101
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Pooley JR, Rivers CA, Kilcooley MT, Paul SN, Cavga AD, Kershaw YM, Muratcioglu S, Gursoy A, Keskin O, Lightman SL. Beyond the heterodimer model for mineralocorticoid and glucocorticoid receptor interactions in nuclei and at DNA. PLoS One 2020; 15:e0227520. [PMID: 31923266 PMCID: PMC6953809 DOI: 10.1371/journal.pone.0227520] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/19/2019] [Indexed: 12/20/2022] Open
Abstract
Glucocorticoid (GR) and mineralocorticoid receptors (MR) are believed to classically bind DNA as homodimers or MR-GR heterodimers to influence gene regulation in response to pulsatile basal or stress-evoked glucocorticoid secretion. Pulsed corticosterone presentation reveals MR and GR co-occupy DNA only at the peaks of glucocorticoid oscillations, allowing interaction. GR DNA occupancy was pulsatile, while MR DNA occupancy was prolonged through the inter-pulse interval. In mouse mammary 3617 cells MR-GR interacted in the nucleus and at a chromatin-associated DNA binding site. Interactions occurred irrespective of ligand type and receptors formed complexes of higher order than heterodimers. We also detected MR-GR interactions ex-vivo in rat hippocampus. An expanded range of MR-GR interactions predicts structural allostery allowing a variety of transcriptional outcomes and is applicable to the multiple tissue types that co-express both receptors in the same cells whether activated by the same or different hormones.
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Affiliation(s)
- John R. Pooley
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, United Kingdom
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Caroline A. Rivers
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, United Kingdom
| | - Michael T. Kilcooley
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, United Kingdom
| | - Susana N. Paul
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, United Kingdom
| | - Ayse Derya Cavga
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Yvonne M. Kershaw
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, United Kingdom
| | - Serena Muratcioglu
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Attila Gursoy
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
| | - Stafford L. Lightman
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, United Kingdom
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102
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Guillien M, le Maire A, Mouhand A, Bernadó P, Bourguet W, Banères JL, Sibille N. IDPs and their complexes in GPCR and nuclear receptor signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:105-155. [DOI: 10.1016/bs.pmbts.2020.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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103
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Van Moortel L, Gevaert K, De Bosscher K. Improved Glucocorticoid Receptor Ligands: Fantastic Beasts, but How to Find Them? Front Endocrinol (Lausanne) 2020; 11:559673. [PMID: 33071974 PMCID: PMC7541956 DOI: 10.3389/fendo.2020.559673] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/26/2020] [Indexed: 01/01/2023] Open
Abstract
Exogenous glucocorticoids are widely used in the clinic for the treatment of inflammatory disorders and hematological cancers. Unfortunately, their use is associated with debilitating side effects, including hyperglycemia, osteoporosis, mood swings, and weight gain. Despite the continued efforts of pharma as well as academia, the search for so-called selective glucocorticoid receptor modulators (SEGRMs), compounds with strong anti-inflammatory or anti-cancer properties but a reduced number or level of side effects, has had limited success so far. Although monoclonal antibody therapies have been successfully introduced for the treatment of certain disorders (such as anti-TNF for rheumatoid arthritis), glucocorticoids remain the first-in-line option for many other chronic diseases including asthma, multiple sclerosis, and multiple myeloma. This perspective offers our opinion on why a continued search for SEGRMs remains highly relevant in an era where small molecules are sometimes unrightfully considered old-fashioned. Besides a discussion on which bottlenecks and pitfalls might have been overlooked in the past, we elaborate on potential solutions and recent developments that may push future research in the right direction.
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Affiliation(s)
- Laura Van Moortel
- Translational Nuclear Receptor Research (TNRR) Laboratory, VIB, Ghent, Belgium
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Karolien De Bosscher
- Translational Nuclear Receptor Research (TNRR) Laboratory, VIB, Ghent, Belgium
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- *Correspondence: Karolien De Bosscher
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104
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Kraemer WJ, Ratamess NA, Hymer WC, Nindl BC, Fragala MS. Growth Hormone(s), Testosterone, Insulin-Like Growth Factors, and Cortisol: Roles and Integration for Cellular Development and Growth With Exercise. Front Endocrinol (Lausanne) 2020; 11:33. [PMID: 32158429 PMCID: PMC7052063 DOI: 10.3389/fendo.2020.00033] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/16/2020] [Indexed: 12/16/2022] Open
Abstract
Hormones are largely responsible for the integrated communication of several physiological systems responsible for modulating cellular growth and development. Although the specific hormonal influence must be considered within the context of the entire endocrine system and its relationship with other physiological systems, three key hormones are considered the "anabolic giants" in cellular growth and repair: testosterone, the growth hormone superfamily, and the insulin-like growth factor (IGF) superfamily. In addition to these anabolic hormones, glucocorticoids, mainly cortisol must also be considered because of their profound opposing influence on human skeletal muscle anabolism in many instances. This review presents emerging research on: (1) Testosterone signaling pathways, responses, and adaptations to resistance training; (2) Growth hormone: presents new complexity with exercise stress; (3) Current perspectives on IGF-I and physiological adaptations and complexity these hormones as related to training; and (4) Glucocorticoid roles in integrated communication for anabolic/catabolic signaling. Specifically, the review describes (1) Testosterone as the primary anabolic hormone, with an anabolic influence largely dictated primarily by genomic and possible non-genomic signaling, satellite cell activation, interaction with other anabolic signaling pathways, upregulation or downregulation of the androgen receptor, and potential roles in co-activators and transcriptional activity; (2) Differential influences of growth hormones depending on the "type" of the hormone being assayed and the magnitude of the physiological stress; (3) The exquisite regulation of IGF-1 by a family of binding proteins (IGFBPs 1-6), which can either stimulate or inhibit biological action depending on binding; and (4) Circadian patterning and newly discovered variants of glucocorticoid isoforms largely dictating glucocorticoid sensitivity and catabolic, muscle sparing, or pathological influence. The downstream integrated anabolic and catabolic mechanisms of these hormones not only affect the ability of skeletal muscle to generate force; they also have implications for pharmaceutical treatments, aging, and prevalent chronic conditions such as metabolic syndrome, insulin resistance, and hypertension. Thus, advances in our understanding of hormones that impact anabolic: catabolic processes have relevance for athletes and the general population, alike.
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Affiliation(s)
- William J. Kraemer
- Department of Human Sciences, The Ohio State University, Columbus, OH, United States
- *Correspondence: William J. Kraemer
| | - Nicholas A. Ratamess
- Department of Health and Exercise Science, The College of New Jersey, Ewing, NJ, United States
| | - Wesley C. Hymer
- Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Bradley C. Nindl
- Department of Sports Medicine, School of Health and Rehabilitation Sciences, University of Pittsburgh, Pittsburgh, PA, United States
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105
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Jiang L, Dai S, Li J, Liang X, Qu L, Chen X, Guo M, Chen Z, Chen L, Wei H, Chen Y. Structural basis of binding of homodimers of the nuclear receptor NR4A2 to selective Nur-responsive DNA elements. J Biol Chem 2019; 294:19795-19803. [PMID: 31723028 PMCID: PMC6926456 DOI: 10.1074/jbc.ra119.010730] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/11/2019] [Indexed: 01/07/2023] Open
Abstract
Proteins of nuclear receptor subfamily 4 group A (NR4A), including NR4A1/NGFI-B, NR4A2/Nurr1, and NR4A3/NOR-1, are nuclear transcription factors that play important roles in metabolism, apoptosis, and proliferation. NR4A proteins recognize DNA response elements as monomers or dimers to regulate the transcription of a variety of genes involved in multiple biological processes. In this study, we determined two crystal structures of the NR4A2 DNA-binding domain (NR4A2-DBD) bound to two Nur-responsive elements: an inverted repeat and an everted repeat at 2.6-2.8 Å resolution. The structures revealed that two NR4A2-DBD molecules bind independently to the everted repeat, whereas two other NR4A2-DBD molecules form a novel dimer interface on the inverted repeat. Moreover, substitution of the interfacial residue valine 298 to lysine as well as mutation of DNA bases involved in the interactions abolished the dimerization. Overall, our structural, biochemical, and bioinformatics analyses provide a molecular basis for the binding of the NR4A2 protein dimers to NurREs and advance our understanding of the dimerization specificity of nuclear receptors.
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Affiliation(s)
- Longying Jiang
- Department of Oncology, Laboratory of Structural Biology, NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Shuyan Dai
- Department of Oncology, Laboratory of Structural Biology, NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jun Li
- Department of Oncology, Laboratory of Structural Biology, NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xujun Liang
- Department of Oncology, Laboratory of Structural Biology, NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Lingzhi Qu
- Department of Oncology, Laboratory of Structural Biology, NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xiaojuan Chen
- Department of Oncology, Laboratory of Structural Biology, NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Ming Guo
- Department of Oncology, Laboratory of Structural Biology, NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhuchu Chen
- Department of Oncology, Laboratory of Structural Biology, NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Lin Chen
- Department of Oncology, Laboratory of Structural Biology, NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China,Molecular and Computational Biology Program, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, California 90089
| | - Hudie Wei
- Department of Oncology, Laboratory of Structural Biology, NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China, To whom correspondence may be addressed. Tel.:
86-731-84327542; Fax:
86-731-84327542; E-mail:
| | - Yongheng Chen
- Department of Oncology, Laboratory of Structural Biology, NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China, To whom correspondence may be addressed. Tel.:
86-731-84327542; Fax:
86-731-84327542; E-mail:
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106
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Parsonnet NV, Lammer NC, Holmes ZE, Batey RT, Wuttke DS. The glucocorticoid receptor DNA-binding domain recognizes RNA hairpin structures with high affinity. Nucleic Acids Res 2019; 47:8180-8192. [PMID: 31147715 DOI: 10.1093/nar/gkz486] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/17/2019] [Accepted: 05/21/2019] [Indexed: 01/04/2023] Open
Abstract
The glucocorticoid receptor (GR) binds the noncoding RNA Gas5 via its DNA-binding domain (DBD) with functional implications in pro-apoptosis signaling. Here, we report a comprehensive in vitro binding study where we have determined that GR-DBD is a robust structure-specific RNA-binding domain. GR-DBD binds to a diverse range of RNA hairpin motifs, both synthetic and biologically derived, with apparent mid-nanomolar affinity while discriminating against uniform dsRNA. As opposed to dimeric recognition of dsDNA, GR-DBD binds to RNA as a monomer and confers high affinity primarily through electrostatic contacts. GR-DBD adopts a discrete RNA-bound state, as assessed by NMR, distinct from both free and DNA-bound. NMR and alanine mutagenesis suggest a heightened involvement of the C-terminal α-helix of the GR-DBD in RNA-binding. RNA competes for binding with dsDNA and occurs in a similar affinity range as dimer binding to the canonical DNA element. Given the prevalence of RNA hairpins within the transcriptome, our findings strongly suggest that many RNAs have potential to impact GR biology.
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Affiliation(s)
- Nicholas V Parsonnet
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA
| | - Nickolaus C Lammer
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA
| | - Zachariah E Holmes
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA
| | - Robert T Batey
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA
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107
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Porter BA, Ortiz MA, Bratslavsky G, Kotula L. Structure and Function of the Nuclear Receptor Superfamily and Current Targeted Therapies of Prostate Cancer. Cancers (Basel) 2019; 11:cancers11121852. [PMID: 31771198 PMCID: PMC6966469 DOI: 10.3390/cancers11121852] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/14/2019] [Accepted: 11/20/2019] [Indexed: 12/26/2022] Open
Abstract
The nuclear receptor superfamily comprises a large group of proteins with functions essential for cell signaling, survival, and proliferation. There are multiple distinctions between nuclear superfamily classes defined by hallmark differences in function, ligand binding, tissue specificity, and DNA binding. In this review, we utilize the initial classification system, which defines subfamilies based on structure and functional difference. The defining feature of the nuclear receptor superfamily is that these proteins function as transcription factors. The loss of transcriptional regulation or gain of functioning of these receptors is a hallmark in numerous diseases. For example, in prostate cancer, the androgen receptor is a primary target for current prostate cancer therapies. Targeted cancer therapies for nuclear hormone receptors have been more feasible to develop than others due to the ligand availability and cell permeability of hormones. To better target these receptors, it is critical to understand their structural and functional regulation. Given that late-stage cancers often develop hormone insensitivity, we will explore the strengths and pitfalls of targeting other transcription factors outside of the nuclear receptor superfamily such as the signal transducer and activator of transcription (STAT).
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Affiliation(s)
- Baylee A. Porter
- Department of Urology, Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (B.A.P.); (M.A.O.); (G.B.)
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Maria A. Ortiz
- Department of Urology, Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (B.A.P.); (M.A.O.); (G.B.)
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Gennady Bratslavsky
- Department of Urology, Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (B.A.P.); (M.A.O.); (G.B.)
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Leszek Kotula
- Department of Urology, Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (B.A.P.); (M.A.O.); (G.B.)
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Correspondence: ; Tel.: +1-315-464-1690
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108
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Martin EW, Chakraborty S, Presman DM, Tomassoni Ardori F, Oh KS, Kaileh M, Tessarollo L, Sung MH. Assaying Homodimers of NF-κB in Live Single Cells. Front Immunol 2019; 10:2609. [PMID: 31787981 PMCID: PMC6853996 DOI: 10.3389/fimmu.2019.02609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/21/2019] [Indexed: 11/25/2022] Open
Abstract
NF-κB is a family of heterodimers and homodimers which are generated from subunits encoded by five genes. The predominant classical dimer RelA:p50 is presumed to operate as “NF-κB” in many contexts. However, there are several other dimer species which exist and may even be more functionally relevant in specific cell types. Accurate characterization of stimulus-specific and tissue-specific dimer repertoires is fundamentally important for understanding the downstream gene regulation by NF-κB proteins. In vitro assays such as immunoprecipitation have been widely used to analyze subunit composition, but these methods do not provide information about dimerization status within the natural intracellular environment of intact live cells. Here we apply a live single cell microscopy technique termed Number and Brightness to examine dimers translocating to the nucleus in fibroblasts after pro-inflammatory stimulation. This quantitative assay suggests that RelA:RelA homodimers are more prevalent than might be expected. We also found that the relative proportion of RelA:RelA homodimers can be perturbed by small molecule inhibitors known to disrupt the NF-κB pathway. Our findings show that Number and Brightness is a useful method for investigating NF-κB dimer species in live cells. This approach may help identify the relevant targets in pathophysiological contexts where the dimer specificity of NF-κB intervention is desired.
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Affiliation(s)
- Erik W Martin
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Sayantan Chakraborty
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Francesco Tomassoni Ardori
- Mouse Cancer Genetics Program, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Kyu-Seon Oh
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Mary Kaileh
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
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109
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Liu X, Gupta STP, Bhimsaria D, Reed JL, Rodríguez-Martínez J, Ansari AZ, Raman S. De novo design of programmable inducible promoters. Nucleic Acids Res 2019; 47:10452-10463. [PMID: 31552424 PMCID: PMC6821364 DOI: 10.1093/nar/gkz772] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/16/2019] [Accepted: 08/29/2019] [Indexed: 01/05/2023] Open
Abstract
Ligand-responsive allosteric transcription factors (aTF) play a vital role in genetic circuits and high-throughput screening because they transduce biochemical signals into gene expression changes. Programmable control of gene expression from aTF-regulated promoter is important because different downstream effector genes function optimally at different expression levels. However, tuning gene expression of native promoters is difficult due to complex layers of homeostatic regulation encoded within them. We engineered synthetic promoters de novo by embedding operator sites with varying affinities and radically reshaped binding preferences within a minimal, constitutive Escherichia coli promoter. Multiplexed cell-based screening of promoters for three TetR-like aTFs generated with this approach gave rich diversity of gene expression levels, dynamic ranges and ligand sensitivities and were 50- to 100-fold more active over their respective native promoters. Machine learning on our dataset revealed that relative position of the core motif and bases flanking the core motif play an important role in modulating induction response. Our generalized approach yields customizable and programmable aTF-regulated promoters for engineering cellular pathways and enables the discovery of new small molecule biosensors.
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Affiliation(s)
- Xiangyang Liu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- The Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sanjan T P Gupta
- The Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Devesh Bhimsaria
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jennifer L Reed
- The Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Aseem Z Ansari
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- The Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
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110
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Senapati D, Kumari S, Heemers HV. Androgen receptor co-regulation in prostate cancer. Asian J Urol 2019; 7:219-232. [PMID: 32742924 PMCID: PMC7385509 DOI: 10.1016/j.ajur.2019.09.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/30/2019] [Accepted: 07/22/2019] [Indexed: 12/11/2022] Open
Abstract
Prostate cancer (PCa) progression relies on androgen receptor (AR) action. Preventing AR's ligand-activation is the frontline treatment for metastatic PCa. Androgen deprivation therapy (ADT) that inhibits AR ligand-binding initially induces remission but eventually fails, mainly because of adaptive PCa responses that restore AR action. The vast majority of castration-resistant PCa (CRPC) continues to rely on AR activity. Novel therapeutic strategies are being explored that involve targeting other critical AR domains such as those that mediate its constitutively active transactivation function, its DNA binding ability, or its interaction with co-operating transcriptional regulators. Considerable molecular and clinical variability has been found in AR's interaction with its ligands, DNA binding motifs, and its associated coregulators and transcription factors. Here, we review evidence that each of these levels of AR regulation can individually and differentially impact transcription by AR. In addition, we examine emerging insights suggesting that each can also impact the other, and that all three may collaborate to induce gene-specific AR target gene expression, likely via AR allosteric effects. For the purpose of this review, we refer to the modulating influence of these differential and/or interdependent contributions of ligands, cognate DNA-binding motifs and critical regulatory protein interactions on AR's transcriptional output, which may influence the efficiency of the novel PCa therapeutic approaches under consideration, as co-regulation of AR activity.
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Affiliation(s)
| | - Sangeeta Kumari
- Department of Cancer Biology, Cleveland Clinic, Cleveland, OH, USA
| | - Hannelore V Heemers
- Department of Cancer Biology, Cleveland Clinic, Cleveland, OH, USA.,Department of Urology, Cleveland Clinic, Cleveland, OH, USA.,Department of Hematology/Medical Oncology, Cleveland Clinic, Cleveland, OH, USA
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111
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Koning ASCAM, Buurstede JC, van Weert LTCM, Meijer OC. Glucocorticoid and Mineralocorticoid Receptors in the Brain: A Transcriptional Perspective. J Endocr Soc 2019; 3:1917-1930. [PMID: 31598572 PMCID: PMC6777400 DOI: 10.1210/js.2019-00158] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/18/2019] [Indexed: 02/07/2023] Open
Abstract
Adrenal glucocorticoid hormones are crucial for maintenance of homeostasis and adaptation to stress. They act via the mineralocorticoid receptors (MRs) and glucocorticoid receptors (GRs)-members of the family of nuclear receptors. MRs and GRs can mediate distinct, sometimes opposite, effects of glucocorticoids. Both receptor types can mediate nongenomic steroid effects, but they are best understood as ligand-activated transcription factors. MR and GR protein structure is similar; the receptors can form heterodimers on the DNA at glucocorticoid response elements (GREs), and they share a number of target genes. The transcriptional basis for opposite effects on cellular physiology remains largely unknown, in particular with respect to MR-selective gene transcription. In this review, we discuss proven and potential mechanisms of transcriptional specificity for MRs and GRs. These include unique GR binding to "negative GREs," direct binding to other transcription factors, and binding to specific DNA sequences in conjunction with other transcription factors, as is the case for MRs and NeuroD proteins in the brain. MR- and GR-specific effects may also depend on specific interactions with transcriptional coregulators, downstream mediators of transcriptional receptor activity. Current data suggest that the relative importance of these mechanisms depends on the tissue and physiological context. Insight into these processes may not only allow a better understanding of homeostatic regulation but also the development of drugs that target specific aspects of disease.
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Affiliation(s)
- Anne-Sophie C A M Koning
- Einthoven Laboratory and Department of Medicine, Division of Endocrinology, Leiden University Medical Center, RC Leiden, Netherlands
| | - Jacobus C Buurstede
- Einthoven Laboratory and Department of Medicine, Division of Endocrinology, Leiden University Medical Center, RC Leiden, Netherlands
| | - Lisa T C M van Weert
- Einthoven Laboratory and Department of Medicine, Division of Endocrinology, Leiden University Medical Center, RC Leiden, Netherlands
| | - Onno C Meijer
- Einthoven Laboratory and Department of Medicine, Division of Endocrinology, Leiden University Medical Center, RC Leiden, Netherlands
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112
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Alqassim AY, Wilson MJ, Wickliffe JK, Pangeni D, Overton EB, Miller CA. Aryl hydrocarbon receptor signaling, toxicity, and gene expression responses to mono-methylchrysenes. ENVIRONMENTAL TOXICOLOGY 2019; 34:992-1000. [PMID: 31087746 DOI: 10.1002/tox.22770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/25/2019] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) comprise a large family of toxic compounds that come from natural and anthropogenic sources. Chrysene is a PAH with multiple effects, but the toxic potentials of mono-methylchrysenes are less characterized. A comparison of chrysene and six mono-methylchrysenes was performed using assays for cytotoxicity, human aryl hydrocarbon receptor (AhR) reporter gene signaling, and AhR-regulated target gene and protein expression. Sulforhodamine B and trypan blue dye binding assays revealed these chrysenes to be similar in their cytotoxic effects on HepG2 cells. A yeast-based reporter assay detecting human AhR-mediated gene expression identified 4-methylchrysene as being six times more potent and 5-methylchrysene about one-third as potent as chrysene. Other methylchrysenes were more similar to chrysene in the ability to act as AhR ligands. The mono-methylchrysenes all strongly induced CYP1A1 mRNA and protein and moderately induced CYP1B1 expression in HepG2 cells. Levels of CYP1A2 mRNA were induced at higher concentrations of the chrysenes, but protein expression was not significantly altered. The PCR-based gene expression and immunoblotting analyses indicated induced expression differences across the chrysene members were similar to each other. Overall, the effects of methylated chrysenes were comparable to unsubstituted chrysene, suggesting members of this group may be considered approximately equivalent in their effects. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Ahmad Y Alqassim
- Global Environmental Health Sciences, Tulane University, New Orleans, Louisiana
- Faculty of Medicine, Jazan University, Jizan, Saudi Arabia
| | - Mark J Wilson
- Global Environmental Health Sciences, Tulane University, New Orleans, Louisiana
| | - Jeffrey K Wickliffe
- Global Environmental Health Sciences, Tulane University, New Orleans, Louisiana
| | - Deepa Pangeni
- Environmental Sciences, Louisiana State University, Baton Rouge, Louisiana
| | - Edward B Overton
- Environmental Sciences, Louisiana State University, Baton Rouge, Louisiana
| | - Charles A Miller
- Global Environmental Health Sciences, Tulane University, New Orleans, Louisiana
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Ling T, Miller DJ, Lang WH, Griffith E, Rodriguez-Cortes A, El Ayachi I, Palacios G, Min J, Miranda-Carboni G, Lee RE, Rivas F. Mechanistic Insight on the Mode of Action of Colletoic Acid. J Med Chem 2019; 62:6925-6940. [PMID: 31294974 DOI: 10.1021/acs.jmedchem.9b00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The natural product colletoic acid (CA) is a selective inhibitor of 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1), which primarily converts cortisone to the active glucocorticoid (GC) cortisol. Here, CA's mode of action and its potential as a chemical tool to study intracellular GC signaling in adipogenesis are disclosed. 11β-HSD1 biochemical studies of CA indicated that its functional groups at C-1, C-4, and C-9 were important for enzymatic activity; an X-ray crystal structure of 11β-HSD1 bound to CA at 2.6 Å resolution revealed the nature of those interactions, namely, a close-fitting and favorable interactions between the constrained CA spirocycle and the catalytic triad of 11β-HSD1. Structure-activity relationship studies culminated in the development of a superior CA analogue with improved target engagement. Furthermore, we demonstrate that CA selectively inhibits preadipocyte differentiation through 11β-HSD1 inhibition, suppressing other relevant key drivers of adipogenesis (i.e., PPARγ, PGC-1α), presumably by negatively modulating the glucocorticoid signaling pathway. The combined findings provide an in-depth evaluation of the mode of action of CA and its potential as a tool compound to study adipose tissue and its implications in metabolic syndrome.
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Affiliation(s)
| | | | | | | | | | - Ikbale El Ayachi
- Department of Medicine , The University of Tennessee Health Science Center , Memphis , Tennessee 38163 , United States
| | | | | | - Gustavo Miranda-Carboni
- Department of Medicine , The University of Tennessee Health Science Center , Memphis , Tennessee 38163 , United States
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114
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Escoter-Torres L, Caratti G, Mechtidou A, Tuckermann J, Uhlenhaut NH, Vettorazzi S. Fighting the Fire: Mechanisms of Inflammatory Gene Regulation by the Glucocorticoid Receptor. Front Immunol 2019; 10:1859. [PMID: 31440248 PMCID: PMC6693390 DOI: 10.3389/fimmu.2019.01859] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/23/2019] [Indexed: 12/12/2022] Open
Abstract
For many decades, glucocorticoids have been widely used as the gold standard treatment for inflammatory conditions. Unfortunately, their clinical use is limited by severe adverse effects such as insulin resistance, cardiometabolic diseases, muscle and skin atrophies, osteoporosis, and depression. Glucocorticoids exert their effects by binding to the Glucocorticoid Receptor (GR), a ligand-activated transcription factor which both positively, and negatively regulates gene expression. Extensive research during the past several years has uncovered novel mechanisms by which the GR activates and represses its target genes. Genome-wide studies and mouse models have provided valuable insight into the molecular mechanisms of inflammatory gene regulation by GR. This review focusses on newly identified target genes and GR co-regulators that are important for its anti-inflammatory effects in innate immune cells, as well as mutations within the GR itself that shed light on its transcriptional activity. This research progress will hopefully serve as the basis for the development of safer immune suppressants with reduced side effect profiles.
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Affiliation(s)
- Laura Escoter-Torres
- Molecular Endocrinology, Helmholtz Zentrum München (HMGU), German Center for Diabetes Research (DZD), Institute for Diabetes and Cancer IDC, Munich, Germany
| | - Giorgio Caratti
- Department of Biology, Institute for Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
| | - Aikaterini Mechtidou
- Molecular Endocrinology, Helmholtz Zentrum München (HMGU), German Center for Diabetes Research (DZD), Institute for Diabetes and Cancer IDC, Munich, Germany
| | - Jan Tuckermann
- Department of Biology, Institute for Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
| | - Nina Henriette Uhlenhaut
- Molecular Endocrinology, Helmholtz Zentrum München (HMGU), German Center for Diabetes Research (DZD), Institute for Diabetes and Cancer IDC, Munich, Germany.,Gene Center, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Sabine Vettorazzi
- Department of Biology, Institute for Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
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115
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Thormann V, Rothkegel MC, Schöpflin R, Glaser LV, Djuric P, Li N, Chung HR, Schwahn K, Vingron M, Meijsing SH. Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer-promoter contacts. Nucleic Acids Res 2019; 46:2868-2882. [PMID: 29385519 PMCID: PMC5888794 DOI: 10.1093/nar/gky051] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 01/19/2018] [Indexed: 12/19/2022] Open
Abstract
Genomic binding of transcription factors, like the glucocorticoid receptor (GR), is linked to the regulation of genes. However, as we show here, GR binding is a poor predictor of GR-dependent gene regulation even when taking the 3D organization of the genome into account. To connect GR binding sites to the regulation of genes in the endogenous genomic context, we turned to genome editing. By deleting GR binding sites, individually or in combination, we uncovered how cooperative interactions between binding sites contribute to the regulation of genes. Specifically, for the GR target gene GILZ, we show that the simultaneous presence of a cluster of GR binding sites is required for the activity of an individual enhancer and that the GR-dependent regulation of GILZ depends on multiple GR-bound enhancers. Further, by deleting GR binding sites that are shared between different cell types, we show how cell type-specific genome organization and enhancer-blocking can result in cell type-specific wiring of promoter–enhancer contacts. This rewiring allows an individual GR binding site shared between different cell types to direct the expression of distinct transcripts and thereby contributes to the cell type-specific consequences of glucocorticoid signaling.
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Affiliation(s)
- Verena Thormann
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
| | - Maika C Rothkegel
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
| | - Robert Schöpflin
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
| | - Laura V Glaser
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
| | - Petar Djuric
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
| | - Na Li
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
| | - Ho-Ryun Chung
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
| | - Kevin Schwahn
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
| | - Sebastiaan H Meijsing
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-67, 14195 Berlin, Germany
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116
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Tonsing-Carter E, Hernandez KM, Kim CR, Harkless RV, Oh A, Bowie KR, West-Szymanski DC, Betancourt-Ponce MA, Green BD, Lastra RR, Fleming GF, Chandarlapaty S, Conzen SD. Glucocorticoid receptor modulation decreases ER-positive breast cancer cell proliferation and suppresses wild-type and mutant ER chromatin association. Breast Cancer Res 2019; 21:82. [PMID: 31340854 PMCID: PMC6651939 DOI: 10.1186/s13058-019-1164-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/25/2019] [Indexed: 12/25/2022] Open
Abstract
Background Non-ER nuclear receptor activity can alter estrogen receptor (ER) chromatin association and resultant ER-mediated transcription. Consistent with GR modulation of ER activity, high tumor glucocorticoid receptor (GR) expression correlates with improved relapse-free survival in ER+ breast cancer (BC) patients. Methods In vitro cell proliferation assays were used to assess ER-mediated BC cell proliferation following GR modulation. ER chromatin association following ER/GR co-liganding was measured using global ChIP sequencing and directed ChIP analysis of proliferative gene enhancers. Results We found that GR liganding with either a pure agonist or a selective GR modulator (SGRM) slowed estradiol (E2)-mediated proliferation in ER+ BC models. SGRMs that antagonized transcription of GR-unique genes both promoted GR chromatin association and inhibited ER chromatin localization at common DNA enhancer sites. Gene expression analysis revealed that ER and GR co-activation decreased proliferative gene activation (compared to ER activation alone), specifically reducing CCND1, CDK2, and CDK6 gene expression. We also found that ligand-dependent GR occupancy of common ER-bound enhancer regions suppressed both wild-type and mutant ER chromatin association and decreased corresponding gene expression. In vivo, treatment with structurally diverse SGRMs also reduced MCF-7 Y537S ER-expressing BC xenograft growth. Conclusion These studies demonstrate that liganded GR can suppress ER chromatin occupancy at shared ER-regulated enhancers, including CCND1 (Cyclin D1), regardless of whether the ligand is a classic GR agonist or antagonist. Resulting GR-mediated suppression of ER+ BC proliferative gene expression and cell division suggests that SGRMs could decrease ER-driven gene expression. Electronic supplementary material The online version of this article (10.1186/s13058-019-1164-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eva Tonsing-Carter
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Kyle M Hernandez
- Center for Research Informatics, The University of Chicago, Chicago, IL, 60637, USA.,Department of Pediatrics, The University of Chicago, Chicago, IL, 60637, USA
| | - Caroline R Kim
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Ryan V Harkless
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Alyce Oh
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Kathleen R Bowie
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | | | | | - Bradley D Green
- Ben May Department for Cancer Research, The University of Chicago, 900 E 57th St, Chicago, IL, 60637, USA
| | - Ricardo R Lastra
- Department of Pathology, The University of Chicago, Chicago, IL, 60637, USA
| | - Gini F Fleming
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Sarat Chandarlapaty
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Suzanne D Conzen
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA. .,Ben May Department for Cancer Research, The University of Chicago, 900 E 57th St, Chicago, IL, 60637, USA.
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117
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Paakinaho V, Johnson TA, Presman DM, Hager GL. Glucocorticoid receptor quaternary structure drives chromatin occupancy and transcriptional outcome. Genome Res 2019; 29:1223-1234. [PMID: 31337711 PMCID: PMC6673716 DOI: 10.1101/gr.244814.118] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 04/09/2019] [Indexed: 01/11/2023]
Abstract
Most transcription factors, including nuclear receptors, are widely modeled as binding regulatory elements as monomers, homodimers, or heterodimers. Recent findings in live cells show that the glucocorticoid receptor NR3C1 (also known as GR) forms tetramers on enhancers, owing to an allosteric alteration induced by DNA binding, and suggest that higher oligomerization states are important for the gene regulatory responses of GR. By using a variant (GRtetra) that mimics this allosteric transition, we performed genome-wide studies using a GR knockout cell line with reintroduced wild-type GR or reintroduced GRtetra. GRtetra acts as a super receptor by binding to response elements not accessible to the wild-type receptor and both induces and represses more genes than GRwt. These results argue that DNA binding induces a structural transition to the tetrameric state, forming a transient higher-order structure that drives both the activating and repressive actions of glucocorticoids.
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Affiliation(s)
- Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA.,Institute of Biomedicine, University of Eastern Finland, Kuopio, FI-70211 Kuopio, Finland
| | - Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA.,IFIBYNE, UBA-CONICET, Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, C1428EGA, Argentina
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA
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118
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Louw A. GR Dimerization and the Impact of GR Dimerization on GR Protein Stability and Half-Life. Front Immunol 2019; 10:1693. [PMID: 31379877 PMCID: PMC6653659 DOI: 10.3389/fimmu.2019.01693] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/08/2019] [Indexed: 12/14/2022] Open
Abstract
Pharmacologically, glucocorticoids, which mediate their effects via the glucocorticoid receptor (GR), are a most effective therapy for inflammatory diseases despite the fact that chronic use causes side-effects and acquired GC resistance. The design of drugs with fewer side-effects and less potential for the development of resistance is therefore considered crucial for improved therapy. Dimerization of the GR is an integral step in glucocorticoid signaling and has been identified as a possible molecular site to target for drug development of anti-inflammatory drugs with an improved therapeutic index. Most of the current understanding regarding the role of GR dimerization in GC signaling derives for dimerization deficient mutants, although the role of ligands biased toward monomerization has also been described. Even though designing for loss of dimerization has mostly been applied for reduction of side-effect profile, designing for loss of dimerization may also be a fruitful strategy for the development of GC drugs with less potential to develop GC resistance. GC-induced resistance affects up to 30% of users and is due to a reduction in the GR functional pool. Several molecular mechanisms of GC-mediated reductions in GR pool have been described, one of which is the autologous down-regulation of GR density by the ubiquitin-proteasome-system (UPS). Loss of GR dimerization prevents autologous down-regulation of the receptor through modulation of interactions with components of the UPS and post-translational modifications (PTMs), such as phosphorylation, which prime the GR for degradation. Rational design of conformationally biased ligands that select for a monomeric GR conformation, which increases GC sensitivity through improving GR protein stability and increasing half-life, may be a productive avenue to explore. However, potential drawbacks to this approach should be considered as well as the advantages and disadvantages in chronic vs. acute treatment regimes.
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Affiliation(s)
- Ann Louw
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
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119
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Andrilenas KK, Ramlall V, Kurland J, Leung B, Harbaugh AG, Siggers T. DNA-binding landscape of IRF3, IRF5 and IRF7 dimers: implications for dimer-specific gene regulation. Nucleic Acids Res 2019; 46:2509-2520. [PMID: 29361124 PMCID: PMC5861432 DOI: 10.1093/nar/gky002] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/09/2018] [Indexed: 12/26/2022] Open
Abstract
Transcription factors IRF3, IRF5 and IRF7 (IRF3/5/7) have overlapping, yet distinct, roles in the mammalian response to pathogens. To examine the role that DNA-binding specificity plays in delineating IRF3/5/7-specific gene regulation we used protein-binding microarrays (PBMs) to characterize the DNA binding of IRF3/5/7 homodimers. We identified both common and dimer-specific DNA binding sites, and show that DNA-binding differences can translate into dimer-specific gene regulation. Central to the antiviral response, IRF3/5/7 regulate type I interferon (IFN) genes. We show that IRF3 and IRF7 bind to many interferon-stimulated response element (ISRE)-type sites in the virus-response elements (VREs) of IFN promoters. However, strikingly, IRF5 does not bind the VREs, suggesting evolutionary selection against IRF5 homodimer binding. Mutational analysis reveals a critical specificity-determining residue that inhibits IRF5 binding to the ISRE-variants present in the IFN gene promoters. Integrating PBM and reporter gene data we find that both DNA-binding affinity and affinity-independent mechanisms determine the function of DNA-bound IRF dimers, suggesting that DNA-based allostery plays a role in IRF binding site function. Our results provide new insights into the role and limitations of DNA-binding affinity in delineating IRF3/5/7-specific gene expression.
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Affiliation(s)
| | | | - Jesse Kurland
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Brandon Leung
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Trevor Siggers
- Department of Biology, Boston University, Boston, MA 02215, USA
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120
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Hua G, Zein N, Daubeuf F, Chambon P. Glucocorticoid receptor modulators CpdX and CpdX-D3 exhibit the same in vivo antiinflammatory activities as synthetic glucocorticoids. Proc Natl Acad Sci U S A 2019; 116:14191-14199. [PMID: 31227605 PMCID: PMC6628818 DOI: 10.1073/pnas.1908258116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We previously reported that the nonsteroidal compound CpdX, which was initially characterized 20 y ago as a possible gestagen and, shortly afterward, as a possible drug for treatments of inflammatory diseases, selectively triggers the NFκB/AP1-mediated tethered indirect transrepression function of the glucocorticoid receptor (GR), and could therefore be a selective glucocorticoid receptor agonistic modulator (SEGRAM). We now demonstrate that, upon administration to the mouse, CpdX and one of its deuterated derivatives, CpdX-D3, repress as efficiently as a synthetic glucocorticoid (e.g., Dexamethasone) an induced skin atopic dermatitis, an induced psoriasis-like inflammation, a house dust mite (HDM)-induced asthma-like allergic lung inflammation, a collagen-induced arthritis, an induced ulcerative colitis, and an ovalbumin-induced allergic conjunctivitis. Interestingly, in the cases of an HDM-induced asthma-like allergic lung inflammation and of a collagen-induced arthritis, the CpdX antiinflammatory activity was selectively exerted by one of the two CpdX enantiomers, namely, CpdX(eA) or CpdX-D3(eA).
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MESH Headings
- Animals
- Anti-Inflammatory Agents/chemistry
- Anti-Inflammatory Agents/pharmacology
- Arthritis, Experimental/drug therapy
- Arthritis, Experimental/genetics
- Arthritis, Experimental/pathology
- Asthma/drug therapy
- Asthma/genetics
- Asthma/pathology
- Conjunctivitis, Allergic/drug therapy
- Conjunctivitis, Allergic/genetics
- Conjunctivitis, Allergic/pathology
- Dermatitis, Atopic/chemically induced
- Dermatitis, Atopic/drug therapy
- Dermatitis, Atopic/genetics
- Dermatitis, Atopic/pathology
- Dexamethasone/pharmacology
- Disease Models, Animal
- Glucocorticoids/genetics
- Glucocorticoids/pharmacology
- Humans
- Inflammation/drug therapy
- Inflammation/genetics
- Inflammation/pathology
- Mice
- NF-kappa B/genetics
- Ovalbumin/toxicity
- Progestins/chemistry
- Progestins/pharmacology
- Receptors, Glucocorticoid/agonists
- Receptors, Glucocorticoid/chemistry
- Receptors, Glucocorticoid/genetics
- Skin/drug effects
- Skin/pathology
- Transcriptional Activation/drug effects
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Affiliation(s)
- Guoqiang Hua
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U1258, 67404 Illkirch, France
| | - Naimah Zein
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U1258, 67404 Illkirch, France
| | - François Daubeuf
- Laboratoire d'Innovation Thérapeutique, Unité Mixte de Recherche 7200, Faculté de Pharmacie, Centre National de la Recherche Scientifique-Université de Strasbourg, F-67400 Illkirch, France
| | - Pierre Chambon
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U1258, 67404 Illkirch, France;
- University of Strasbourg Institute for Advanced Study, 67404 Illkirch, France
- Collège de France, 67404 Illkirch, France
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121
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Timmermans S, Souffriau J, Libert C. A General Introduction to Glucocorticoid Biology. Front Immunol 2019; 10:1545. [PMID: 31333672 PMCID: PMC6621919 DOI: 10.3389/fimmu.2019.01545] [Citation(s) in RCA: 358] [Impact Index Per Article: 59.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 06/20/2019] [Indexed: 12/13/2022] Open
Abstract
Glucocorticoids (GCs) are steroid hormones widely used for the treatment of inflammation, autoimmune diseases, and cancer. To exert their broad physiological and therapeutic effects, GCs bind to the GC receptor (GR) which belongs to the nuclear receptor superfamily of transcription factors. Despite their success, GCs are hindered by the occurrence of side effects and glucocorticoid resistance (GCR). Increased knowledge on GC and GR biology together with a better understanding of the molecular mechanisms underlying the GC side effects and GCR are necessary for improved GC therapy development. We here provide a general overview on the current insights in GC biology with a focus on GC synthesis, regulation and physiology, role in inflammation inhibition, and on GR function and plasticity. Furthermore, novel and selective therapeutic strategies are proposed based on recently recognized distinct molecular mechanisms of the GR. We will explain the SEDIGRAM concept, which was launched based on our research results.
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Affiliation(s)
- Steven Timmermans
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jolien Souffriau
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Claude Libert
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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122
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Rudnizky S, Khamis H, Malik O, Squires AH, Meller A, Melamed P, Kaplan A. Single-molecule DNA unzipping reveals asymmetric modulation of a transcription factor by its binding site sequence and context. Nucleic Acids Res 2019; 46:1513-1524. [PMID: 29253225 PMCID: PMC5815098 DOI: 10.1093/nar/gkx1252] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/11/2017] [Indexed: 12/31/2022] Open
Abstract
Most functional transcription factor (TF) binding sites deviate from their ‘consensus’ recognition motif, although their sites and flanking sequences are often conserved across species. Here, we used single-molecule DNA unzipping with optical tweezers to study how Egr-1, a TF harboring three zinc fingers (ZF1, ZF2 and ZF3), is modulated by the sequence and context of its functional sites in the Lhb gene promoter. We find that both the core 9 bp bound to Egr-1 in each of the sites, and the base pairs flanking them, modulate the affinity and structure of the protein–DNA complex. The effect of the flanking sequences is asymmetric, with a stronger effect for the sequence flanking ZF3. Characterization of the dissociation time of Egr-1 revealed that a local, mechanical perturbation of the interactions of ZF3 destabilizes the complex more effectively than a perturbation of the ZF1 interactions. Our results reveal a novel role for ZF3 in the interaction of Egr-1 with other proteins and the DNA, providing insight on the regulation of Lhb and other genes by Egr-1. Moreover, our findings reveal the potential of small changes in DNA sequence to alter transcriptional regulation, and may shed light on the organization of regulatory elements at promoters.
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Affiliation(s)
- Sergei Rudnizky
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Hadeel Khamis
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Faculty of Physics, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Omri Malik
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Allison H Squires
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Amit Meller
- Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.,Faculty of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Philippa Melamed
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Ariel Kaplan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
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The glucocorticoid receptor agonistic modulators CpdX and CpdX-D3 do not generate the debilitating effects of synthetic glucocorticoids. Proc Natl Acad Sci U S A 2019; 116:14200-14209. [PMID: 31221758 DOI: 10.1073/pnas.1908264116] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Seventy years after the discovery of their anti-inflammatory properties, glucocorticoids (GCs) remain the mainstay treatment for major allergic and inflammatory disorders, such as atopic dermatitis, asthma, rheumatoid arthritis, colitis, and conjunctivitis, among others. However, their long-term therapeutical administration is limited by major debilitating side effects, e.g., skin atrophy, osteoporosis, Addison-like adrenal insufficiency, fatty liver, and type 2 diabetes syndrome, as well as growth inhibition in children. These undesirable side effects are mostly related to GC-induced activation of both the direct transactivation and the direct transrepression functions of the GC receptor (GR), whereas the activation of its GC-induced indirect tethered transrepression function results in beneficial anti-inflammatory effects. We have reported in the accompanying paper that the nonsteroidal compound CpdX as well as its deuterated form CpdX-D3 selectively activate the GR indirect transrepression function and are as effective as synthetic GCs at repressing inflammations generated in several mouse models of major pathologies. We now demonstrate that these CpdX compounds are bona fide selective GC receptor agonistic modulators (SEGRAMs) as none of the known GC-induced debilitating side effects were observed in the mouse upon 3-mo CpdX treatments. We notably report that, unlike that of GCs, the administration of CpdX to ovariectomized (OVX) mice does not induce a fatty liver nor type 2 diabetes, which indicates that CpdX could be used in postmenopausal women as an efficient "harmless" GC substitute.
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Penvose A, Keenan JL, Bray D, Ramlall V, Siggers T. Comprehensive study of nuclear receptor DNA binding provides a revised framework for understanding receptor specificity. Nat Commun 2019; 10:2514. [PMID: 31175293 PMCID: PMC6555819 DOI: 10.1038/s41467-019-10264-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 05/02/2019] [Indexed: 01/06/2023] Open
Abstract
The type II nuclear receptors (NRs) function as heterodimeric transcription factors with the retinoid X receptor (RXR) to regulate diverse biological processes in response to endogenous ligands and therapeutic drugs. DNA-binding specificity has been proposed as a primary mechanism for NR gene regulatory specificity. Here we use protein-binding microarrays (PBMs) to comprehensively analyze the DNA binding of 12 NR:RXRα dimers. We find more promiscuous NR-DNA binding than has been reported, challenging the view that NR binding specificity is defined by half-site spacing. We show that NRs bind DNA using two distinct modes, explaining widespread NR binding to half-sites in vivo. Finally, we show that the current models of NR specificity better reflect binding-site activity rather than binding-site affinity. Our rich dataset and revised NR binding models provide a framework for understanding NR regulatory specificity and will facilitate more accurate analyses of genomic datasets. The type II nuclear receptors (NRs) and the retinoid X receptor (RXR) form heterodimeric transcription factors to regulate development, metabolism, and inflammation. Here the authors employ protein-binding microarrays to comprehensively analyze the DNA binding of 12 NR:RXRα heterodimers, and report promiscuous NR-DNA binding.
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Affiliation(s)
- Ashley Penvose
- Department of Biology, Boston University, Boston, MA, 02215, USA.,Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Jessica L Keenan
- Biological Design Center, Boston University, Boston, MA, 02215, USA.,Bioinformatics Program, Boston University, Boston, MA, 02215, USA
| | - David Bray
- Biological Design Center, Boston University, Boston, MA, 02215, USA.,Bioinformatics Program, Boston University, Boston, MA, 02215, USA
| | - Vijendra Ramlall
- Department of Biology, Boston University, Boston, MA, 02215, USA.,Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Trevor Siggers
- Department of Biology, Boston University, Boston, MA, 02215, USA. .,Biological Design Center, Boston University, Boston, MA, 02215, USA. .,Bioinformatics Program, Boston University, Boston, MA, 02215, USA.
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125
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Lai X, Stigliani A, Vachon G, Carles C, Smaczniak C, Zubieta C, Kaufmann K, Parcy F. Building Transcription Factor Binding Site Models to Understand Gene Regulation in Plants. MOLECULAR PLANT 2019; 12:743-763. [PMID: 30447332 DOI: 10.1016/j.molp.2018.10.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/20/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
Transcription factors (TFs) are key cellular components that control gene expression. They recognize specific DNA sequences, the TF binding sites (TFBSs), and thus are targeted to specific regions of the genome where they can recruit transcriptional co-factors and/or chromatin regulators to fine-tune spatiotemporal gene regulation. Therefore, the identification of TFBSs in genomic sequences and their subsequent quantitative modeling is of crucial importance for understanding and predicting gene expression. Here, we review how TFBSs can be determined experimentally, how the TFBS models can be constructed in silico, and how they can be optimized by taking into account features such as position interdependence within TFBSs, DNA shape, and/or by introducing state-of-the-art computational algorithms such as deep learning methods. In addition, we discuss the integration of context variables into the TFBS modeling, including nucleosome positioning, chromatin states, methylation patterns, 3D genome architectures, and TF cooperative binding, in order to better predict TF binding under cellular contexts. Finally, we explore the possibilities of combining the optimized TFBS model with technological advances, such as targeted TFBS perturbation by CRISPR, to better understand gene regulation, evolution, and plant diversity.
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Affiliation(s)
- Xuelei Lai
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France.
| | - Arnaud Stigliani
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Gilles Vachon
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Cristel Carles
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Cezary Smaczniak
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Chloe Zubieta
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - François Parcy
- CNRS, Univ. Grenoble Alpes, CEA, INRA, BIG-LPCV, 38000 Grenoble, France.
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126
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Fischer C, Metsger M, Bauch S, Vidal R, Böttcher M, Grote P, Kliem M, Sauer S. Signals trigger state-specific transcriptional programs to support diversity and homeostasis in immune cells. Sci Signal 2019; 12:12/581/eaao5820. [DOI: 10.1126/scisignal.aao5820] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Macrophages play key roles in the immune systems of humans and other mammals. Here, we performed single-cell analyses of the mRNAs and proteins of human macrophages to compare their responses to the signaling molecules lipopolysaccharide (LPS), a component of Gram-negative bacteria, and palmitate (PAL), a free fatty acid. We found that, although both molecules signal through the cell surface protein Toll-like receptor 4 (TLR4), they stimulated the expression of different genes, resulting in specific pro- and anti-inflammatory cellular states for each signal. The effects of the glucocorticoid receptor, which antagonizes LPS signaling, and cyclic AMP–dependent transcription factor 3, which inhibits PAL-induced inflammation, on inflammatory response seemed largely determined by digital on-off events. Furthermore, the quantification of transcriptional variance and signaling entropy enabled the identification of cell state–specific deregulated molecular pathways. These data suggest that the preservation of signaling in distinct cells might confer diversity on macrophage populations essential to maintaining major cellular functions.
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127
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Enguix-Riego MDV, Cacicedo J, Delgado León BD, Nieto-Guerrero Gómez JM, Herrero Rivera D, Perez M, Praena-Fernández JM, Sanchez Carmona G, Rivin Del Campo E, Ortiz Gordillo MJ, Lopez Guerra JL. The single nucleotide variant rs2868371 associates with the risk of mortality in non-small cell lung cancer patients: A multicenter prospective validation. Radiother Oncol 2019; 136:29-36. [PMID: 31015126 DOI: 10.1016/j.radonc.2019.03.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/23/2019] [Accepted: 03/26/2019] [Indexed: 11/16/2022]
Abstract
BACKGROUND AND PURPOSE Definitive radiation therapy (RT) with or without chemotherapy has become the standard treatment for non-metastatic unresectable non-small cell lung cancer (NSCLC). However, treatment outcomes can differ substantially and patients' genetic background could play a crucial role. Potential associations between single-nucleotide polymorphisms (SNP) in Heat shock protein beta-1 (HSPB1) and survival have been reported in prior single-institution retrospective reports. MATERIALS AND METHODS The current assay aims to validate such connection in a prospective multicenter study in a European cohort including 181 NSCLC patients. Median follow-up time for all patients was 13 months (range, 3-57 months). RESULTS The results obtained show an association between the rs2868371 GG genotype and better overall survival (HR: 0.35; 95%CI: 0.13-0.96; p = 0.042) in multivariate analysis. Two-year overall survival rate was 72% for patients carrying the rs2868371 GG genotype versus 36% for those patients harboring the rs2868371 CC/CG genotypes (p = 0.013). Additionally, the rs2868371 GG genotype was found to be associated with better disease-free survival in the multivariate analysis (HR: 0.36; 95%CI: 0.13-0.99; p = 0.048). In silico analysis of the potential functional SNP suggested significant difference in the affinity of the Glucocorticoid Receptor binding site between alternative allelic variants, confirmed by chromatin immunoprecipitation analysis displaying stronger affinity for the risk allele (C). Furthermore, our findings indicate that the rs2868371 influences (mRNA) HSPB1 expression, offering insight into the regulation of HSPB1 transcription. CONCLUSION The functional HSPB1 rs2868371 promoter variant may affect lung cancer survival by regulation of HSPB1 expression levels through glucocorticoid receptor interaction.
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Affiliation(s)
- María Del Valle Enguix-Riego
- Department of Radiation Oncology, University Hospital Virgen del Rocío, Seville, Spain; Instituto de Biomedicina de Sevilla (IBIS/HUVR/CSIC/Universidad de Sevilla), Spain
| | - Jon Cacicedo
- Departament of Radiation Oncology, Cruces University Hospital, Barakaldo, Spain
| | | | | | - Daniel Herrero Rivera
- Department of Medical Oncology, University Hospital Virgen del Rocío, Seville, Spain
| | - Marco Perez
- Instituto de Biomedicina de Sevilla (IBIS/HUVR/CSIC/Universidad de Sevilla), Spain
| | | | | | | | - María José Ortiz Gordillo
- Department of Radiation Oncology, University Hospital Virgen del Rocío, Seville, Spain; Instituto de Biomedicina de Sevilla (IBIS/HUVR/CSIC/Universidad de Sevilla), Spain
| | - Jose Luis Lopez Guerra
- Department of Radiation Oncology, University Hospital Virgen del Rocío, Seville, Spain; Instituto de Biomedicina de Sevilla (IBIS/HUVR/CSIC/Universidad de Sevilla), Spain.
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128
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Meijer FA, Leijten-van de Gevel IA, de Vries RMJM, Brunsveld L. Allosteric small molecule modulators of nuclear receptors. Mol Cell Endocrinol 2019; 485:20-34. [PMID: 30703487 DOI: 10.1016/j.mce.2019.01.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/23/2019] [Accepted: 01/25/2019] [Indexed: 02/08/2023]
Abstract
Nuclear Receptors (NRs) are multi-domain proteins, whose natural regulation occurs via ligands for a classical, orthosteric, binding pocket and via intra- and inter-domain allosteric mechanisms. Allosteric modulation of NRs via synthetic small molecules has recently emerged as an interesting entry to address the need for small molecules targeting NRs in pathology, via novel modes of action and with beneficial profiles. In this review the general concept of allosteric modulation in drug discovery is first discussed, serving as a background and inspiration for NRs. Subsequently, the review focuses on examples of small molecules that allosterically modulate NRs, with a strong focus on structural information and the ligand binding domain. Recently discovered nanomolar potent allosteric site NR modulators are catapulting allosteric targeting of NRs to the center of attention. The obtained insights serve as a basis for recommendations for the next steps to take in allosteric small molecular targeting of NRs.
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Affiliation(s)
- Femke A Meijer
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Iris A Leijten-van de Gevel
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Rens M J M de Vries
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands.
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129
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Okafor CD, Colucci JK, Ortlund EA. Ligand-Induced Allosteric Effects Governing SR Signaling. NUCLEAR RECEPTOR RESEARCH 2019. [DOI: 10.32527/2019/101382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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130
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Thormann V, Glaser LV, Rothkegel MC, Borschiwer M, Bothe M, Fuchs A, Meijsing SH. Expanding the repertoire of glucocorticoid receptor target genes by engineering genomic response elements. Life Sci Alliance 2019; 2:2/2/e201800283. [PMID: 30867223 PMCID: PMC6417287 DOI: 10.26508/lsa.201800283] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/05/2019] [Accepted: 03/05/2019] [Indexed: 01/25/2023] Open
Abstract
This study shows that addition of a single transcription factor binding site can be sufficient to convert a gene into a glucocorticoid receptor target. The glucocorticoid receptor (GR), a hormone-activated transcription factor, binds to a myriad of genomic binding sites yet seems to regulate a much smaller number of genes. Genome-wide analysis of GR binding and gene regulation has shown that the likelihood of GR-dependent regulation increases with decreased distance of its binding to the transcriptional start site of a gene. To test if we can adopt this knowledge to expand the repertoire of GR target genes, we used CRISPR/Cas-mediated homology-directed repair to add a single GR-binding site directly upstream of the transcriptional start site of each of four genes. To our surprise, we found that the addition of a single GR-binding site can be enough to convert a gene into a GR target. The gain of GR-dependent regulation was observed for two of four genes analyzed and coincided with acquired GR binding at the introduced binding site. However, the gene-specific gain of GR-dependent regulation could not be explained by obvious differences in chromatin accessibility between converted genes and their non-converted counterparts. Furthermore, by introducing GR-binding sequences with different nucleotide compositions, we show that activation can be facilitated by distinct sequences without obvious differences in activity between the GR-binding sequence variants we tested. The approach to use genome engineering to build genomic response elements facilitates the generation of cell lines with tailored repertoires of GR-responsive genes and a framework to test and refine our understanding of the cis-regulatory logic of gene regulation by testing if engineered response elements behave as predicted.
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Affiliation(s)
- Verena Thormann
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Laura V Glaser
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | | | - Melissa Bothe
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alisa Fuchs
- Max Planck Institute for Molecular Genetics, Berlin, Germany
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131
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Monczor F, Chatzopoulou A, Zappia CD, Houtman R, Meijer OC, Fitzsimons CP. A Model of Glucocorticoid Receptor Interaction With Coregulators Predicts Transcriptional Regulation of Target Genes. Front Pharmacol 2019; 10:214. [PMID: 30930776 PMCID: PMC6425864 DOI: 10.3389/fphar.2019.00214] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/20/2019] [Indexed: 12/14/2022] Open
Abstract
Regulatory factors that control gene transcription in multicellular organisms are assembled in multicomponent complexes by combinatorial interactions. In this context, nuclear receptors provide well-characterized and physiologically relevant systems to study ligand-induced transcription resulting from the integration of cellular and genomic information in a cell- and gene-specific manner. Here, we developed a mathematical model describing the interactions between the glucocorticoid receptor (GR) and other components of a multifactorial regulatory complex controlling the transcription of GR-target genes, such as coregulator peptides. We support the validity of the model in relation to gene-specific GR transactivation with gene transcription data from A549 cells and in vitro real time quantification of coregulator-GR interactions. The model accurately describes and helps to interpret ligand-specific and gene-specific transcriptional regulation by the GR. The comprehensive character of the model allows future insight into the function and relative contribution of the molecular species proposed in ligand- and gene-specific transcriptional regulation.
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Affiliation(s)
- Federico Monczor
- Laboratorio de Farmacología de Receptores, Instituto de Investigaciones Farmacológicas, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Antonia Chatzopoulou
- Leiden Academic Center for Drug Research, Leiden University, Leiden, Netherlands
| | - Carlos Daniel Zappia
- Laboratorio de Farmacología de Receptores, Instituto de Investigaciones Farmacológicas, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - René Houtman
- PamGene International B.V., 's-Hertogenbosch, Netherlands
| | - Onno C Meijer
- Division of Endocrinology, Department of Internal Medicine, Leiden University Medical Centre, Leiden, Netherlands
| | - Carlos P Fitzsimons
- Neuroscience Collaboration, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
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Wang C, Nanni L, Novakovic B, Megchelenbrink W, Kuznetsova T, Stunnenberg HG, Ceri S, Logie C. Extensive epigenomic integration of the glucocorticoid response in primary human monocytes and in vitro derived macrophages. Sci Rep 2019; 9:2772. [PMID: 30809020 PMCID: PMC6391480 DOI: 10.1038/s41598-019-39395-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 01/22/2019] [Indexed: 12/12/2022] Open
Abstract
Glucocorticoid receptor is a transcription factor that is ubiquitously expressed. Glucocorticoids are circadian steroids that regulate a wide range of bodily functions, including immunity. Here we report that synthetic glucocorticoids affect 1035 mRNAs in isolated healthy human blood monocytes but only 165 in the respective six day-old monocyte-derived macrophages. The majority of the glucocorticoid response in monocytes concerns genes that are dynamic upon monocyte to macrophage differentiation, whereby macrophage-like mRNA levels are often reached in monocytes within four hours of treatment. Concomitantly, over 5000 chromosomal H3K27ac regions undergo remodelling, of which 60% involve increased H3K27ac signal. We find that chromosomal glucocorticoid receptor binding sites correlate with positive but not with negative local epigenomic effects. To investigate further we assigned our data to topologically associating domains (TADs). This shows that about 10% of macrophage TADs harbour at least one GR binding site and that half of all the glucocorticoid-induced H3K27ac regions are confined to these TADs. Our analyses are therefore consistent with the notion that TADs naturally accommodate information from sets of distal glucocorticoid response elements.
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Affiliation(s)
- Cheng Wang
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science Radboud University, PO box 9101, 6500 HG, Nijmegen, The Netherlands
| | - Luca Nanni
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy
| | - Boris Novakovic
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science Radboud University, PO box 9101, 6500 HG, Nijmegen, The Netherlands
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Wout Megchelenbrink
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science Radboud University, PO box 9101, 6500 HG, Nijmegen, The Netherlands
| | - Tatyana Kuznetsova
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science Radboud University, PO box 9101, 6500 HG, Nijmegen, The Netherlands
- Department of Medical Biochemistry, Academic Medical Centre of the University of Amsterdam, Amsterdam, The Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science Radboud University, PO box 9101, 6500 HG, Nijmegen, The Netherlands
| | - Stefano Ceri
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy
| | - Colin Logie
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science Radboud University, PO box 9101, 6500 HG, Nijmegen, The Netherlands.
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Mosure SA, Shang J, Eberhardt J, Brust R, Zheng J, Griffin PR, Forli S, Kojetin DJ. Structural Basis of Altered Potency and Efficacy Displayed by a Major in Vivo Metabolite of the Antidiabetic PPARγ Drug Pioglitazone. J Med Chem 2019; 62:2008-2023. [PMID: 30676741 PMCID: PMC6898968 DOI: 10.1021/acs.jmedchem.8b01573] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Pioglitazone (Pio) is a Food and Drug Administration-approved drug for type-2 diabetes that binds and activates the nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ), yet it remains unclear how in vivo Pio metabolites affect PPARγ structure and function. Here, we present a structure-function comparison of Pio and its most abundant in vivo metabolite, 1-hydroxypioglitazone (PioOH). PioOH displayed a lower binding affinity and reduced potency in co-regulator recruitment assays. X-ray crystallography and molecular docking analysis of PioOH-bound PPARγ ligand-binding domain revealed an altered hydrogen bonding network, including the formation of water-mediated bonds, which could underlie its altered biochemical phenotype. NMR spectroscopy and hydrogen/deuterium exchange mass spectrometry analysis coupled to activity assays revealed that PioOH better stabilizes the PPARγ activation function-2 (AF-2) co-activator binding surface and better enhances co-activator binding, affording slightly better transcriptional efficacy. These results indicating that Pio hydroxylation affects its potency and efficacy as a PPARγ agonist contributes to our understanding of PPARγ-drug metabolite interactions.
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Affiliation(s)
| | | | - Jerome Eberhardt
- Department of Integrative Structural and Computational Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
| | | | | | | | - Stefano Forli
- Department of Integrative Structural and Computational Biology , The Scripps Research Institute , La Jolla , California 92037 , United States
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Osz J, McEwen AG, Wolf J, Poussin-Courmontagne P, Peluso-Iltis C, Chebaro Y, Kieffer B, Rochel N. Modulation of RXR-DNA complex assembly by DNA context. Mol Cell Endocrinol 2019; 481:44-52. [PMID: 30476562 DOI: 10.1016/j.mce.2018.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/15/2018] [Accepted: 11/22/2018] [Indexed: 01/16/2023]
Abstract
Retinoid X Receptors (RXRs) act as dimer partners for several nuclear receptors including itself, binding to genomic DNA response elements and regulating gene transcription with cell and gene specificity. As homodimers, RXRs bind direct repeats of the half-site (A/G)G(G/T)TCA separated by 1 nucleotide (DR1) and little variability of this consensus site is observed for natural DR1s. However, these variations are responsible of the modulation of RXR receptors function through differential binding affinity and conformational changes. To further our understanding of the molecular mechanisms underlying RXR-DNA interactions, we examined how RXR DBDs bind to different DR1s using thermodynamics, X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. We show that the half-site sequences modulate the binding cooperativity that results from the protein-protein contacts between the two DBDs. Chemical shifts perturbation NMR experiments revealed that sequence variations in half-sites induce changes that propagate from the protein-DNA interface to the dimerization interface throughout the DBD fold.
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Affiliation(s)
- Judit Osz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM), U1258/Centre National de la Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, 67404, Illkirch, France
| | - Alastair G McEwen
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM), U1258/Centre National de la Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, 67404, Illkirch, France
| | - Justine Wolf
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM), U1258/Centre National de la Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, 67404, Illkirch, France
| | - Pierre Poussin-Courmontagne
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM), U1258/Centre National de la Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, 67404, Illkirch, France
| | - Carole Peluso-Iltis
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM), U1258/Centre National de la Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, 67404, Illkirch, France
| | - Yassmine Chebaro
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM), U1258/Centre National de la Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, 67404, Illkirch, France
| | - Bruno Kieffer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM), U1258/Centre National de la Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, 67404, Illkirch, France.
| | - Natacha Rochel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM), U1258/Centre National de la Recherche Scientifique (CNRS), UMR7104/Université de Strasbourg, 67404, Illkirch, France.
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Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT. The Human Transcription Factors. Cell 2019; 172:650-665. [PMID: 29425488 DOI: 10.1016/j.cell.2018.01.029] [Citation(s) in RCA: 1873] [Impact Index Per Article: 312.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 01/15/2018] [Accepted: 01/22/2018] [Indexed: 12/13/2022]
Abstract
Transcription factors (TFs) recognize specific DNA sequences to control chromatin and transcription, forming a complex system that guides expression of the genome. Despite keen interest in understanding how TFs control gene expression, it remains challenging to determine how the precise genomic binding sites of TFs are specified and how TF binding ultimately relates to regulation of transcription. This review considers how TFs are identified and functionally characterized, principally through the lens of a catalog of over 1,600 likely human TFs and binding motifs for two-thirds of them. Major classes of human TFs differ markedly in their evolutionary trajectories and expression patterns, underscoring distinct functions. TFs likewise underlie many different aspects of human physiology, disease, and variation, highlighting the importance of continued effort to understand TF-mediated gene regulation.
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Affiliation(s)
- Samuel A Lambert
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Arttu Jolma
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Laura F Campitelli
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Pratyush K Das
- Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland
| | - Yimeng Yin
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Mihai Albu
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jussi Taipale
- Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland; Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden; Department of Biochemistry, Cambridge University, Cambridge CB2 1GA, United Kingdom.
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Donnelly Centre, University of Toronto, Toronto, ON, Canada.
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.
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136
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Keizer VIP, Coppola S, Houtsmuller AB, Geverts B, van Royen ME, Schmidt T, Schaaf MJM. Repetitive switching between DNA binding modes enables target finding by the glucocorticoid receptor. J Cell Sci 2019; 132:jcs.217455. [DOI: 10.1242/jcs.217455] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 01/16/2019] [Indexed: 12/21/2022] Open
Abstract
Transcription factor mobility is a determining factor in the regulation of gene expression. Here, we have studied the intranuclear dynamics of the glucocorticoid receptor (GR) using fluorescence recovery after photobleaching and single-molecule microscopy. First we have described the dynamic states in which the GR occurs. Subsequently we have analyzed the transitions between these states using a continuous time Markov chain model, and functionally investigated these states by making specific mutations in the DNA-binding domain. This analysis revealed that the GR diffuses freely through the nucleus, and once it leaves this free diffusion state it most often enters a repetitive switching mode. In this mode it alternates between slow diffusion as a result of brief nonspecific DNA binding events, and a state of stable binding to specific DNA target sites. This repetitive switching mechanism results in a compact searching strategy which facilitates finding DNA target sites by the GR.
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Affiliation(s)
| | - Stefano Coppola
- Institute of Physics, Leiden University, Leiden, The Netherlands
| | - Adriaan B. Houtsmuller
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
- Erasmus Optical Imaging Center, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bart Geverts
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
- Erasmus Optical Imaging Center, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Martin E. van Royen
- Department of Pathology, Erasmus Medical Center, Rotterdam, The Netherlands
- Erasmus Optical Imaging Center, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Thomas Schmidt
- Institute of Physics, Leiden University, Leiden, The Netherlands
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137
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Fuller PJ, Yang J, Young MJ. Mechanisms of Mineralocorticoid Receptor Signaling. VITAMINS AND HORMONES 2019; 109:37-68. [DOI: 10.1016/bs.vh.2018.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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138
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Schöne S, Bothe M, Einfeldt E, Borschiwer M, Benner P, Vingron M, Thomas-Chollier M, Meijsing SH. Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise. PLoS Genet 2018; 14:e1007793. [PMID: 30427832 PMCID: PMC6261644 DOI: 10.1371/journal.pgen.1007793] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 11/28/2018] [Accepted: 10/26/2018] [Indexed: 12/29/2022] Open
Abstract
The binding of transcription factors to short recognition sequences plays a pivotal role in controlling the expression of genes. The sequence and shape characteristics of binding sites influence DNA binding specificity and have also been implicated in modulating the activity of transcription factors downstream of binding. To quantitatively assess the transcriptional activity of tens of thousands of designed synthetic sites in parallel, we developed a synthetic version of STARR-seq (synSTARR-seq). We used the approach to systematically analyze how variations in the recognition sequence of the glucocorticoid receptor (GR) affect transcriptional regulation. Our approach resulted in the identification of a novel highly active functional GR binding sequence and revealed that sequence variation both within and flanking GR’s core binding site can modulate GR activity without apparent changes in DNA binding affinity. Notably, we found that the sequence composition of variants with similar activity profiles was highly diverse. In contrast, groups of variants with similar activity profiles showed specific DNA shape characteristics indicating that DNA shape may be a better predictor of activity than DNA sequence. Finally, using single cell experiments with individual enhancer variants, we obtained clues indicating that the architecture of the response element can independently tune expression mean and cell-to cell variability in gene expression (noise). Together, our studies establish synSTARR as a powerful method to systematically study how DNA sequence and shape modulate transcriptional output and noise. The expression level of genes is controlled by transcription factors, which are proteins that bind to genomic response elements that contain their recognition DNA sequence. Importantly, genes are not simply turned on but need to be expressed at the right level. This is, at least in part, assured by the sequence composition of genomic response elements. Here, we studied how the recognition DNA sequence influences gene regulation by a transcription factor called the glucocorticoid receptor. Specifically, we developed a method to test the activity of variants in a highly parallelized setting where everything is kept identical except for the sequence of the binding site. The systematic analysis of tens of thousands of sequence variants facilitated the identification of a previously unknown sequence variant with high activity. Moreover, we report how sequence variation of the response element influences cell-to-cell variability in expression levels. Finally, we observe similar activity profiles for distinct sequence variants that share similar three-dimensional DNA shape characteristics arguing that the three-dimensional perception of DNA by the glucocorticoid receptor, modulates its activity towards individual target genes.
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Affiliation(s)
- Stefanie Schöne
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Melissa Bothe
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Edda Einfeldt
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Philipp Benner
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Morgane Thomas-Chollier
- Institut de biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
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139
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Weikum ER, Liu X, Ortlund EA. The nuclear receptor superfamily: A structural perspective. Protein Sci 2018; 27:1876-1892. [PMID: 30109749 PMCID: PMC6201731 DOI: 10.1002/pro.3496] [Citation(s) in RCA: 299] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/01/2018] [Accepted: 08/06/2018] [Indexed: 12/28/2022]
Abstract
Nuclear receptors (NRs) are a family of transcription factors that regulate numerous physiological processes such as metabolism, reproduction, inflammation, as well as the circadian rhythm. NRs sense changes in lipid metabolite levels to drive differential gene expression, producing distinct physiologic effects. This is an allosteric process whereby binding a cognate ligand and specific DNA sequences drives the recruitment of diverse transcriptional co-regulators at chromatin and ultimately transactivation or transrepression of target genes. Dysregulation of NR signaling leads to various malignances, metabolic disorders, and inflammatory disease. Given their important role in physiology and ability to respond to small lipophilic ligands, NRs have emerged as valuable therapeutic targets. Here, we summarize and discuss the recent progress on understanding the complex mechanism of action of NRs, primarily from a structural perspective. Finally, we suggest future studies to improve our understanding of NR signaling and better design drugs by integrating multiple structural and biophysical approaches.
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Affiliation(s)
- Emily R. Weikum
- Department of BiochemistryEmory School of MedicineAtlanta30322Georgia
| | - Xu Liu
- Department of BiochemistryEmory School of MedicineAtlanta30322Georgia
| | - Eric A. Ortlund
- Department of BiochemistryEmory School of MedicineAtlanta30322Georgia
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140
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Li J, Hilser VJ. Assessing Allostery in Intrinsically Disordered Proteins With Ensemble Allosteric Model. Methods Enzymol 2018; 611:531-557. [PMID: 30471699 DOI: 10.1016/bs.mie.2018.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Intrinsically disordered (ID) proteins have been shown to play a major role in signaling in a broad range of proteins, using a process known as allostery, wherein the protein can integrate one or a number of inputs to regulate its function. The disorder-mediated allostery can be understood energetically with ensemble allosteric model (EAM). In this model, the molecule without effectors is considered as an ensemble of preexisting conformations, and effector binding is treated as an energetic perturbation of the ensemble to redistribute the microstates that are favorable or unfavorable to the second binding partner. As it only considers the intrinsic energetics of the system and does not depend on a crystallographic structure, it can be applied to both structured proteins, ID proteins, and mixed proteins with both structured and ID domains. Simulation with EAM on the basis of experimental data can help quantitatively explain experimental observations, as well as to make predictions to direct future research. This has recently been illustrated with the case of human glucocorticoid receptor, a multidomain transcription factor that contains both structured and disordered regions. In this chapter, we describe the assays for measuring the transcriptional activity, binding affinity to cognate DNA, conformational stability, either on single domain or tandem coupled domains in the GR two-domain isoforms. We then explain how these data are utilized as input parameters or constraints in the EAM for quantitative estimates of stabilities and coupling energies for each domain through global minimization method.
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Affiliation(s)
- Jing Li
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States
| | - Vincent J Hilser
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States; Department of Biology, Johns Hopkins University, Baltimore, MD, United States.
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141
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Glucocorticoids Induce Stress Oncoproteins Associated with Therapy-Resistance in African American and European American Prostate Cancer Cells. Sci Rep 2018; 8:15063. [PMID: 30305646 PMCID: PMC6180116 DOI: 10.1038/s41598-018-33150-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 09/19/2018] [Indexed: 12/22/2022] Open
Abstract
Glucocorticoid receptor (GR) is emerging as a key driver of prostate cancer (PCa) progression and therapy resistance in the absence of androgen receptor (AR) signaling. Acting as a bypass mechanism, GR activates AR-regulated genes, although GR-target genes contributing to PCa therapy resistance remain to be identified. Emerging evidence also shows that African American (AA) men, who disproportionately develop aggressive PCa, have hypersensitive GR signaling linked to cumulative stressful life events. Using racially diverse PCa cell lines (MDA-PCa-2b, 22Rv1, PC3, and DU145) we examined the effects of glucocorticoids on the expression of two stress oncoproteins associated with PCa therapy resistance, Clusterin (CLU) and Lens Epithelium-Derived Growth Factor p75 (LEDGF/p75). We observed that glucocorticoids upregulated LEDGF/p75 and CLU in PCa cells. Blockade of GR activation abolished this upregulation. We also detected increased GR transcript expression in AA PCa tissues, compared to European American (EA) tissues, using Oncomine microarray datasets. These results demonstrate that glucocorticoids upregulate the therapy resistance-associated oncoproteins LEDGF/p75 and CLU, and suggest that this effect may be enhanced in AA PCa. This study provides an initial framework for understanding the contribution of glucocorticoid signaling to PCa health disparities.
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142
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Meijer OC, Buurstede JC, Schaaf MJM. Corticosteroid Receptors in the Brain: Transcriptional Mechanisms for Specificity and Context-Dependent Effects. Cell Mol Neurobiol 2018; 39:539-549. [PMID: 30291573 PMCID: PMC6469829 DOI: 10.1007/s10571-018-0625-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/25/2018] [Indexed: 12/22/2022]
Abstract
Corticosteroid hormones act in the brain to support adaptation to stress via binding to mineralocorticoid and glucocorticoid receptors (MR and GR). These receptors act in large measure as transcription factors. Corticosteroid effects can be highly divergent, depending on the receptor type, but also on brain region, cell type, and physiological context. These differences ultimately depend on differential interactions of MR and GR with other proteins, which determine ligand binding, nuclear translocation, and transcriptional activities. In this review, we discuss established and potential mechanisms that confer receptor and cell type-specific effects of the MR and GR-mediated transcriptional effects in the brain.
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Affiliation(s)
- Onno C Meijer
- Division of Endocrinology, Department of Medicine, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands. .,Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands.
| | - J C Buurstede
- Division of Endocrinology, Department of Medicine, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands.,Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Marcel J M Schaaf
- Department of Animal Sciences and Health (M.J.M.S.), Institute of Biology, Leiden University, 2333 CC, Leiden, The Netherlands
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143
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Spaanderman DCE, Nixon M, Buurstede JC, Sips HC, Schilperoort M, Kuipers EN, Backer EA, Kooijman S, Rensen PCN, Homer NZM, Walker BR, Meijer OC, Kroon J. Androgens modulate glucocorticoid receptor activity in adipose tissue and liver. J Endocrinol 2018; 240:JOE-18-0503.R1. [PMID: 30400038 DOI: 10.1530/joe-18-0503] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/04/2018] [Indexed: 12/16/2022]
Abstract
Glucocorticoid signaling is context-dependent, and in certain scenarios glucocorticoid receptors (GR) are able to engage with other members of the nuclear receptor subfamily. Glucocorticoid signaling can exert sexually dimorphic effects, suggesting a possible interaction with androgen sex hormones. We therefore set out to determine the crosstalk between glucocorticoids and androgens in metabolic tissues including white adipose tissue, liver and brown adipose tissue. Thereto we exposed male C57BL/6J mice to elevated levels of corticosterone in combination with an androgen receptor (AR) agonist or an AR antagonist. Systemic and local glucocorticoid levels were determined by mass spectrometry, tissue expression of glucocorticoid-responsive genes and protein was measured by RT-qPCR and Western blot, respectively. To evaluate crosstalk in vitro, cultured white and brown adipocytes were exposed to a combination of corticosterone and an androgen agonist. We found that AR agonism potentiated transcriptional response to GR in vitro in white and brown adipocytes and in vivo in white and brown adipose tissue. Conversely, AR antagonism substantially attenuated glucocorticoid signaling in white adipose tissue and liver. In white adipose tissue this effect could partially be attributed to decreased 11B-hydroxysteroid dehydrogenase type 1-mediated glucocorticoid regeneration upon AR antagonism. In liver, attenuated GR activity was independent of active glucocorticoid ligand levels. We conclude that androgen signaling modulates GR transcriptional output in a tissue-specific manner.
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Affiliation(s)
- Dieuwertje C E Spaanderman
- D Spaanderman, Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, Netherlands
| | - Mark Nixon
- M Nixon, BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom of Great Britain and Northern Ireland
| | - Jacobus C Buurstede
- J Buurstede, Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, Netherlands
| | - Hetty Cm Sips
- H Sips, Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, Netherlands
| | - Maaike Schilperoort
- M Schilperoort, Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, Netherlands
| | - Eline N Kuipers
- E Kuipers, Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, Netherlands
| | - Emma A Backer
- E Backer, Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, Netherlands
| | - Sander Kooijman
- S Kooijman, Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, Netherlands
| | - Patrick C N Rensen
- P Rensen, Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, Netherlands
| | - Natalie Z M Homer
- N Homer, BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom of Great Britain and Northern Ireland
| | - Brian R Walker
- B Walker, BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom of Great Britain and Northern Ireland
| | - Onno C Meijer
- O Meijer, Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, Netherlands
| | - Jan Kroon
- J Kroon, Urology, Leiden University Medical Center, Leiden, 2333ZA, Netherlands
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144
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Niu B, Coslo DM, Bataille AR, Albert I, Pugh BF, Omiecinski CJ. In vivo genome-wide binding interactions of mouse and human constitutive androstane receptors reveal novel gene targets. Nucleic Acids Res 2018; 46:8385-8403. [PMID: 30102401 PMCID: PMC6144799 DOI: 10.1093/nar/gky692] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/17/2018] [Accepted: 07/20/2018] [Indexed: 12/13/2022] Open
Abstract
The constitutive androstane receptor (CAR; NR1I3) is a nuclear receptor orchestrating complex roles in cell and systems biology. Species differences in CAR's effector pathways remain poorly understood, including its role in regulating liver tumor promotion. We developed transgenic mouse models to assess genome-wide binding of mouse and human CAR, following receptor activation in liver with direct ligands and with phenobarbital, an indirect CAR activator. Genomic interaction profiles were integrated with transcriptional and biological pathway analyses. Newly identified CAR target genes included Gdf15 and Foxo3, important regulators of the carcinogenic process. Approximately 1000 genes exhibited differential binding interactions between mouse and human CAR, including the proto-oncogenes, Myc and Ikbke, which demonstrated preferential binding by mouse CAR as well as mouse CAR-selective transcriptional enhancement. The ChIP-exo analyses also identified distinct binding motifs for the respective mouse and human receptors. Together, the results provide new insights into the important roles that CAR contributes as a key modulator of numerous signaling pathways in mammalian organisms, presenting a genomic context that specifies species variation in biological processes under CAR's control, including liver cell proliferation and tumor promotion.
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Affiliation(s)
- Ben Niu
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Denise M Coslo
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Alain R Bataille
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Istvan Albert
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - B Franklin Pugh
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Curtis J Omiecinski
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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145
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Frank F, Okafor CD, Ortlund EA. The first crystal structure of a DNA-free nuclear receptor DNA binding domain sheds light on DNA-driven allostery in the glucocorticoid receptor. Sci Rep 2018; 8:13497. [PMID: 30201977 PMCID: PMC6131172 DOI: 10.1038/s41598-018-31812-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/22/2018] [Indexed: 12/05/2022] Open
Abstract
The glucocorticoid receptor (GR) is a steroid hormone receptor of the nuclear receptor family that regulates gene expression in response to glucocorticoid hormone signaling. Interaction with specific GR DNA binding sequences causes conformational changes in the GR DNA binding domain (DBD) that result in recruitment of specific sets of co-regulators that determine transcriptional outcomes. We have solved the crystal structure of GR DBD in its DNA-free state, the first such crystal structure from any nuclear receptor. In contrast to previous NMR structures, this crystal structure reveals that free GR DBD adopts a conformation very similar to DNA-bound states. The lever arm region is the most variable element in the free GR DBD. Molecular dynamics of the free GR DBD as well as GR DBD bound to activating and repressive DNA elements confirm lever arm flexibility in all functional states. Cluster analysis of lever arm conformations during simulations shows that DNA binding and dimerization cause a reduction in the number of conformations sampled by the lever arm. These results reveal that DNA binding and dimerization drive conformational selection in the GR DBD lever arm region and show how DNA allosterically controls GR structure and dynamics.
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Affiliation(s)
- Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - C Denise Okafor
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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146
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Vincent BJ, Staller MV, Lopez-Rivera F, Bragdon MDJ, Pym ECG, Biette KM, Wunderlich Z, Harden TT, Estrada J, DePace AH. Hunchback is counter-repressed to regulate even-skipped stripe 2 expression in Drosophila embryos. PLoS Genet 2018; 14:e1007644. [PMID: 30192762 PMCID: PMC6145585 DOI: 10.1371/journal.pgen.1007644] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 09/19/2018] [Accepted: 08/17/2018] [Indexed: 01/18/2023] Open
Abstract
Hunchback is a bifunctional transcription factor that can activate and repress gene expression in Drosophila development. We investigated the regulatory DNA sequence features that control Hunchback function by perturbing enhancers for one of its target genes, even-skipped (eve). While Hunchback directly represses the eve stripe 3+7 enhancer, we found that in the eve stripe 2+7 enhancer, Hunchback repression is prevented by nearby sequences-this phenomenon is called counter-repression. We also found evidence that Caudal binding sites are responsible for counter-repression, and that this interaction may be a conserved feature of eve stripe 2 enhancers. Our results alter the textbook view of eve stripe 2 regulation wherein Hb is described as a direct activator. Instead, to generate stripe 2, Hunchback repression must be counteracted. We discuss how counter-repression may influence eve stripe 2 regulation and evolution.
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Affiliation(s)
- Ben J. Vincent
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Max V. Staller
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Francheska Lopez-Rivera
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Meghan D. J. Bragdon
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Edward C. G. Pym
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kelly M. Biette
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Zeba Wunderlich
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Timothy T. Harden
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Javier Estrada
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Angela H. DePace
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
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147
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Souffriau J, Eggermont M, Van Ryckeghem S, Van Looveren K, Van Wyngene L, Van Hamme E, Vuylsteke M, Beyaert R, De Bosscher K, Libert C. A screening assay for Selective Dimerizing Glucocorticoid Receptor Agonists and Modulators (SEDIGRAM) that are effective against acute inflammation. Sci Rep 2018; 8:12894. [PMID: 30150712 PMCID: PMC6110732 DOI: 10.1038/s41598-018-31150-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 08/13/2018] [Indexed: 02/07/2023] Open
Abstract
It has been suggested that glucocorticoid receptor (GR) agonists that promote GR homodimerization more than standard glucocorticoids such as Dexamethasone could be more effective anti-inflammatory molecules against acute and life-threatening inflammatory conditions. To test this hypothesis, we set up a screening pipeline aimed at discovering such Selective Dimerizing GR Agonists and Modulators (SEDIGRAM). The pipeline consists of a reporter gene assay based on a palindromic glucocorticoid responsive element (GRE). This assay represents GR dimerization in human A549 lung epithelial cells. In the pipeline, this is followed by analysis of endogenous GRE-driven gene expression, a FRET assay confirming dimerization, and monitoring of in vitro and in vivo anti-inflammatory activity. In a proof of principle experiment, starting from seven candidate compounds, we identified two potentially interesting compounds (Cortivazol and AZD2906) that confer strong protection in a mouse model of aggressive TNF-induced lethal inflammation. A screening pipeline for SEDIGRAM may assist the search for compounds that promote GR dimerization and limit overwhelming acute inflammatory responses.
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Affiliation(s)
- Jolien Souffriau
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Melanie Eggermont
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Sara Van Ryckeghem
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Kelly Van Looveren
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Lise Van Wyngene
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Evelien Van Hamme
- Bio Imaging Core, Center for Inflammation Research, VIB, Ghent, Belgium
| | | | - Rudi Beyaert
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Karolien De Bosscher
- Receptor Research Laboratories, Nuclear Receptor Lab, Center for Medical Biotechnology Center, VIB, Ghent, Belgium.,Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Claude Libert
- Center for Inflammation Research, VIB, Ghent, Belgium. .,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
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148
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Sevilla LM, Pérez P. Roles of the Glucocorticoid and Mineralocorticoid Receptors in Skin Pathophysiology. Int J Mol Sci 2018; 19:ijms19071906. [PMID: 29966221 PMCID: PMC6073661 DOI: 10.3390/ijms19071906] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 06/25/2018] [Accepted: 06/27/2018] [Indexed: 12/15/2022] Open
Abstract
The nuclear hormone receptor (NR) superfamily comprises approximately 50 evolutionarily conserved proteins that play major roles in gene regulation by prototypically acting as ligand-dependent transcription factors. Besides their central role in physiology, NRs have been largely used as therapeutic drug targets in many chronic inflammatory conditions and derivatives of their specific ligands, alone or in combination, are frequently prescribed for the treatment of skin diseases. In particular, glucocorticoids (GCs) are the most commonly used compounds for treating prevalent skin diseases such as psoriasis due to their anti-proliferative and anti-inflammatory actions. However, and despite their therapeutic efficacy, the long-term use of GCs is limited because of the cutaneous adverse effects including atrophy, delayed wound healing, and increased susceptibility to stress and infections. The GC receptor (GR/NR3C1) and the mineralocorticoid receptor (MR/NR3C2) are members of the NR subclass NR3C that are highly related, both structurally and functionally. While the GR is ubiquitously expressed and is almost exclusively activated by GCs; an MR has a more restricted tissue expression pattern and can bind GCs and the mineralocorticoid aldosterone with similar high affinity. As these receptors share 95% identity in their DNA binding domains; both can recognize the same hormone response elements; theoretically resulting in transcriptional regulation of the same target genes. However, a major mechanism for specific activation of GRs and/or MRs is at the pre-receptor level by modulating the local availability of active GCs. Furthermore, the selective interactions of each receptor with spatio-temporally regulated transcription factors and co-regulators are crucial for the final transcriptional outcome. While there are abundant genome wide studies identifying GR transcriptional targets in a variety of tissue and cell types; including keratinocytes; the data for MR is more limited thus far. Our group and others have studied the role of GRs and MRs in skin development and disease by generating and characterizing mouse and cellular models with gain- and loss-of-function for each receptor. Both NRs are required for skin barrier competence during mouse development and also play a role in adult skin homeostasis. Moreover, the combined loss of epidermal GRs and MRs caused a more severe skin phenotype relative to single knock-outs (KOs) in developing skin and in acute inflammation and psoriasis, indicating that these corticosteroid receptors play cooperative roles. Understanding GR- and MR-mediated signaling in skin should contribute to deciphering their tissue-specific relative roles and ultimately help to improve GC-based therapies.
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Affiliation(s)
- Lisa M Sevilla
- Instituto de Biomedicina de Valencia (IBV)-CSIC, 46010 Valencia, Spain.
| | - Paloma Pérez
- Instituto de Biomedicina de Valencia (IBV)-CSIC, 46010 Valencia, Spain.
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149
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White JT, Li J, Grasso E, Wrabl JO, Hilser VJ. Ensemble allosteric model: energetic frustration within the intrinsically disordered glucocorticoid receptor. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170175. [PMID: 29735729 PMCID: PMC5941170 DOI: 10.1098/rstb.2017.0175] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2018] [Indexed: 01/21/2023] Open
Abstract
Allostery is an important regulatory phenomenon enabling precise control of biological function. Initial understanding of allostery was gained from seminal work on conformational changes exhibited by structured proteins. Within the last decade, protein allostery has also been demonstrated to occur within intrinsically disordered proteins. This emerging concept of disorder-mediated allostery can be usefully understood in the context of a thermodynamic ensemble. The advantage of this ensemble allosteric model is that it unifies the explanations of allostery occurring within both structured and disordered proteins. One central finding from this model is that energetic coupling, the transmission of a signal between separate regions (or domains) of a protein, is maximized when one or more domains are disordered. This is due to a disorder-order transition that contributes additional coupling energy to the allosteric system through formation of a molecular interaction surface or interface. A second key finding is that multiple interfaces may constructively or destructively interfere with each other, resulting in a new form of allosteric regulation called 'energetic frustration'. Articulating protein allostery in terms of the thermodynamic ensemble permits formulation of experimentally testable hypotheses which can increase fundamental understanding and direct drug-design efforts. These ideas are illustrated here with the specific case of human glucocorticoid receptor, a medically important multi-domain allosteric protein that contains both structured and disordered regions and exemplifies 'energetic frustration'.This article is part of a discussion meeting issue 'Allostery and molecular machines'.
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Affiliation(s)
- Jordan T White
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Jing Li
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Emily Grasso
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - James O Wrabl
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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150
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Ramachandran R, Ciaccia PN, Filsuf TA, Jha JK, Chattoraj DK. Chromosome 1 licenses chromosome 2 replication in Vibrio cholerae by doubling the crtS gene dosage. PLoS Genet 2018; 14:e1007426. [PMID: 29795553 PMCID: PMC5991422 DOI: 10.1371/journal.pgen.1007426] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/06/2018] [Accepted: 05/17/2018] [Indexed: 12/20/2022] Open
Abstract
Initiation of chromosome replication in bacteria is precisely timed in the cell cycle. Bacteria that harbor multiple chromosomes face the additional challenge of orchestrating replication initiation of different chromosomes. In Vibrio cholerae, the smaller of its two chromosomes, Chr2, initiates replication after Chr1 such that both chromosomes terminate replication synchronously. The delay is due to the dependence of Chr2 initiation on the replication of a site, crtS, on Chr1. The mechanism by which replication of crtS allows Chr2 replication remains unclear. Here, we show that blocking Chr1 replication indeed blocks Chr2 replication, but providing an extra crtS copy in replication-blocked Chr1 permitted Chr2 replication. This demonstrates that unreplicated crtS copies have significant activity, and suggests that a role of replication is to double the copy number of the site that sufficiently increases its activity for licensing Chr2 replication. We further show that crtS activity promotes the Chr2-specific initiator function and that this activity is required in every cell cycle, as would be expected of a cell-cycle regulator. This study reveals how increase of gene dosage through replication can be utilized in a critical regulatory switch.
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Affiliation(s)
- Revathy Ramachandran
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Peter N. Ciaccia
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tara A. Filsuf
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jyoti K. Jha
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Dhruba K. Chattoraj
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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