorticoid receptor (GR) has motivated a search for small molecules that selectively modulate its ability to activate or repress gene transcription. Recently, breakthrough studies in the field of genomics have reinvigorated debate over longstanding transcriptional models explaining how GR controls tissue-specific gene expression. Here, we highlight these genomic studies with the dual goals of advancing understanding of nuclear receptor-mediated transcription and stimulating thought on the development of anti-inflammatory and immunosuppressive ligands for GR that have reduced harmful effects on metabolism.
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Affiliation(s)
- Daniel M Cohen
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, and The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David J Steger
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, and The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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185
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Poulard C, Bittencourt D, Wu DY, Hu Y, Gerke DS, Stallcup MR. A post-translational modification switch controls coactivator function of histone methyltransferases G9a and GLP. EMBO Rep 2017; 18:1442-1459. [PMID: 28615290 DOI: 10.15252/embr.201744060] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/10/2017] [Accepted: 05/16/2017] [Indexed: 11/09/2022] Open
Abstract
Like many transcription regulators, histone methyltransferases G9a and G9a-like protein (GLP) can act gene-specifically as coregulators, but mechanisms controlling this specificity are mostly unknown. We show that adjacent post-translational methylation and phosphorylation regulate binding of G9a and GLP to heterochromatin protein 1 gamma (HP1γ), formation of a ternary complex with the glucocorticoid receptor (GR) on chromatin, and function of G9a and GLP as coactivators for a subset of GR target genes. HP1γ is recruited by G9a and GLP to GR binding sites associated with genes that require G9a, GLP, and HP1γ for glucocorticoid-stimulated transcription. At the physiological level, G9a and GLP coactivator function is required for glucocorticoid activation of genes that repress cell migration in A549 lung cancer cells. Thus, regulated methylation and phosphorylation serve as a switch controlling G9a and GLP coactivator function, suggesting that this mechanism may be a general paradigm for directing specific transcription factor and coregulator actions on different genes.
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Affiliation(s)
- Coralie Poulard
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Danielle Bittencourt
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Dai-Ying Wu
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Yixin Hu
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Daniel S Gerke
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Michael R Stallcup
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
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186
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Mazumder A, Batabyal S, Mondal M, Mondol T, Choudhury S, Ghosh R, Chatterjee T, Bhattacharyya D, Pal SK, Roy S. Specific DNA sequences allosterically enhance protein-protein interaction in a transcription factor through modulation of protein dynamics: implications for specificity of gene regulation. Phys Chem Chem Phys 2017; 19:14781-14792. [PMID: 28548177 DOI: 10.1039/c7cp01193h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Most genes are regulated by multiple transcription factors, often assembling into multi-protein complexes in the gene regulatory region. Understanding of the molecular origin of specificity of gene regulatory complex formation in the context of the whole genome is currently inadequate. A phage transcription factor λ-CI forms repressive multi-protein complexes by binding to multiple binding sites in the genome to regulate the lifecycle of the phage. The protein-protein interaction between two DNA-bound λ-CI molecules is stronger when they are bound to the correct pair of binding sites, suggesting allosteric transmission of recognition of correct DNA sequences to the protein-protein interaction interface. Exploration of conformation and dynamics by time-resolved fluorescence anisotropy decay and molecular dynamics suggests a change in protein dynamics to be a crucial factor in mediating allostery. A lattice-based model suggests that DNA-sequence induced allosteric effects could be crucial underlying factors in differentially stabilizing the correct site-specific gene regulatory complexes. We conclude that transcription factors have evolved multiple mechanisms to augment the specificity of DNA-protein interactions in order to achieve an extraordinarily high degree of spatial and temporal specificities of gene regulatory complexes, and DNA-sequence induced allostery plays an important role in the formation of sequence-specific gene regulatory complexes.
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Affiliation(s)
- Abhishek Mazumder
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700 032, India
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187
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Fernandez EJ, Gahlot V, Rodriguez C, Amburn J. DNA-induced unfolding of the thyroid hormone receptor α A/B domain through allostery. FEBS Open Bio 2017; 7:854-864. [PMID: 28593140 PMCID: PMC5458466 DOI: 10.1002/2211-5463.12229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 01/22/2023] Open
Affiliation(s)
- Elias J. Fernandez
- Biochemistry & Cellular and Molecular Biology; University of Tennessee; Knoxville TN USA
| | - Vandna Gahlot
- Biochemistry & Cellular and Molecular Biology; University of Tennessee; Knoxville TN USA
| | - Celeste Rodriguez
- Biochemistry & Cellular and Molecular Biology; University of Tennessee; Knoxville TN USA
| | - Jacob Amburn
- Biochemistry & Cellular and Molecular Biology; University of Tennessee; Knoxville TN USA
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188
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Kang SH, Lee HA, Kim M, Lee E, Sohn UD, Kim I. Forkhead box O3 plays a role in skeletal muscle atrophy through expression of E3 ubiquitin ligases MuRF-1 and atrogin-1 in Cushing's syndrome. Am J Physiol Endocrinol Metab 2017; 312:E495-E507. [PMID: 28246104 DOI: 10.1152/ajpendo.00389.2016] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/21/2017] [Accepted: 02/21/2017] [Indexed: 11/22/2022]
Abstract
Cushing's syndrome is caused by overproduction of the adrenocorticotropic hormone (ACTH), which stimulates the adrenal grand to make cortisol. Skeletal muscle wasting occurs in pathophysiological response to Cushing's syndrome. The forkhead box (FOX) protein family has been implicated as a key regulator of muscle loss under conditions such as diabetes and sepsis. However, the mechanistic role of the FOXO family in ACTH-induced muscle atrophy is not understood. We hypothesized that FOXO3a plays a role in muscle atrophy through expression of the E3 ubiquitin ligases, muscle RING finger protein-1 (MuRF-1), and atrogin-1 in Cushing's syndrome. For establishment of a Cushing's syndrome animal model, Sprague-Dawley rats were implanted with osmotic minipumps containing ACTH (40 ng·kg-1·day-1). ACTH infusion significantly reduced muscle weight. In ACTH-infused rats, MuRF-1, atrogin-1, and FOXO3a were upregulated and the FOXO3a promoter was targeted by the glucocorticoid receptor (GR). Transcriptional activity and expression of FOXO3a were significantly decreased by the GR antagonist RU486. Treatment with RU486 reduced MuRF-1 and atrogin-1 expression in accordance with reduced enrichment of FOXO3a and Pol II on the promoters. Knockdown of FOXO3a prevented dexamethasone-induced MuRF-1 and atrogin-1 expression. These results indicate that FOXO3a plays a role in muscle atrophy through expression of MuRF-1 and atrogin-1 in Cushing's syndrome.
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MESH Headings
- Active Transport, Cell Nucleus/drug effects
- Animals
- Cell Line
- Chromatin Immunoprecipitation
- Cushing Syndrome/metabolism
- Cushing Syndrome/pathology
- Cushing Syndrome/physiopathology
- Disease Models, Animal
- Forkhead Box Protein O3/agonists
- Forkhead Box Protein O3/antagonists & inhibitors
- Forkhead Box Protein O3/genetics
- Forkhead Box Protein O3/metabolism
- Gene Expression Regulation/drug effects
- Genes, Reporter/drug effects
- Glucocorticoids/pharmacology
- Hormone Antagonists/pharmacology
- Male
- Muscle Fibers, Skeletal/drug effects
- Muscle Fibers, Skeletal/metabolism
- Muscle Fibers, Skeletal/pathology
- Muscle Proteins/agonists
- Muscle Proteins/antagonists & inhibitors
- Muscle Proteins/genetics
- Muscle Proteins/metabolism
- Muscle, Skeletal/drug effects
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscular Atrophy/etiology
- Promoter Regions, Genetic/drug effects
- RNA Interference
- Rats, Sprague-Dawley
- Receptors, Glucocorticoid/agonists
- Receptors, Glucocorticoid/antagonists & inhibitors
- Receptors, Glucocorticoid/metabolism
- Response Elements/drug effects
- SKP Cullin F-Box Protein Ligases/antagonists & inhibitors
- SKP Cullin F-Box Protein Ligases/genetics
- SKP Cullin F-Box Protein Ligases/metabolism
- Tripartite Motif Proteins/agonists
- Tripartite Motif Proteins/antagonists & inhibitors
- Tripartite Motif Proteins/genetics
- Tripartite Motif Proteins/metabolism
- Ubiquitin-Protein Ligases/antagonists & inhibitors
- Ubiquitin-Protein Ligases/genetics
- Ubiquitin-Protein Ligases/metabolism
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Affiliation(s)
- Seol-Hee Kang
- Department of Pharmacology, Cardiovascular Research Institute, Cell and Matrix Research Institute, Kyungpook National University School of Medicine, Daegu, Republic of Korea
- BK21 Plus Kyungpook National University Biomedical Convergence Program, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Hae-Ahm Lee
- Department of Pharmacology, Cardiovascular Research Institute, Cell and Matrix Research Institute, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Mina Kim
- Department of Pharmacology, Cardiovascular Research Institute, Cell and Matrix Research Institute, Kyungpook National University School of Medicine, Daegu, Republic of Korea
- BK21 Plus Kyungpook National University Biomedical Convergence Program, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Eunjo Lee
- Department of Pharmacology, Cardiovascular Research Institute, Cell and Matrix Research Institute, Kyungpook National University School of Medicine, Daegu, Republic of Korea
- BK21 Plus Kyungpook National University Biomedical Convergence Program, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Uy Dong Sohn
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea; and
| | - Inkyeom Kim
- Department of Pharmacology, Cardiovascular Research Institute, Cell and Matrix Research Institute, Kyungpook National University School of Medicine, Daegu, Republic of Korea;
- BK21 Plus Kyungpook National University Biomedical Convergence Program, Kyungpook National University School of Medicine, Daegu, Republic of Korea
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189
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Whirledge S, Cidlowski JA. Glucocorticoids and Reproduction: Traffic Control on the Road to Reproduction. Trends Endocrinol Metab 2017; 28:399-415. [PMID: 28274682 PMCID: PMC5438761 DOI: 10.1016/j.tem.2017.02.005] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/06/2017] [Accepted: 02/12/2017] [Indexed: 02/06/2023]
Abstract
Glucocorticoids are steroid hormones that regulate diverse cellular functions and are essential to facilitate normal physiology. However, stress-induced levels of glucocorticoids result in several pathologies including profound reproductive dysfunction. Compelling new evidence indicates that glucocorticoids are crucial to the establishment and maintenance of reproductive function. The fertility-promoting or -inhibiting activity of glucocorticoids depends on timing, dose, and glucocorticoid responsiveness within a given tissue, which is mediated by the glucocorticoid receptor (GR). The GR gene and protein are subject to cellular processing, contributing to signaling diversity and providing a mechanism by which both physiological and stress-induced levels of glucocorticoids function in a cell-specific manner. Understanding how glucocorticoids regulate fertility and infertility may lead to novel approaches to the regulation of reproductive function.
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Affiliation(s)
- Shannon Whirledge
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - John A Cidlowski
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC 27709, USA.
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190
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Klaßen C, Karabinskaya A, Dejager L, Vettorazzi S, Van Moorleghem J, Lühder F, Meijsing SH, Tuckermann JP, Bohnenberger H, Libert C, Reichardt HM. Airway Epithelial Cells Are Crucial Targets of Glucocorticoids in a Mouse Model of Allergic Asthma. THE JOURNAL OF IMMUNOLOGY 2017; 199:48-61. [PMID: 28515280 DOI: 10.4049/jimmunol.1601691] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 04/25/2017] [Indexed: 11/19/2022]
Abstract
Although glucocorticoids (GCs) are a mainstay in the clinical management of asthma, the target cells that mediate their therapeutic effects are unknown. Contrary to our expectation, we found that GC receptor (GR) expression in immune cells was dispensable for successful therapy of allergic airway inflammation (AAI) with dexamethasone. Instead, GC treatment was compromised in mice expressing a defective GR in the nonhematopoietic compartment or selectively lacking the GR in airway epithelial cells. Further, we found that an intact GR dimerization interface was a prerequisite for the suppression of AAI and airway hyperresponsiveness by GCs. Our observation that the ability of dexamethasone to modulate gene expression in airway epithelial cells coincided with its potency to resolve AAI supports a crucial role for transcriptional regulation by the GR in this cell type. Taken together, we identified an unknown mode of GC action in the treatment of allergic asthma that might help to develop more specific therapies in the future.
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Affiliation(s)
- Carina Klaßen
- Institute for Cellular and Molecular Immunology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Anna Karabinskaya
- Institute for Cellular and Molecular Immunology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Lien Dejager
- Inflammation Research Center, Flanders Institute for Biotechnology, 9052 Ghent, Belgium.,Department of Biomedical Molecular Biology, University of Ghent, 9052 Ghent, Belgium
| | - Sabine Vettorazzi
- Institute of Comparative Endocrinology, University of Ulm, 89081 Ulm, Germany
| | | | - Fred Lühder
- Institute for Multiple Sclerosis Research and Neuroimmunology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | | | - Jan P Tuckermann
- Institute of Comparative Endocrinology, University of Ulm, 89081 Ulm, Germany
| | - Hanibal Bohnenberger
- Institute of Pathology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Claude Libert
- Inflammation Research Center, Flanders Institute for Biotechnology, 9052 Ghent, Belgium.,Department of Biomedical Molecular Biology, University of Ghent, 9052 Ghent, Belgium
| | - Holger M Reichardt
- Institute for Cellular and Molecular Immunology, University Medical Center Göttingen, 37073 Göttingen, Germany;
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191
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Choi EJ, Jung BJ, Lee SH, Yoo HS, Shin EA, Ko HJ, Chang S, Kim SY, Jeon SM. A clinical drug library screen identifies clobetasol propionate as an NRF2 inhibitor with potential therapeutic efficacy in KEAP1 mutant lung cancer. Oncogene 2017; 36:5285-5295. [PMID: 28504720 DOI: 10.1038/onc.2017.153] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/10/2017] [Accepted: 04/14/2017] [Indexed: 01/07/2023]
Abstract
The Kelch-like ECH-associated protein 1 (KEAP1)-nuclear factor E2-related factor 2 (NRF2)pathway has a central role in cellular antioxidant defense. NRF2 activation due to KEAP1 or NRF2 mutations occurs frequently in many cancers, suggesting that NRF2 inhibition could be a promising therapeutic strategy. However, no potent NRF2 inhibitors are clinically available to date. To develop potent NRF2 inhibitors for therapeutic purpose, we screened ~4000 clinical compounds and determined clobetasol propionate (CP) as the most potent NRF2 inhibitor. Mechanistically, CP prevented nuclear accumulation and promoted β-TrCP-dependent degradation of NRF2 in a glucocorticoid receptor- and a glycogen synthase kinase 3 (GSK3)-dependent manner. As a result, CP induced oxidative stress and strongly suppressed the anchorage-independent growth of tumors with KEAP1 mutation, but not with the wild-type KEAP1. Further, CP alone or in combination with rapamycin strongly inhibited the in vitro and in vivo growth of tumors harboring mutations in KEAP1 or both KEAP1 and LKB1 that are frequently observed in lung cancer. Thus, CP could be a repurposed therapeutic agent for cancers with high NRF2 activity. We also proposed that the use CP and rapamycin in combination could be a potential therapeutic strategy for tumors harboring both KEAP1 and LKB1 mutations.
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Affiliation(s)
- E-J Choi
- College of Pharmacy, Ajou University, Suwon, Republic of Korea
| | - B-J Jung
- College of Pharmacy, Ajou University, Suwon, Republic of Korea
| | - S-H Lee
- Cancer Cell and Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - H-S Yoo
- College of Pharmacy, Ajou University, Suwon, Republic of Korea
| | - E-A Shin
- College of Pharmacy, Ajou University, Suwon, Republic of Korea
| | - H-J Ko
- College of Pharmacy, Kangwon National University, Chuncheon, Republic of Korea.,Convergence Research Center for Functional Plant Products, Advanced Institutes of Convergence Technology, Yeongtong-gu, Suwon, Republic of Korea
| | - S Chang
- Department of Biomedical Sciences, University of Ulsan School of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - S-Y Kim
- Cancer Cell and Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - S-M Jeon
- College of Pharmacy, Ajou University, Suwon, Republic of Korea.,Institute of Pharmaceutical Science and Technology, Ajou University, Suwon, Republic of Korea
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192
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Structural hierarchy controlling dimerization and target DNA recognition in the AHR transcriptional complex. Proc Natl Acad Sci U S A 2017; 114:5431-5436. [PMID: 28396409 DOI: 10.1073/pnas.1617035114] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) belongs to the PAS (PER-ARNT-SIM) family transcription factors and mediates broad responses to numerous environmental pollutants and cellular metabolites, modulating diverse biological processes from adaptive metabolism, acute toxicity, to normal physiology of vascular and immune systems. The AHR forms a transcriptionally active heterodimer with ARNT (AHR nuclear translocator), which recognizes the dioxin response element (DRE) in the promoter of downstream genes. We determined the crystal structure of the mammalian AHR-ARNT heterodimer in complex with the DRE, in which ARNT curls around AHR into a highly intertwined asymmetric architecture, with extensive heterodimerization interfaces and AHR interdomain interactions. Specific recognition of the DRE is determined locally by the DNA-binding residues, which discriminates it from the closely related hypoxia response element (HRE), and is globally affected by the dimerization interfaces and interdomain interactions. Changes at the interdomain interactions caused either AHR constitutive nuclear localization or failure to translocate to nucleus, underlying an allosteric structural pathway for mediating ligand-induced exposure of nuclear localization signal. These observations, together with the global higher flexibility of the AHR PAS-A and its loosely packed structural elements, suggest a dynamic structural hierarchy for complex scenarios of AHR activation induced by its diverse ligands.
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193
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Lee BH, Stallcup MR. Glucocorticoid receptor binding to chromatin is selectively controlled by the coregulator Hic-5 and chromatin remodeling enzymes. J Biol Chem 2017; 292:9320-9334. [PMID: 28381557 DOI: 10.1074/jbc.m117.782607] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 03/31/2017] [Indexed: 11/06/2022] Open
Abstract
The steroid hormone-activated glucocorticoid receptor (GR) regulates cellular stress pathways by binding to genomic regulatory elements of target genes and recruiting coregulator proteins to remodel chromatin and regulate transcription complex assembly. The coregulator hydrogen peroxide-inducible clone 5 (Hic-5) is required for glucocorticoid (GC) regulation of some genes but not others and blocks the regulation of a third gene set by inhibiting GR binding. How Hic-5 exerts these gene-specific effects and specifically how it blocks GR binding to some genes but not others is unclear. Here we show that site-specific blocking of GR binding is due to gene-specific requirements for ATP-dependent chromatin remodeling enzymes. By depletion of 11 different chromatin remodelers, we found that ATPases chromodomain helicase DNA-binding protein 9 (CHD9) and Brahma homologue (BRM, a product of the SMARCA2 gene) are required for GC-regulated expression of the blocked genes but not for other GC-regulated genes. Furthermore, CHD9 and BRM were required for GR occupancy and chromatin remodeling at GR-binding regions associated with blocked genes but not at GR-binding regions associated with other GC-regulated genes. Hic-5 selectively inhibits GR interaction with CHD9 and BRM, thereby blocking chromatin remodeling and robust GR binding at GR-binding sites associated with blocked genes. Thus, Hic-5 regulates GR binding site selection by a novel mechanism, exploiting gene-specific requirements for chromatin remodeling enzymes to selectively influence DNA occupancy and gene regulation by a transcription factor.
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Affiliation(s)
- Brian H Lee
- From the Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089-9176
| | - Michael R Stallcup
- From the Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089-9176
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194
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Jin HL, Yang L, Jeong KW. Flightless-I homolog regulates glucocorticoid receptor-mediated transcription via direct interaction of the leucine-rich repeat domain. Mol Biol Rep 2017; 44:243-250. [PMID: 28455686 DOI: 10.1007/s11033-017-4106-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 04/26/2017] [Indexed: 01/22/2023]
Abstract
Flightless-I homolog (FLII) is a member of the gelsolin family of proteins, and has been identified as a coactivator of estrogen receptor-mediated transcription. Here, we investigate the role of FLII in the glucocorticoid receptor (GR) signaling pathway. Reporter gene assay and real-time quantitative PCR in A549 were performed to investigate the function of FLII in the expression of GR target genes. Co-immunoprecipitation assay and in vitro binding assay were used to identify binding domain of FLII. Chromatin immunoprecipitation assay were carried out with FLII-depleted A549 cells to determine the role of FLII at GR binding sites. We demonstrate that FLII potentiates GR-mediated reporter gene activity synergistically with CARM1 and p300 to enhance GR transcriptional activity in the presence of dexamethasone (Dex) in A549 cells. Depletion of endogenous FLII inhibited the expression of Dex-regulated GR target genes in A549 cells, indicating that FLII is required for GR-mediated transcription. Further, we observed that FLII binds to GR via its N-terminal leucine-rich repeat (LRR) region, suggesting that the enhancement of GR activation may occur through the interaction of GR and FLII. Moreover, chromatin immunoprecipitation analysis demonstrated that FLII is recruited to the GR binding sites. In addition, depletion of endogenous FLII decreased the recruitment of p300, and subsequently RNA polymerase II, to specific sites of GR target genes. Taken together, these studies reveal a functional involvement of FLII in activating transcription of GR target genes, suggesting a physiological role for FLII in the GR signaling pathway.
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Affiliation(s)
- Hong Lan Jin
- Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University, 191 Hambakmoero, Yeonsu-gu, Incheon, 21936, Republic of Korea
| | - Liu Yang
- Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University, 191 Hambakmoero, Yeonsu-gu, Incheon, 21936, Republic of Korea
| | - Kwang Won Jeong
- Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University, 191 Hambakmoero, Yeonsu-gu, Incheon, 21936, Republic of Korea.
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195
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Kurmis AA, Yang F, Welch TR, Nickols NG, Dervan PB. A Pyrrole-Imidazole Polyamide Is Active against Enzalutamide-Resistant Prostate Cancer. Cancer Res 2017; 77:2207-2212. [PMID: 28360139 DOI: 10.1158/0008-5472.can-16-2503] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/24/2016] [Accepted: 03/08/2017] [Indexed: 12/20/2022]
Abstract
The LREX' prostate cancer model is resistant to the antiandrogen enzalutamide via activation of an alternative nuclear hormone receptor, glucocorticoid receptor (GR), which has similar DNA-binding specificity to the androgen receptor (AR). Small molecules that target DNA to interfere with protein-DNA interactions may retain activity against enzalutamide-resistant prostate cancers where ligand-binding domain antagonists are ineffective. We reported previously that a pyrrole-imidazole (Py-Im) polyamide designed to bind the consensus androgen response element half-site has antitumor activity against hormone-sensitive prostate cancer. In enzalutamide-resistant LREX' cells, Py-Im polyamide interfered with both AR- and GR-driven gene expression, whereas enzalutamide interfered with only that of AR. Genomic analyses indicated immediate interference with the AR transcriptional pathway. Long-term treatment with Py-Im polyamide demonstrated a global decrease in RNA levels consistent with inhibition of transcription. The polyamide was active against two enzalutamide-resistant xenografts with minimal toxicity. Overall, our results identify Py-Im polyamide as a promising therapeutic strategy in enzalutamide-resistant prostate cancer. Cancer Res; 77(9); 2207-12. ©2017 AACR.
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Affiliation(s)
- Alexis A Kurmis
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
| | - Fei Yang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
| | - Timothy R Welch
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
| | - Nicholas G Nickols
- Department of Radiation Oncology, David Geffen School of Medicine at UCLA, VA Greater Los Angeles Healthcare System, Los Angeles, California
| | - Peter B Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California.
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196
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Popović V, Goeman J, Thommis J, Heyerick A, Caroen J, Van der Eycken J, De Bosscher K. Daucane esters from laserwort (Laserpitium latifolium L.) inhibit cytokine and chemokine production in human lung epithelial cells. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2017; 26:28-36. [PMID: 28257662 DOI: 10.1016/j.phymed.2017.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/21/2016] [Accepted: 01/04/2017] [Indexed: 06/06/2023]
Abstract
BACKGROUND Laserwort, Laserpitium latifolium L. (Apiaceae), is a European medicinal plant. Its roots and rhizomes were traditionally used as a general tonic and to treat inflammatory and infective diseases. PURPOSE The anti-inflammatory potential of daucane esters, isolated from underground parts extract of L. latifolium and specific structural features that contribute to their activity were investigated. In addition, we studied their interference with the transactivation capacity of the Glucocorticoid Receptor when added together with a classic glucocorticoid (GC), dexamethasone (DEX). This particular property may be relevant in combination strategies, attempting to circumvent diabetogenic side effects of glucocorticoids upon long-term anti-inflammatory treatments. MATERIALS AND METHODS Nine L. latifolium daucane esters were isolated and elucidated as derivatives of desoxodehydrolaserpitin, laserpitin and a novel 2β-esterified laserpitinol analogue. Of all compounds effects on NF-κB- and AP-1-driven pro-inflammatory pathways were assessed using TNF- or PMA-induced reporter gene analysis in A549 cells. Daucanes with a strong and concentration-dependent inhibition of both NF-κB and AP-1, were tested for a potential effect on DEX-stimulated GR-driven Glucocorticoid Response Element (GRE) reporter gene activity. In addition, GRE-driven anti-inflammatory mRNA expression was determined (GILZ and DUSP1). Also anti-inflammatory properties were validated by monitoring effects on CCL-2, IL-6, IL-1β mRNA expression levels (qPCR) and on CCL-2 chemokine production (ELISA). RESULTS Daucanes featuring an ester moiety and/or a hydroxy group at positions 2β, 6α and 10α and especially the novel 2β-esterified laserpitinol derivative that, in comparison to other isolated compounds, features an additional 9α-hydroxy group, demonstrated suppression of both NF-κB- and AP-1-dependent pro-inflammatory pathways. Remarkably, those entities competitively and concentration-dependently repressed GR-driven GRE-dependent reporter gene activities. The most active compounds inhibited CCL-2 protein excretion and compound 4 downregulated genes coding for IL-1β and IL-6 induced upon TNF treatment in A549. In absence of TNF, compound 4 upregulated the GRE-mediated anti-inflammatory gene GILZ, but not DUSP1. CONCLUSIONS Daucane esters are novel anti-inflammatory agents that may, in combination with GCs, potentially improve therapeutic benefit. These results contribute to the ongoing search for novel anti-inflammatory agents as safer alternatives to, or with, GCs.
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Affiliation(s)
- Višnja Popović
- Receptor Research Laboratories, Nuclear Receptor Lab, VIB-Medical Biotechnology Center, VIB, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium; Laboratory for Organic and Bio-Organic Synthesis, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
| | - Jan Goeman
- Laboratory for Organic and Bio-Organic Synthesis, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Jonathan Thommis
- Receptor Research Laboratories, Nuclear Receptor Lab, VIB-Medical Biotechnology Center, VIB, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
| | - Arne Heyerick
- Reliable Cancer Therapies, Boechoutlaan 221, B-1853 Strombeek-Bever, Belgium
| | - Jurgen Caroen
- Laboratory for Organic and Bio-Organic Synthesis, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Johan Van der Eycken
- Laboratory for Organic and Bio-Organic Synthesis, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Karolien De Bosscher
- Receptor Research Laboratories, Nuclear Receptor Lab, VIB-Medical Biotechnology Center, VIB, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium; Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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197
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Molecular basis for the genome engagement by Sox proteins. Semin Cell Dev Biol 2017; 63:2-12. [DOI: 10.1016/j.semcdb.2016.08.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/09/2016] [Accepted: 08/09/2016] [Indexed: 01/11/2023]
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198
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Weikum ER, Knuesel MT, Ortlund EA, Yamamoto KR. Glucocorticoid receptor control of transcription: precision and plasticity via allostery. Nat Rev Mol Cell Biol 2017; 18:159-174. [PMID: 28053348 PMCID: PMC6257982 DOI: 10.1038/nrm.2016.152] [Citation(s) in RCA: 372] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The glucocorticoid receptor (GR) is a constitutively expressed transcriptional regulatory factor (TRF) that controls many distinct gene networks, each uniquely determined by particular cellular and physiological contexts. The precision of GR-mediated responses seems to depend on combinatorial, context-specific assembly of GR-nucleated transcription regulatory complexes at genomic response elements. In turn, evidence suggests that context-driven plasticity is conferred by the integration of multiple signals, each serving as an allosteric effector of GR conformation, a key determinant of regulatory complex composition and activity. This structural and mechanistic perspective on GR regulatory specificity is likely to extend to other eukaryotic TRFs.
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Affiliation(s)
- Emily R Weikum
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
| | - Matthew T Knuesel
- Department of Cellular and Molecular Pharmacology, University of California San Francisco School of Medicine, 600 16th Street, San Francisco, California 94143, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
| | - Keith R Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California San Francisco School of Medicine, 600 16th Street, San Francisco, California 94143, USA
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199
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Comparing the rules of engagement of androgen and glucocorticoid receptors. Cell Mol Life Sci 2017; 74:2217-2228. [PMID: 28168446 PMCID: PMC5425506 DOI: 10.1007/s00018-017-2467-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 12/21/2016] [Accepted: 01/17/2017] [Indexed: 01/22/2023]
Abstract
Despite the diverse physiological activities of androgens and glucocorticoids, the corresponding receptors are very close members of the nuclear-receptor super family. Their action mechanisms show striking similarities, since both receptors recognize very similar DNA-response elements and recruit the same coactivators to their target genes. The specificity of the responses lies mainly in the tissue-specific expression of the receptors and in their ligand specificity. In cells, where both receptors are expressed, the mechanisms leading to the difference in target genes are less obvious. They lie in part in subtle variations of the DNA-binding sites, in cooperativity with other transcription factors and in differential allosteric signals from the DNA and ligand to other receptor domains. We will highlight the different suggestions that might explain the DNA sequence selectivity and will compare the possible allosteric routes between the response elements and the different functions in the transactivation process. The interplay of androgen and glucocorticoid receptors is also highly relevant in clinical settings, where both receptors are therapeutically targeted. We will discuss the possibility that the glucocorticoid and androgen receptors can play partially redundant roles in castration-resistant prostate cancer.
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200
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Mohideen-Abdul K, Tazibt K, Bourguet M, Hazemann I, Lebars I, Takacs M, Cianférani S, Klaholz BP, Moras D, Billas IML. Importance of the Sequence-Directed DNA Shape for Specific Binding Site Recognition by the Estrogen-Related Receptor. Front Endocrinol (Lausanne) 2017; 8:140. [PMID: 28676789 PMCID: PMC5476932 DOI: 10.3389/fendo.2017.00140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/06/2017] [Indexed: 01/01/2023] Open
Abstract
Most nuclear receptors (NRs) bind DNA as dimers, either as hetero- or as homodimers on DNA sequences organized as two half-sites with specific orientation and spacing. The dimerization of NRs on their cognate response elements (REs) involves specific protein-DNA and protein-protein interactions. The estrogen-related receptor (ERR) belongs to the steroid hormone nuclear receptor (SHR) family and shares strong similarity in its DNA-binding domain (DBD) with that of the estrogen receptor (ER). In vitro, ERR binds with high affinity inverted repeat REs with a 3-bps spacing (IR3), but in vivo, it preferentially binds to single half-site REs extended at the 5'-end by 3 bp [estrogen-related response element (ERREs)], thus explaining why ERR was often inferred as a purely monomeric receptor. Since its C-terminal ligand-binding domain is known to homodimerize with a strong dimer interface, we investigated the binding behavior of the isolated DBDs to different REs using electrophoretic migration, multi-angle static laser light scattering (MALLS), non-denaturing mass spectrometry, and nuclear magnetic resonance. In contrast to ER DBD, ERR DBD binds as a monomer to EREs (IR3), such as the tff1 ERE-IR3, but we identified a DNA sequence composed of an extended half-site embedded within an IR3 element (embedded ERRE/IR3), where stable dimer binding is observed. Using a series of chimera and mutant DNA sequences of ERREs and IR3 REs, we have found the key determinants for the binding of ERR DBD as a dimer. Our results suggest that the sequence-directed DNA shape is more important than the exact nucleotide sequence for the binding of ERR DBD to DNA as a dimer. Our work underlines the importance of the shape-driven DNA readout mechanisms based on minor groove recognition and electrostatic potential. These conclusions may apply not only to ERR but also to other members of the SHR family, such as androgen or glucocorticoid, for which a strong well-conserved half-site is followed by a weaker one with degenerated sequence.
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Affiliation(s)
- Kareem Mohideen-Abdul
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Karima Tazibt
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Maxime Bourguet
- Université de Strasbourg, Strasbourg, France
- Laboratoire de Spectrométrie de Masse BioOrganique, Centre National de la Recherche Scientifique (CNRS), IPHC UMR 7178, Strasbourg, France
| | - Isabelle Hazemann
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Isabelle Lebars
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Maria Takacs
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Sarah Cianférani
- Université de Strasbourg, Strasbourg, France
- Laboratoire de Spectrométrie de Masse BioOrganique, Centre National de la Recherche Scientifique (CNRS), IPHC UMR 7178, Strasbourg, France
| | - Bruno P. Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Dino Moras
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Isabelle M. L. Billas
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France
- Université de Strasbourg, Strasbourg, France
- *Correspondence: Isabelle M. L. Billas,
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