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Struhl K. Non-canonical functions of enhancers: regulation of RNA polymerase III transcription, DNA replication, and V(D)J recombination. Trends Genet 2024; 40:471-479. [PMID: 38643034 PMCID: PMC11152991 DOI: 10.1016/j.tig.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/02/2024] [Indexed: 04/22/2024]
Abstract
Enhancers are the key regulators of other DNA-based processes by virtue of their unique ability to generate nucleosome-depleted regions in a highly regulated manner. Enhancers regulate cell-type-specific transcription of tRNA genes by RNA polymerase III (Pol III). They are also responsible for the binding of the origin replication complex (ORC) to DNA replication origins, thereby regulating origin utilization, replication timing, and replication-dependent chromosome breaks. Additionally, enhancers regulate V(D)J recombination by increasing access of the recombination-activating gene (RAG) recombinase to target sites and by generating non-coding enhancer RNAs and localized regions of trimethylated histone H3-K4 recognized by the RAG2 PHD domain. Thus, enhancers represent the first step in decoding the genome, and hence they regulate biological processes that, unlike RNA polymerase II (Pol II) transcription, do not have dedicated regulatory proteins.
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Affiliation(s)
- Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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2
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Jeon DY, Jeong SY, Lee JW, Kim J, Kim JH, Chu HS, Jeong WJ, Lee BJ, Ahn B, Kim J, Choi SH, Park JW. FOXO1 Is a Key Mediator of Glucocorticoid-Induced Expression of Tristetraprolin in MDA-MB-231 Breast Cancer Cells. Int J Mol Sci 2022; 23:ijms232213673. [PMID: 36430156 PMCID: PMC9693238 DOI: 10.3390/ijms232213673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022] Open
Abstract
The mRNA destabilizing factor tristetraprolin (TTP) functions as a tumor suppressor by down-regulating cancer-associated genes. TTP expression is significantly reduced in various cancers, which contributes to cancer processes. Enforced expression of TTP impairs tumorigenesis and abolishes maintenance of the malignant state, emphasizing the need to identify a TTP inducer in cancer cells. To search for novel candidate agents for inducing TTP in cancer cells, we screened a library containing 1019 natural compounds using MCF-7 breast cancer cells transfected with a reporter vector containing the TTP promoter upstream of the luciferase gene. We identified one molecule, of which the enantiomers are betamethasone 21-phosphate (BTM-21-P) and dexamethasone 21-phosphate (BTM-21-P), as a potent inducer of TTP in cancer cells. We confirmed that BTM-21-P, DXM-21-P, and dexamethasone (DXM) induced the expression of TTP in MDA-MB-231 cells in a glucocorticoid receptor (GR)-dependent manner. To identify potential pathways linking BTM-21-P and DXM-21-P to TTP induction, we performed an RNA sequencing-based transcriptome analysis of MDA-MB-231 cells at 3 h after treatment with these compounds. A heat map analysis of FPKM expression showed a similar expression pattern between cells treated with the two compounds. The KEGG pathway analysis results revealed that the upregulated DEGs were strongly associated with several pathways, including the Hippo signaling pathway, PI3K-Akt signaling pathway, FOXO signaling pathway, NF-κB signaling pathway, and p53 signaling pathway. Inhibition of the FOXO pathway using a FOXO1 inhibitor blocked the effects of BTM-21-P and DXM-21-P on the induction of TTP in MDA-MB-231 cells. We found that DXM enhanced the binding of FOXO1 to the TTP promoter in a GR-dependent manner. In conclusion, we identified a natural compound of which the enantiomers are DXM-21-P and BTM-21-P as a potent inducer of TTP in breast cancer cells. We also present new insights into the role of FOXO1 in the DXM-21-P- and BTM-21-P-induced expression of TTP in cancer cells.
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Affiliation(s)
- Do Yong Jeon
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, Korea
| | - So Yeon Jeong
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, Korea
| | - Ju Won Lee
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, Korea
| | - Jeonghwan Kim
- School of System Biomedical Science, Soongsil University, Seoul 06978, Korea
| | - Jee Hyun Kim
- RopheLBio, B102, Seoul Forest M Tower, Seoul 04778, Korea
| | - Hun Su Chu
- RopheLBio, B102, Seoul Forest M Tower, Seoul 04778, Korea
| | - Won Jin Jeong
- RopheLBio, B102, Seoul Forest M Tower, Seoul 04778, Korea
| | - Byung Ju Lee
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, Korea
| | - Byungyong Ahn
- Department of Food Science and Nutrition, University of Ulsan, Ulsan 44610, Korea
| | - Junil Kim
- School of System Biomedical Science, Soongsil University, Seoul 06978, Korea
| | - Seong Hee Choi
- RopheLBio, B102, Seoul Forest M Tower, Seoul 04778, Korea
- Correspondence: (S.H.C.); (J.W.P.)
| | - Jeong Woo Park
- Department of Biological Sciences, University of Ulsan, Ulsan 44610, Korea
- Correspondence: (S.H.C.); (J.W.P.)
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3
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Giguère V, Evans RM. Chronicle of a discovery: the retinoic acid receptor. J Mol Endocrinol 2022; 69:T1-T11. [PMID: 35900848 DOI: 10.1530/jme-22-0117] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 06/18/2022] [Indexed: 11/08/2022]
Abstract
The landmark 1987 discovery of the retinoic acid receptor (RAR) came as a surprise, uncovering a genomic kinship between the fields of vitamin A biology and steroid receptors. This stunning breakthrough triggered a cascade of studies to deconstruct the roles played by the RAR and its natural and synthetic ligands in embryonic development, skin, growth, physiology, vision, and disease as well as providing a template to elucidate the molecular mechanisms by which nuclear receptors regulate gene expression. In this review, written from historic and personal perspectives, we highlight the milestones that led to the discovery of the RAR and the subsequent studies that enriched our knowledge of the molecular mechanisms by which a low-abundant dietary compound could be so essential to the generation and maintenance of life itself.
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Affiliation(s)
- Vincent Giguère
- Goodman Cancer Institute, McGill University, Montréal, Quebec, Canada
- Department of Biochemistry, McGill University, Montréal, Quebec, Canada
| | - Ronald M Evans
- The Salk Institute for Biological Studies, La Jolla, California, USA
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Sánchez-Campillo I, Miguel-Gracia J, Karamanis P, Blanco-Canosa JB. A versatile o-aminoanilide linker for native chemical ligation. Chem Sci 2022; 13:10904-10913. [PMID: 36320694 PMCID: PMC9491214 DOI: 10.1039/d2sc04158h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/25/2022] [Indexed: 12/04/2022] Open
Abstract
Chemical protein synthesis (CPS) is a consolidated field founded on the high chemospecificity of amide-forming reactions, most notably the native chemical ligation (NCL), but also on new technologies such as the Ser/Thr ligation of C-terminal salicylaldehyde esters and the α-ketoacid-hydroxylamine (KAHA) condensation. NCL was conceptually devised for the ligation of peptides having a C-terminal thioester and an N-terminal cysteine. The synthesis of C-terminal peptide thioesters has attracted a lot of interest, resulting in the invention of a wide diversity of different methods for their preparation. The N-acylurea (Nbz) approach relies on the use of the 3,4-diaminobenzoic (Dbz-COOH) and the 3-amino-(4-methylamino)benzoic (MeDbz-COOH) acids; the latter disclosed to eliminate the formation of branching peptides. Dbz-COOH has been also used for the development of the benzotriazole (Bt)-mediated NCL, in which the peptide-Dbz-CONH2 precursor is oxidized to a highly acylating peptide-Bt-CONH2 species. Here, we have brought together the Nbz and Bt approaches in a versatile linker, the 1,2-diaminobenzene (Dbz). The Dbz combines the robustness of MeDbz-COOH and the flexibility of Dbz-COOH: it can be converted into the Nbz or Bt C-terminal peptides. Both are ligated in high yields, and the reaction intermediates can be conveniently characterized. Our results show that the Bt precursors have faster NCL kinetics that is reflected by a rapid transthioesterification (<5 min). Taking advantage of this major acylating capacity, peptide-Bt can be transselenoesterified in the presence of selenols to afford peptide selenoesters which hold enormous potential in NCL.
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Affiliation(s)
- Iván Sánchez-Campillo
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18-26 08034 Barcelona Spain
| | - Judit Miguel-Gracia
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18-26 08034 Barcelona Spain
| | - Periklis Karamanis
- Dept. of Chemistry "G. Ciamician", University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Juan B Blanco-Canosa
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18-26 08034 Barcelona Spain
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Typical Enhancers, Super-Enhancers, and Cancers. Cancers (Basel) 2022; 14:cancers14184375. [PMID: 36139535 PMCID: PMC9496678 DOI: 10.3390/cancers14184375] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
Simple Summary The cancer genome has been exhaustively studied upon the advent of Next-Generation Sequencing technologies. Coding and non-coding sequences have been defined as hotspots of genomic variations that affect the naïve gene expression programs established in normal cells, thus working as endogenous drivers of carcinogenesis. In this review, we comprehensively summarize fundamental aspects of gene expression regulation, with emphasis on the impact of sequence and structural variations mapped across non-coding cis-acting elements of genes encoding for tumor-related transcription factors. Chromatin architecture, epigenome reprogramming, transcriptional enhancers and Super-enhancers, oncogene regulation, cutting-edge technologies, and pharmacological treatment are substantially highlighted. Abstract Non-coding segments of the human genome are enriched in cis-regulatory modules that constitute functional elements, such as transcriptional enhancers and Super-enhancers. A hallmark of cancer pathogenesis is the dramatic dysregulation of the “archetype” gene expression profiles of normal human cells. Genomic variations can promote such deficiencies when occurring across enhancers and Super-enhancers, since they affect their mechanistic principles, their functional capacity and specificity, and the epigenomic features of the chromatin microenvironment across which these regulatory elements reside. Here, we comprehensively describe: fundamental mechanisms of gene expression dysregulation in cancers that involve genomic abnormalities within enhancers’ and Super-enhancers’ (SEs) sequences, which alter the expression of oncogenic transcription factors (TFs); cutting-edge technologies applied for the analysis of variation-enriched hotspots of the cancer genome; and pharmacological approaches for the treatment of Super-enhancers’ aberrant function. Finally, we provide an intratumor meta-analysis, which highlights that genomic variations in transcription-factor-driven tumors are accompanied overexpression of genes, a portion of which encodes for additional cancer-related transcription factors.
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6
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Rose EM, Haakenson CM, Ball GF. Sex differences in seasonal brain plasticity and the neuroendocrine regulation of vocal behavior in songbirds. Horm Behav 2022; 142:105160. [PMID: 35366412 DOI: 10.1016/j.yhbeh.2022.105160] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 11/20/2022]
Abstract
Birdsong is controlled in part by a discrete network of interconnected brain nuclei regulated in turn by steroid hormones and environmental stimuli. This complex interaction results in neural changes that occur seasonally as the environment varies (e.g., photoperiod, food/water availability, etc.). Variation in environment, vocal behavior, and neuroendocrine control has been primarily studied in male songbirds in both laboratory studies of captive birds and field studies of wild caught birds. The bias toward studying seasonality in the neuroendocrine regulation of song in male birds comes from a historic focus on sexually selected male behaviors. In fact, given that male song is often loud and accompanied by somewhat extravagant courtship behaviors, female song has long been overlooked. To compound this bias, the primary model songbird species for studies in the lab, zebra finches (Taeniopygia guttata) and canaries (Serinus canaria), exhibit little or no female song. Therefore, understanding the degree of variation and neuroendocrine control of seasonality in female songbirds is a major gap in our knowledge. In this review, we discuss the importance of studying sex differences in seasonal plasticity and the song control system. Specifically, we discuss sex differences in 1) the neuroanatomy of the song control system, 2) the distribution of receptors for androgens and estrogens and 3) the seasonal neuroplasticity of the hypothalamo-pituitary-gonadal axis as well as in the neural and cellular mechanisms mediating song system changes. We also discuss how these neuroendocrine mechanisms drive sex differences in seasonal behavior. Finally, we highlight specific gaps in our knowledge and suggest experiments critical for filling these gaps.
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Affiliation(s)
- Evangeline M Rose
- Department of Psychology, University of Maryland, College Park, MD, USA; Program in Neuroscience and Cognitive Science, University of Maryland, College Park, MD, USA.
| | - Chelsea M Haakenson
- Department of Psychology, University of Maryland, College Park, MD, USA; Program in Neuroscience and Cognitive Science, University of Maryland, College Park, MD, USA
| | - Gregory F Ball
- Department of Psychology, University of Maryland, College Park, MD, USA; Program in Neuroscience and Cognitive Science, University of Maryland, College Park, MD, USA
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7
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Hoffman JA, Trotter KW, Day CR, Ward JM, Inoue K, Rodriguez J, Archer TK. Multimodal regulatory elements within a hormone-specific super enhancer control a heterogeneous transcriptional response. Mol Cell 2022; 82:803-815.e5. [PMID: 35077705 PMCID: PMC8897972 DOI: 10.1016/j.molcel.2021.12.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 11/02/2021] [Accepted: 12/22/2021] [Indexed: 12/16/2022]
Abstract
The hormone-stimulated glucocorticoid receptor (GR) modulates transcription by interacting with thousands of enhancers and GR binding sites (GBSs) throughout the genome. Here, we examined the effects of GR binding on enhancer dynamics and investigated the contributions of individual GBSs to the hormone response. Hormone treatment resulted in genome-wide reorganization of the enhancer landscape in breast cancer cells. Upstream of the DDIT4 oncogene, GR bound to four sites constituting a hormone-dependent super enhancer. Three GBSs were required as hormone-dependent enhancers that differentially promoted histone acetylation, transcription frequency, and burst size. Conversely, the fourth site suppressed transcription and hormone treatment alleviated this suppression. GR binding within the super enhancer promoted a loop-switching mechanism that allowed interaction of the DDIT4 TSS with the active GBSs. The unique functions of each GR binding site contribute to hormone-induced transcriptional heterogeneity and demonstrate the potential for targeted modulation of oncogene expression.
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Affiliation(s)
- Jackson A Hoffman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA 27709
| | - Kevin W Trotter
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA 27709
| | - Christopher R Day
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA 27709
| | - James M Ward
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA 27709
| | - Kaoru Inoue
- Clinical Research Branch, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA 27709
| | - Joseph Rodriguez
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA 27709
| | - Trevor K Archer
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA.
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8
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Walsh AD, Johnson LJ, Harvey AJ, Kilpatrick TJ, Binder MD. Identification and Characterisation of cis-Regulatory Elements Upstream of the Human Receptor Tyrosine Kinase Gene MERTK. Brain Plast 2021; 7:3-16. [PMID: 34631417 PMCID: PMC8461731 DOI: 10.3233/bpl-200102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND: MERTK encodes a receptor tyrosine kinase that regulates immune homeostasis via phagocytosis of apoptotic cells and cytokine-mediated immunosuppression. MERTK is highly expressed in the central nervous system (CNS), specifically in myeloid derived innate immune cells and its dysregulation is implicated in CNS pathologies including the autoimmune disease multiple sclerosis (MS). OBJECTIVE: While the cell types and tissues that express MERTK have been well described, the genetic elements that define the gene’s promoter and regulate specific transcription domains remain unknown. The primary objective of this study was to define and characterise the human MERTK promoter region. METHODS: We cloned and characterized the 5’ upstream region of MERTK to identify cis-acting DNA elements that promote gene transcription in luciferase reporter assays. In addition, promoter regions were tested for sensitivity to the anti-inflammatory glucocorticoid dexamethasone. RESULTS: This study identified identified both proximal and distal-acting DNA elements that promote transcription. The strongest promoter activity was identified in an ∼850 bp region situated 3 kb upstream of the MERTK transcription start site. Serial deletions of this putative enhancer revealed that the entire region is essential for expression activity. Using in silico analysis, we identified several candidate transcription factor binding sites. Despite a well-established upregulation of MERTK in response to anti-inflammatory glucocorticoids, no DNA region within the 5 kb putative promoter was found to directly respond to dexamethasone treatment. CONCLUSIONS: Elucidating the genetic mechanisms that regulate MERTK expression gives insights into gene regulation during homeostasis and disease, providing potential targets for therapeutic modulation of MERTK transcription.
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Affiliation(s)
- Alexander D. Walsh
- The Florey Institute of Neuroscience and Mental Health, Parkville, Melbourne, Australia
| | - Laura J. Johnson
- The Florey Institute of Neuroscience and Mental Health, Parkville, Melbourne, Australia
| | - Alexandra J. Harvey
- School of BioSciences, University of Melbourne, Parkville, Melbourne, Australia
| | - Trevor J. Kilpatrick
- The Florey Institute of Neuroscience and Mental Health, Parkville, Melbourne, Australia
- The Florey Department of Neuroscience and Mental Health, University of Melbourne, Parkville, Melbourne, Australia
| | - Michele D. Binder
- The Florey Institute of Neuroscience and Mental Health, Parkville, Melbourne, Australia
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Melbourne, Australia
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9
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Stress, memory, and implications for major depression. Behav Brain Res 2021; 412:113410. [PMID: 34116119 DOI: 10.1016/j.bbr.2021.113410] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 06/04/2021] [Accepted: 06/06/2021] [Indexed: 12/22/2022]
Abstract
The stress response comprises a phylogenetically conserved set of cognitive, physiological, and behavioral responses that evolved as a survival strategy. In this context, the memory of stressful events would be adaptive as it could avoid re-exposure to an adverse event, otherwise the event would be facilitated in positively stressful or non-distressful conditions. However, the interaction between stress and memory comprises complex responses, some of them which are not yet completely understood, and which depend on several factors such as the memory system that is recruited, the nature and duration of the stressful event, as well as the timing in which this interaction takes place. In this narrative review, we briefly discuss the mechanisms of the stress response, the main memory systems, and its neural correlates. Then, we show how stress, through the action of its biochemical mediators, influences memory systems and mnemonic processes. Finally, we make use of major depressive disorder to explore the possible implications of non-adaptive interactions between stress and memory to psychiatric disorders, as well as possible roles for memory studies in the field of psychiatry.
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10
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Mostafa MM, Bansal A, Michi AN, Sasse SK, Proud D, Gerber AN, Newton R. Genomic determinants implicated in the glucocorticoid-mediated induction of KLF9 in pulmonary epithelial cells. J Biol Chem 2021; 296:100065. [PMID: 33184061 PMCID: PMC7949084 DOI: 10.1074/jbc.ra120.015755] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
Ligand-activated glucocorticoid receptor (GR) elicits variable glucocorticoid-modulated transcriptomes in different cell types. However, some genes, including Krüppel-like factor 9 (KLF9), a putative transcriptional repressor, demonstrate conserved responses. We show that glucocorticoids induce KLF9 expression in the human airways in vivo and in differentiated human bronchial epithelial (HBE) cells grown at air-liquid interface (ALI). In A549 and BEAS-2B pulmonary epithelial cells, glucocorticoids induce KLF9 expression with similar kinetics to primary HBE cells in submersion culture. A549 and BEAS-2B ChIP-seq data reveal four common glucocorticoid-induced GR binding sites (GBSs). Two GBSs mapped to the 5'-proximal region relative to KLF9 transcription start site (TSS) and two occurred at distal sites. These were all confirmed in primary HBE cells. Global run-on (GRO) sequencing indicated robust enhancer RNA (eRNA) production from three of these GBSs in BEAS-2B cells. This was confirmed in A549 cells, plus submersion, and ALI culture of HBE cells. Cloning each GBS into luciferase reporters revealed glucocorticoid-induced activity requiring a glucocorticoid response element (GRE) within each distal GBS. While the proximal GBSs drove modest reporter induction by glucocorticoids, this region exhibited basal eRNA production, RNA polymerase II enrichment, and looping to the TSS, plausibly underlying constitutive KLF9 expression. Post glucocorticoid treatment, interactions between distal and proximal GBSs and the TSS correlated with KLF9 induction. CBP/P300 silencing reduced proximal GBS activity, but negligibly affected KLF9 expression. Overall, a model for glucocorticoid-mediated regulation of KLF9 involving multiple GBSs is depicted. This work unequivocally demonstrates that mechanistic insights gained from cell lines can translate to physiologically relevant systems.
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Affiliation(s)
- Mahmoud M Mostafa
- Department of Physiology & Pharmacology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Akanksha Bansal
- Department of Physiology & Pharmacology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Aubrey N Michi
- Department of Physiology & Pharmacology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Sarah K Sasse
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - David Proud
- Department of Physiology & Pharmacology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Anthony N Gerber
- Department of Medicine, National Jewish Health, Denver, Colorado, USA; Department of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Robert Newton
- Department of Physiology & Pharmacology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Canada.
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11
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Regulation of Expression and Latency in BLV and HTLV. Viruses 2020; 12:v12101079. [PMID: 32992917 PMCID: PMC7601775 DOI: 10.3390/v12101079] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022] Open
Abstract
Human T-lymphotrophic virus type 1 (HTLV-1) and Bovine leukemia virus (BLV) belong to the Deltaretrovirus genus. HTLV-1 is the etiologic agent of the highly aggressive and currently incurable cancer adult T-cell leukemia (ATL) and a neurological disease HTLV-1-associated myelopathy (HAM)/tropical spastic paraparesis (TSP). BLV causes neoplastic proliferation of B cells in cattle: enzootic bovine leucosis (EBL). Despite the severity of these conditions, infection by HTLV-1 and BLV appear in most cases clinically asymptomatic. These viruses can undergo latency in their hosts. The silencing of proviral gene expression and maintenance of latency are central for the establishment of persistent infection, as well as for pathogenesis in vivo. In this review, we will present the mechanisms that control proviral activation and retroviral latency in deltaretroviruses, in comparison with other exogenous retroviruses. The 5′ long terminal repeats (5′-LTRs) play a main role in controlling viral gene expression. While the regulation of transcription initiation is a major mechanism of silencing, we discuss topics that include (i) the epigenetic control of the provirus, (ii) the cis-elements present in the LTR, (iii) enhancers with cell-type specific regulatory functions, (iv) the role of virally-encoded transactivator proteins, (v) the role of repressors in transcription and silencing, (vi) the effect of hormonal signaling, (vii) implications of LTR variability on transcription and latency, and (viii) the regulatory role of non-coding RNAs. Finally, we discuss how a better understanding of these mechanisms may allow for the development of more effective treatments against Deltaretroviruses.
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12
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Kandasamy T, Sudhamalla B, Naskar D. Designing of RNA aptamer against DNA binding domain of the glucocorticoid receptor: A response element-based in-silico approach. J Biomol Struct Dyn 2020; 40:1120-1127. [PMID: 32964813 DOI: 10.1080/07391102.2020.1822918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Virtual screening, a conventional in-silico approach to design an RNA aptamer against target proteins require huge RNA library containing 1010 to 1015 combination of RNA oligomers and high-performance computing systems. However, in the case of nuclear receptor proteins, screening can be narrowed down by using response element sequences rather than random RNA oligomer library. In this study, we used a novel method to design RNA aptamer against the DNA binding domain of the glucocorticoid receptor α (GRα). GRα plays a vital role in cancer metastasis such as colon, cervical and breast cancer by activating the S100A8 calcium-binding protein, which makes it a potential drug target for those cancers. We started the screening of 24 RNA aptamers (16 nucleotides long), all of which are glucocorticoid response elements (GRE) of S100A8. Among the aptamers screened, Apt-2, Apt-5, Apt-6 and Apt-15 are found to be most suitable by molecular docking and dynamic studies. The stability and compactness of the aptamer-protein complexes were assessed by GROMACS. The binding energies were rescored using the MM-PBSA method, which were -3679.581, -3690.892, -8246.052 and -3412.802 KJ/mol, respectively for Apt-2, Apt- 5, Apt-6 and Apt-15. The designed RNA aptamer may directly bind to the DNA binding domain of GR and prevent the trans-activation of the S100A8 gene by blocking the binding of GR to its response element. Thus, this novel approach of design the response elements-based RNA aptamer against GRα like nuclear receptor proteins will help to generate target-specific RNA aptamers with minimal efforts and cost.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Thirukumaran Kandasamy
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India
| | - Babu Sudhamalla
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Debdut Naskar
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India
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13
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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: 15] [Impact Index Per Article: 3.0] [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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14
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Goustin AS, Thepsuwan P, Kosir MA, Lipovich L. The Growth-Arrest-Specific ( GAS)-5 Long Non-Coding RNA: A Fascinating lncRNA Widely Expressed in Cancers. Noncoding RNA 2019; 5:ncrna5030046. [PMID: 31533355 PMCID: PMC6789762 DOI: 10.3390/ncrna5030046] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 09/08/2019] [Accepted: 09/10/2019] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNA (lncRNA) genes encode non-messenger RNAs that lack open reading frames (ORFs) longer than 300 nucleotides, lack evolutionary conservation in their shorter ORFs, and do not belong to any classical non-coding RNA category. LncRNA genes equal, or exceed in number, protein-coding genes in mammalian genomes. Most mammalian genomes harbor ~20,000 protein-coding genes that give rise to conventional messenger RNA (mRNA) transcripts. These coding genes exhibit sweeping evolutionary conservation in their ORFs. LncRNAs function via different mechanisms, including but not limited to: (1) serving as “enhancer” RNAs regulating nearby coding genes in cis; (2) functioning as scaffolds to create ribonucleoprotein (RNP) complexes; (3) serving as sponges for microRNAs; (4) acting as ribo-mimics of consensus transcription factor binding sites in genomic DNA; (5) hybridizing to other nucleic acids (mRNAs and genomic DNA); and, rarely, (6) as templates encoding small open reading frames (smORFs) that may encode short proteins. Any given lncRNA may have more than one of these functions. This review focuses on one fascinating case—the growth-arrest-specific (GAS)-5 gene, encoding a complicated repertoire of alternatively-spliced lncRNA isoforms. GAS5 is also a host gene of numerous small nucleolar (sno) RNAs, which are processed from its introns. Publications about this lncRNA date back over three decades, covering its role in cell proliferation, cell differentiation, and cancer. The GAS5 story has drawn in contributions from prominent molecular geneticists who attempted to define its tumor suppressor function in mechanistic terms. The evidence suggests that rodent Gas5 and human GAS5 functions may be different, despite the conserved multi-exonic architecture featuring intronic snoRNAs, and positional conservation on syntenic chromosomal regions indicating that the rodent Gas5 gene is the true ortholog of the GAS5 gene in man and other apes. There is no single answer to the molecular mechanism of GAS5 action. Our goal here is to summarize competing, not mutually exclusive, mechanistic explanations of GAS5 function that have compelling experimental support.
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Affiliation(s)
- Anton Scott Goustin
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | - Pattaraporn Thepsuwan
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
| | | | - Leonard Lipovich
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA.
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15
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Mitchell CA, Dasgupta S, Zhang S, Stapleton HM, Volz DC. Disruption of Nuclear Receptor Signaling Alters Triphenyl Phosphate-Induced Cardiotoxicity in Zebrafish Embryos. Toxicol Sci 2019. [PMID: 29529285 DOI: 10.1093/toxsci/kfy037] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Triphenyl phosphate (TPHP) is an unsubstituted aryl phosphate ester used as a flame retardant and plasticizer within the United States. Using zebrafish as a model, the objectives of this study were to rely on (1) mRNA-sequencing to uncover pathways disrupted following embryonic TPHP exposure and (2) high-content screening to identify nuclear receptor ligands that enhance or mitigate TPHP-induced cardiotoxicity. Based on mRNA-sequencing, TPHP exposure from 24 to 72-h postfertilization (hpf) resulted in a concentration-dependent increase in the number of transcripts significantly affected at 72 hpf, and pathway analysis revealed that 5 out of 9 nuclear receptor pathways were associated with the retinoid X receptor (RXR). Based on a screen of 74 unique nuclear receptor ligands as well as follow-up experiments, 2 compounds-ciglitazone (a peroxisome proliferator-activated receptor gamma, or PPARγ, agonist) and fenretinide (a pan-retinoic acid receptor, or RAR, agonist)-reliably mitigated TPHP-induced cardiotoxicity in the absence of effects on TPHP uptake or metabolism. As these data suggested that TPHP may be activating RXR (a heterodimer for both RARs and PPARγ), we coexposed embryos to HX 531-a pan-RXR antagonist-from 24 to 72 hpf and, contrary to our hypothesis, found that coexposure to HX 531 significantly enhanced TPHP-induced cardiotoxicity. Using a luciferase reporter assay, we also found that TPHP did not activate nor inhibit chimeric human RXRα, RXRβ, or RXRγ, suggesting that TPHP does not directly bind nor interact with RXRs. Overall, our data suggest that TPHP may interfere with RXR-dependent pathways involved in cardiac development.
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Affiliation(s)
- Constance A Mitchell
- Environmental Toxicology Graduate Program.,Department of Environmental Sciences, University of California, Riverside, California
| | - Subham Dasgupta
- Department of Environmental Sciences, University of California, Riverside, California
| | - Sharon Zhang
- Division of Environmental Sciences and Policy, Duke University, Durham, North Carolina
| | - Heather M Stapleton
- Division of Environmental Sciences and Policy, Duke University, Durham, North Carolina
| | - David C Volz
- Department of Environmental Sciences, University of California, Riverside, California
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16
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Mostafa MM, Rider CF, Shah S, Traves SL, Gordon PMK, Miller-Larsson A, Leigh R, Newton R. Glucocorticoid-driven transcriptomes in human airway epithelial cells: commonalities, differences and functional insight from cell lines and primary cells. BMC Med Genomics 2019; 12:29. [PMID: 30704470 PMCID: PMC6357449 DOI: 10.1186/s12920-018-0467-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 12/21/2018] [Indexed: 12/16/2022] Open
Abstract
Background Glucocorticoids act on the glucocorticoid receptor (GR; NR3C1) to resolve inflammation and, as inhaled corticosteroids (ICS), are the cornerstone of treatment for asthma. However, reduced efficacy in severe disease or exacerbations indicates a need to improve ICS actions. Methods Glucocorticoid-driven transcriptomes were compared using PrimeView microarrays between primary human bronchial epithelial (HBE) cells and the model cell lines, pulmonary type II A549 and bronchial epithelial BEAS-2B cells. Results In BEAS-2B cells, budesonide induced (≥2-fold, P ≤ 0.05) or, in a more delayed fashion, repressed (≤0.5-fold, P ≤ 0.05) the expression of 63, 133, 240, and 257 or 15, 56, 236, and 344 mRNAs at 1, 2, 6, and 18 h, respectively. Within the early-induced mRNAs were multiple transcriptional activators and repressors, thereby providing mechanisms for the subsequent modulation of gene expression. Using the above criteria, 17 (BCL6, BIRC3, CEBPD, ERRFI1, FBXL16, FKBP5, GADD45B, IRS2, KLF9, PDK4, PER1, RGCC, RGS2, SEC14L2, SLC16A12, TFCP2L1, TSC22D3) induced and 8 (ARL4C, FLRT2, IER3, IL11, PLAUR, SEMA3A, SLC4A7, SOX9) repressed mRNAs were common between A549, BEAS-2B and HBE cells at 6 h. As absolute gene expression change showed greater commonality, lowering the cut-off (≥1.25 or ≤ 0.8-fold) within these groups produced 93 induced and 82 repressed genes in common. Since large changes in few mRNAs and/or small changes in many mRNAs may drive function, gene ontology (GO)/pathway analyses were performed using both stringency criteria. Budesonide-induced genes showed GO term enrichment for positive and negative regulation of transcription, signaling, proliferation, apoptosis, and movement, as well as FOXO and PI3K-Akt signaling pathways. Repressed genes were enriched for inflammatory signaling pathways (TNF, NF-κB) and GO terms for cytokine activity, chemotaxis and cell signaling. Reduced growth factor expression and effects on proliferation and apoptosis were highlighted. Conclusions While glucocorticoids repress mRNAs associated with inflammation, prior induction of transcriptional activators and repressors may explain longer-term responses to these agents. Furthermore, positive and negative effects on signaling, proliferation, migration and apoptosis were revealed. Since many such gene expression changes occurred in human airways post-ICS inhalation, the effects observed in cell lines and primary HBE cells in vitro may be relevant to ICS in vivo. Electronic supplementary material The online version of this article (10.1186/s12920-018-0467-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mahmoud M Mostafa
- Airways Inflammation Research Group, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada.,Cardiovascular and Respiratory Sciences graduate program, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Christopher F Rider
- Department of Medicine, Vancouver General Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Suharsh Shah
- Airways Inflammation Research Group, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Suzanne L Traves
- Airways Inflammation Research Group, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Paul M K Gordon
- Centre for Health Genomics and Informatics, University of Calgary, Calgary, Alberta, Canada
| | | | - Richard Leigh
- Airways Inflammation Research Group, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Robert Newton
- Airways Inflammation Research Group, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada.
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17
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Fletcher ELK, Kanki M, Morgan J, Ray DW, Delbridge L, Fuller PJ, Clyne CD, Young MJ. Cardiomyocyte transcription is controlled by combined MR and circadian clock signalling. J Endocrinol 2019; 241:JOE-18-0584.R3. [PMID: 30689544 DOI: 10.1530/joe-18-0584] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/28/2019] [Indexed: 12/21/2022]
Abstract
We previously identified a critical pathogenic role for MR activation in cardiomyocytes that included a potential interaction between the MR and the molecular circadian clock. While glucocorticoid regulation of the circadian clock is undisputed, MR interactions with circadian clock signalling are limited. We hypothesised that the MR influences cardiac circadian clock signalling, and vice versa. 10nM aldosterone or corticosterone regulated CRY 1, PER1, PER2 and ReverbA (NR1D1) gene expression patterns in H9c2 cells over 24hr. MR-dependent regulation of circadian gene promoters containing GREs and E-box sequences was established for CLOCK, Bmal, CRY 1 and CRY2, PER1 and PER2 and transcriptional activators CLOCK and Bmal modulated MR-dependent transcription of a subset of these promoters. We also demonstrated differential regulation of MR target gene expression in hearts of mice 4hr after administration of aldosterone at 8AM versus 8PM. Our data support combined MR regulation of a subset of circadian genes and that endogenous circadian transcription factors CLOCK and Bmal modulate this response. This unsuspected relationship links MR in the heart to circadian rhythmicity at the molecular level and has important implications for the biology of MR signalling in response to aldosterone as well as cortisol. These data are consistent with MR signalling in the brain where, like the heart, it preferentially responds to cortisol. Given the undisputed requirement for diurnal cortisol release in the entrainment of peripheral clocks, the present study highlights the MR as an important mechanism for transducing the circadian actions of cortisol in addition to the GR in the heart.
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Affiliation(s)
- ELizabeth K Fletcher
- E Fletcher, Sackler School of Graduate Biomedical Sciences, Tuft Medical Centre, Boston, United States
| | - Monica Kanki
- M Kanki, Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Melbourne, Australia
| | - James Morgan
- J Morgan, Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Melbourne, Australia
| | - David W Ray
- D Ray, Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom of Great Britain and Northern Ireland
| | - Lea Delbridge
- L Delbridge, Dept Of Physiology, University of Melbourne, Melbourne, xxx, Australia
| | - Peter James Fuller
- P Fuller, Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Melbourne, Australia
| | - Colin D Clyne
- C Clyne , Cancer Drug Discovery, Hudson Institute of Medical Research, Clayton, Australia
| | - Morag J Young
- M Young, Cardiovascular Endocrinology, Hudson Institute of Medical Research, Clayton, 3166, Australia
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18
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Human genome-wide measurement of drug-responsive regulatory activity. Nat Commun 2018; 9:5317. [PMID: 30575722 PMCID: PMC6303339 DOI: 10.1038/s41467-018-07607-x] [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: 03/21/2018] [Accepted: 11/07/2018] [Indexed: 01/09/2023] Open
Abstract
Environmental stimuli commonly act via changes in gene regulation. Human-genome-scale assays to measure such responses are indirect or require knowledge of the transcription factors (TFs) involved. Here, we present the use of human genome-wide high-throughput reporter assays to measure environmentally-responsive regulatory element activity. We focus on responses to glucocorticoids (GCs), an important class of pharmaceuticals and a paradigmatic genomic response model. We assay GC-responsive regulatory activity across >108 unique DNA fragments, covering the human genome at >50×. Those assays directly detected thousands of GC-responsive regulatory elements genome-wide. We then validate those findings with measurements of transcription factor occupancy, histone modifications, chromatin accessibility, and gene expression. We also detect allele-specific environmental responses. Notably, the assays did not require knowledge of GC response mechanisms. Thus, this technology can be used to agnostically quantify genomic responses for which the underlying mechanism remains unknown. Quantification of genomic responses to environmental stimuli by current genome-scale assays is limited to indirect measurements or requires knowledge of the transcription factors involved. Here, the authors use genome-wide high-throughput reporter assays to agnostically map enhancer activity in response to glucocorticoid treatment across the human genome.
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19
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Gorbacheva AM, Kuprash DV, Mitkin NA. Glucocorticoid Receptor Binding Inhibits an Intronic IL33 Enhancer and is Disrupted by rs4742170 (T) Allele Associated with Specific Wheezing Phenotype in Early Childhood. Int J Mol Sci 2018; 19:ijms19123956. [PMID: 30544846 PMCID: PMC6321062 DOI: 10.3390/ijms19123956] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 12/05/2018] [Accepted: 12/06/2018] [Indexed: 12/19/2022] Open
Abstract
Interleukin 33 (IL-33) is a cytokine constitutively expressed by various cells of barrier tissues that contribute to the development of inflammatory immune responses. According to its function as an alarmin secreted by lung and airway epithelium, IL-33 plays a significant role in pathogenesis of allergic disorders. IL-33 is strongly involved in the pathogenesis of asthma, anaphylaxis, allergy and dermatitis, and genetic variations in IL33 locus are associated with increased susceptibility to asthma. Genome-wide association studies have identified risk "T" allele of the single-nucleotide polymorphism rs4742170 located in putative IL33 enhancer area as susceptible variant for development of specific wheezing phenotype in early childhood. Here, we demonstrate that risk "T" rs4742170 allele disrupts binding of glucocorticoid receptor (GR) transcription factor to IL33 putative enhancer. The IL33 promoter/enhancer constructs containing either 4742170 (T) allele or point mutations in the GR-binding site, were significantly more active and did not respond to cortisol in a pulmonary epithelial cell line. At the same time, the constructs containing rs4742170 (C) allele with a functional GR-binding site were less active and further inhibitable by cortisol. The latter effect was GR-dependent as it was completely abolished by GR-specific siRNA. This mechanism may explain the negative effect of the rs4742170 (T) risk allele on the development of wheezing phenotype that strongly correlates with allergic sensitization in childhood.
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Affiliation(s)
- Alisa M Gorbacheva
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
- Biological Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia.
| | - Dmitry V Kuprash
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
- Biological Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia.
| | - Nikita A Mitkin
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
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20
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Zhao X, Hwang DY, Kao HY. The Role of Glucocorticoid Receptors in Podocytes and Nephrotic Syndrome. NUCLEAR RECEPTOR RESEARCH 2018; 5. [PMID: 30417008 PMCID: PMC6224173 DOI: 10.11131/2018/101323] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Glucocorticoid receptor (GC), a founding member of the nuclear hormone receptor superfamily, is a glucocorticoid-activated transcription factor that regulates gene expression and controls the development and homeostasis of human podocytes. Synthetic glucocorticoids are the standard treatment regimens for proteinuria (protein in the urine) and nephrotic syndrome (NS) caused by kidney diseases. These include minimal change disease (MCD), focal segmental glomerulosclerosis (FSGS), membranous nephropathy (MN) and immunoglobulin A nephropathy (IgAN) or subsequent complications due to diabetes mellitus or HIV infection. However, unwanted side effects and steroid-resistance remain major issues for their long-term use. Furthermore, the mechanism by which glucocorticoids elicit their renoprotective activity in podocyte and glomeruli is poorly understood. Podocytes are highly differentiated epithelial cells that contribute to the integrity of kidney glomerular filtration barrier. Injury or loss of podocytes leads to proteinuria and nephrotic syndrome. Recent studies in multiple experimental models have begun to explore the mechanism of GC action in podocytes. This review will discuss progress in our understanding of the role of glucocorticoid receptor and glucocorticoids in podocyte physiology and their renoprotective activity in nephrotic syndrome.
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Affiliation(s)
- Xuan Zhao
- Department of Biochemistry, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Daw-Yang Hwang
- Division of Nephrology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hung-Ying Kao
- Department of Biochemistry, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
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21
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den Boon FS, Sarabdjitsingh RA. Circadian and ultradian patterns of HPA-axis activity in rodents: Significance for brain functionality. Best Pract Res Clin Endocrinol Metab 2017; 31:445-457. [PMID: 29223280 DOI: 10.1016/j.beem.2017.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The hypothalamo-pituitary-adrenal (HPA) axis comprises interactions between the hypothalamus, the pituitary and the adrenal glands and its activation results in the release of corticosteroid hormones. Corticosteroids are secreted from the adrenal gland in a distinct 24-h circadian rhythm overarching an ultradian rhythm, which consists of hourly corticosteroid pulses exposing target tissues to rapidly changing steroid levels. On top of these rhythms surges can take place after stress. HPA-axis rhythms promote adaptation to predictable (i.e. the earth's rotation) and unpredictable (i.e. stressors) changes in environmental factors. Two steroid hormone receptors, the mineralocorticoid receptor (MR) and the glucocorticoid receptor (GR), are activated by corticosteroids and mediate effects at fast and slow timescales on e.g. glucose availability, gene transcription and synaptic plasticity. The current review discusses the origin of the circadian and ultradian corticosteroid rhythms and their relevance for gene regulation, neuroendocrine and physiological responses to stress and the involvement in the maintenance of brain functionality in rodents.
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Affiliation(s)
- Femke S den Boon
- Dept. Translational Neuroscience, Brain Center Rudolf Magnus, UMC Utrecht, The Netherlands
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22
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Bekhbat M, Rowson SA, Neigh GN. Checks and balances: The glucocorticoid receptor and NFĸB in good times and bad. Front Neuroendocrinol 2017; 46:15-31. [PMID: 28502781 PMCID: PMC5523465 DOI: 10.1016/j.yfrne.2017.05.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/21/2017] [Accepted: 05/09/2017] [Indexed: 01/23/2023]
Abstract
Mutual regulation and balance between the endocrine and immune systems facilitate an organism's stress response and are impaired following chronic stress or prolonged immune activation. Concurrent alterations in stress physiology and immunity are increasingly recognized as contributing factors to several stress-linked neuropsychiatric disorders including depression, anxiety, and post-traumatic stress disorder. Accumulating evidence suggests that impaired balance and crosstalk between the glucocorticoid receptor (GR) and nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) - effectors of the stress and immune axes, respectively - may play a key role in mediating the harmful effects of chronic stress on mood and behavior. Here, we first review the molecular mechanisms of GR and NFκB interactions in health, then describe potential shifts in the GR-NFκB dynamics in chronic stress conditions within the context of brain circuitry relevant to neuropsychiatric diseases. Furthermore, we discuss developmental influences and sex differences in the regulation of these two transcription factors.
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Affiliation(s)
- Mandakh Bekhbat
- Emory University, Graduate Division of Biological Sciences, Neuroscience Graduate Program, United States
| | - Sydney A Rowson
- Emory University, Graduate Division of Biological Sciences, Molecular and Systems Pharmacology Graduate Studies Program, United States
| | - Gretchen N Neigh
- Virginia Commonwealth University, Department of Anatomy & Neurobiology, United States.
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23
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Weikum ER, Knuesel MT, Ortlund EA, Yamamoto KR. Glucocorticoid receptor control of transcription: precision and plasticity via allostery. Nat Rev Mol Cell Biol 2017; 18:159-174. [PMID: 28053348 PMCID: PMC6257982 DOI: 10.1038/nrm.2016.152] [Citation(s) in RCA: 342] [Impact Index Per Article: 48.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The glucocorticoid receptor (GR) is a constitutively expressed transcriptional regulatory factor (TRF) that controls many distinct gene networks, each uniquely determined by particular cellular and physiological contexts. The precision of GR-mediated responses seems to depend on combinatorial, context-specific assembly of GR-nucleated transcription regulatory complexes at genomic response elements. In turn, evidence suggests that context-driven plasticity is conferred by the integration of multiple signals, each serving as an allosteric effector of GR conformation, a key determinant of regulatory complex composition and activity. This structural and mechanistic perspective on GR regulatory specificity is likely to extend to other eukaryotic TRFs.
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Affiliation(s)
- Emily R Weikum
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
| | - Matthew T Knuesel
- Department of Cellular and Molecular Pharmacology, University of California San Francisco School of Medicine, 600 16th Street, San Francisco, California 94143, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
| | - Keith R Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California San Francisco School of Medicine, 600 16th Street, San Francisco, California 94143, USA
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24
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Vockley CM, D'Ippolito AM, McDowell IC, Majoros WH, Safi A, Song L, Crawford GE, Reddy TE. Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome. Cell 2016; 166:1269-1281.e19. [PMID: 27565349 DOI: 10.1016/j.cell.2016.07.049] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/12/2016] [Accepted: 07/27/2016] [Indexed: 12/21/2022]
Abstract
The glucocorticoid receptor (GR) binds the human genome at >10,000 sites but only regulates the expression of hundreds of genes. To determine the functional effect of each site, we measured the glucocorticoid (GC) responsive activity of nearly all GR binding sites (GBSs) captured using chromatin immunoprecipitation (ChIP) in A549 cells. 13% of GBSs assayed had GC-induced activity. The responsive sites were defined by direct GR binding via a GC response element (GRE) and exclusively increased reporter-gene expression. Meanwhile, most GBSs lacked GC-induced reporter activity. The non-responsive sites had epigenetic features of steady-state enhancers and clustered around direct GBSs. Together, our data support a model in which clusters of GBSs observed with ChIP-seq reflect interactions between direct and tethered GBSs over tens of kilobases. We further show that those interactions can synergistically modulate the activity of direct GBSs and may therefore play a major role in driving gene activation in response to GCs.
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Affiliation(s)
- Christopher M Vockley
- Department of Cell Biology, Duke University, Durham, NC 27708, USA; Center for Genomic & Computational Biology, Duke University, Durham, NC 27708, USA
| | - Anthony M D'Ippolito
- Center for Genomic & Computational Biology, Duke University, Durham, NC 27708, USA; University Program in Genetics & Genomics, Duke University, Durham, NC 27708, USA
| | - Ian C McDowell
- Center for Genomic & Computational Biology, Duke University, Durham, NC 27708, USA; Program in Computational Biology & Bioinformatics, Duke University, Durham, NC 27708, USA
| | - William H Majoros
- Center for Genomic & Computational Biology, Duke University, Durham, NC 27708, USA; Program in Computational Biology & Bioinformatics, Duke University, Durham, NC 27708, USA
| | - Alexias Safi
- Center for Genomic & Computational Biology, Duke University, Durham, NC 27708, USA; Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC 27708, USA
| | - Lingyun Song
- Center for Genomic & Computational Biology, Duke University, Durham, NC 27708, USA; Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC 27708, USA
| | - Gregory E Crawford
- Center for Genomic & Computational Biology, Duke University, Durham, NC 27708, USA; Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC 27708, USA
| | - Timothy E Reddy
- Center for Genomic & Computational Biology, Duke University, Durham, NC 27708, USA; Department of Biostatistics & Bioinformatics, Duke University, Durham, NC 27708, USA.
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25
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Murayi R, Chittiboina P. Glucocorticoids in the management of peritumoral brain edema: a review of molecular mechanisms. Childs Nerv Syst 2016; 32:2293-2302. [PMID: 27613642 PMCID: PMC5136308 DOI: 10.1007/s00381-016-3240-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 08/31/2016] [Indexed: 12/15/2022]
Abstract
Peritumoral brain edema (PTBE) is mediated by blood-brain barrier breakdown. PTBE results from interstitial vasogenic brain edema due to vascular endothelial growth factor and other inflammatory products of brain tumors. Glucocorticoids (GCs) are the mainstay for treatment of PTBE despite significant systemic side effects. GCs are thought to affect multiple cell types in the edematous brain. Here, we review preclinical studies of GC effects on edematous brain and review mechanisms underlying GC action on tumor cells, endothelial cells, and astrocytes. GCs may reduce tumor cell viability and suppress vascular endothelial growth factor (VEGF) production in tumor cells. Modulation of expression and distribution of tight junction proteins occludin, claudin-5, and ZO-1 in endothelial cells likely plays a central role in GC action on endothelial cells. GCs may also have an effect on astrocyte angiopoietin production and limited effect on astrocyte aquaporin. A better understanding of these molecular mechanisms may lead to the development of novel therapeutics for management of PTBE with a better side effect profile.
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Affiliation(s)
- Roger Murayi
- Surgical Neurology Branch, Neurosurgery Unit for Pituitary and Inheritable Diseases, National Institute of Neurological Diseases and Stroke, National Institutes of Health, 10 Center Drive, Room 3D20, Bethesda, MD, 20892-1414, USA
| | - Prashant Chittiboina
- Surgical Neurology Branch, Neurosurgery Unit for Pituitary and Inheritable Diseases, National Institute of Neurological Diseases and Stroke, National Institutes of Health, 10 Center Drive, Room 3D20, Bethesda, MD, 20892-1414, USA.
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26
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Broecker F, Hardt C, Herwig R, Timmermann B, Kerick M, Wunderlich A, Schweiger MR, Borsig L, Heikenwalder M, Lehrach H, Moelling K. Transcriptional signature induced by a metastasis-promoting c-Src mutant in a human breast cell line. FEBS J 2016; 283:1669-88. [PMID: 26919036 DOI: 10.1111/febs.13694] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 01/20/2016] [Accepted: 02/23/2016] [Indexed: 01/06/2023]
Abstract
UNLABELLED Deletions at the C-terminus of the proto-oncogene protein c-Src kinase are found in the viral oncogene protein v-Src as well as in some advanced human colon cancers. They are associated with increased kinase activity and cellular invasiveness. Here, we analyzed the mRNA expression signature of a constitutively active C-terminal mutant of c-Src, c-Src(mt), in comparison with its wild-type protein, c-Src(wt), in the human non-transformed breast epithelial cell line MCF-10A. We demonstrated previously that the mutant altered migratory and metastatic properties. Genome-wide transcriptome analysis revealed that c-Src(mt) de-regulated the expression levels of approximately 430 mRNAs whose gene products are mainly involved in the cellular processes of migration and adhesion, apoptosis and protein synthesis. 82.9% of these genes have previously been linked to cellular migration, while the others play roles in RNA transport and splicing processes, for instance. Consistent with the transcriptome data, cells expressing c-Src(mt), but not those expressing c-Src(wt), showed the capacity to metastasize into the lungs of mice in vivo. The mRNA expression profile of c-Src(mt)-expressing cells shows significant overlap with that of various primary human tumor samples, possibly reflecting elevated Src activity in some cancerous cells. Expression of c-Src(mt) led to elevated migratory potential. We used this model system to analyze the transcriptional changes associated with an invasive cellular phenotype. These genes and pathways de-regulated by c-Src(mt) may provide suitable biomarkers or targets of therapeutic approaches for metastatic cells. DATABASE This project was submitted to the National Center for Biotechnology Information BioProject under ID PRJNA288540. The Illumina RNA-Seq reads are available in the National Center for Biotechnology Information Sequence Read Archive under study ID SRP060008 with accession numbers SRS977414 for MCF-10A cells, SRS977717 for mock cells, SRS978053 for c-Src(wt) cells and SRS978046 for c-Src(mt) cells.
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Affiliation(s)
- Felix Broecker
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,University of Zurich, Switzerland
| | | | - Ralf Herwig
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Martin Kerick
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | | | - Lubor Borsig
- Institute of Physiology, Zurich Center for Integrative Human Physiology, University of Zurich, Switzerland
| | - Mathias Heikenwalder
- Institute of Virology, Technische Universität München, Germany.,Institute of Virology, Helmholtz Zentrum Munich, Germany.,Department Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Dahlem Centre for Genome Research and Medical Systems Biology, Berlin, Germany.,Alacris Theranostics GmbH, Berlin, Germany
| | - Karin Moelling
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,University of Zurich, Switzerland
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Investigating the role of early childhood abuse and HPA axis genes in suicide attempters with bipolar disorder. Psychiatr Genet 2015; 25:106-11. [PMID: 25714448 DOI: 10.1097/ypg.0000000000000082] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Genes and the environment both play a major role in the risk for attempted suicide, and environments harboring stressors, such as early childhood abuse, have been linked to suicidal behavior. Such environments also disrupt the hypothalamic-pituitary-adrenal (HPA) axis pathway, which has been hypothesized to play a role in suicidal behavior. We investigated whether the risk for attempted suicide was attributable in part to the interaction between childhood physical and/or sexual abuse and genetic variation in 19 genes (±5 kb) integral to the HPA axis pathway. MATERIALS AND METHODS Using the Genetic Association Information Network Bipolar Disorder and Translational Genomics Research Institute cohorts, we implemented PLINK's logistic regression-based 'interaction' approach to search for evidence of an interaction between 235 genotyped HPA axis single-nucleotide polymorphisms and early childhood abuse. Our study included 631 bipolar disorder suicide attempters and 657 bipolar disorder nonattempters with information on abuse. RESULTS After correction for multiple testing, no significant interaction between the 235 HPA axis single-nucleotide polymorphisms and early childhood abuse was found. In our study, the strongest interaction was found with rs2664008 in the corticotropin-releasing hormone receptor 1 (CRHR1) gene, with a nominal interaction P-value of 1.22×10 and an interaction odds ratio of 0.47. CONCLUSION Our findings suggest that further work and larger sample sizes are required to elucidate the link between early childhood abuse and the HPA axis in suicidal behavior.
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Modulation of Immunity and Inflammation by the Mineralocorticoid Receptor and Aldosterone. BIOMED RESEARCH INTERNATIONAL 2015; 2015:652738. [PMID: 26448944 PMCID: PMC4581510 DOI: 10.1155/2015/652738] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/07/2015] [Accepted: 06/03/2015] [Indexed: 02/07/2023]
Abstract
The mineralocorticoid receptor (MR) is a ligand dependent transcription factor. MR has been traditionally associated with the control of water and electrolyte homeostasis in order to keep blood pressure through aldosterone activation. However, there is growing evidence indicating that MR expression is not restricted to vascular and renal tissues, as it can be also expressed by cells of the immune system, where it responds to stimulation or antagonism, controlling immune cell function. On the other hand, aldosterone also has been associated with proinflammatory immune effects, such as the release of proinflammatory cytokines, generating oxidative stress and inducing fibrosis. The inflammatory participation of MR and aldosterone in the cardiovascular disease suggests an association with alterations in the immune system. Hypertensive patients show higher levels of proinflammatory mediators that can be modulated by MR antagonism. Although these proinflammatory properties have been observed in other autoimmune and chronic inflammatory diseases, the cellular and molecular mechanisms that mediate these effects remain unknown. Here we review and discuss the scientific work aimed at determining the immunological role of MR and aldosterone in humans, as well as animal models.
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29
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Kook I, Henley C, Meyer F, Hoffmann FG, Jones C. Bovine herpesvirus 1 productive infection and immediate early transcription unit 1 promoter are stimulated by the synthetic corticosteroid dexamethasone. Virology 2015; 484:377-385. [PMID: 26226582 DOI: 10.1016/j.virol.2015.06.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/21/2015] [Accepted: 06/05/2015] [Indexed: 01/21/2023]
Abstract
The primary site for life-long latency of bovine herpesvirus 1 (BHV-1) is sensory neurons. The synthetic corticosteroid dexamethasone consistently induces reactivation from latency; however the mechanism by which corticosteroids mediate reactivation is unclear. In this study, we demonstrate for the first time that dexamethasone stimulates productive infection, in part, because the BHV-1 genome contains more than 100 potential glucocorticoid receptor (GR) response elements (GREs). Immediate early transcription unit 1 (IEtu1) promoter activity, but not IEtu2 or VP16 promoter activity, was stimulated by dexamethasone. Two near perfect consensus GREs located within the IEtu1 promoter were necessary for dexamethasone-mediated stimulation. Electrophoretic mobility shift assays and chromatin immunoprecipitation studies demonstrated that the GR interacts with IEtu1 promoter sequences containing the GREs. Although we hypothesize that DEX-mediated stimulation of IEtu1 promoter activity is important during productive infection and perhaps reactivation from latency, stress likely has pleiotropic effects on virus-infected cells.
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Affiliation(s)
- Insun Kook
- School of Veterinary Medicine and Biomedical Sciences, Nebraska Center for Virology, University of Nebraska, Morisson Life Science Center, RM234, Lincoln, NE 68583-09065, USA
| | - Caitlin Henley
- Mississippi State University, Department of Biochemistry and Molecular Biology, Entomology and Plant Pathology, 408 Dorman Hall-Mailstop 9655, 32 Creelman St., Starkville, MS 39762, USA
| | - Florencia Meyer
- Mississippi State University, Department of Biochemistry and Molecular Biology, Entomology and Plant Pathology, 408 Dorman Hall-Mailstop 9655, 32 Creelman St., Starkville, MS 39762, USA
| | - Federico G Hoffmann
- Mississippi State University, Department of Biochemistry and Molecular Biology, Entomology and Plant Pathology, 408 Dorman Hall-Mailstop 9655, 32 Creelman St., Starkville, MS 39762, USA
| | - Clinton Jones
- School of Veterinary Medicine and Biomedical Sciences, Nebraska Center for Virology, University of Nebraska, Morisson Life Science Center, RM234, Lincoln, NE 68583-09065, USA.
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Meijsing SH. Mechanisms of Glucocorticoid-Regulated Gene Transcription. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015. [PMID: 26215990 DOI: 10.1007/978-1-4939-2895-8_3] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
One fascinating aspect of glucocorticoid signaling is their broad range of physiological and pharmacological effects. These effects are at least in part a consequence of transcriptional regulation by the glucocorticoid receptor (GR). Activation of GR by glucocorticoids results in tissue-specific changes in gene expression levels with some genes being activated whereas others are repressed. This raises two questions: First, how does GR regulate different subsets of target genes in different tissues? And second, how can GR both activate and repress the expression of genes?To answer these questions, this chapter will describe the function of the various "components" and how they cooperate to mediate the transcriptional responses to glucocorticoids. The first "component" is GR itself. The second "component" is the chromatin and its role in specifying where in the genome GR binds. Binding to the genome however is just the first step in regulating the expression of genes and transcriptional regulation by GR depends on the recruitment of coregulator proteins that either directly or indirectly influence the recruitment and or activity of RNA polymerase II. Ultimately, the integration of inputs including GR isoform, DNA sequence, chromatin and cooperation with coregulators determines which genes are regulated and the direction of their regulation.
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Affiliation(s)
- Sebastiaan H Meijsing
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Biology, Ihnestrasse 63-73, Berlin, 14195, Germany,
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31
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Regulatory Actions of Glucocorticoid Hormones: From Organisms to Mechanisms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015. [DOI: 10.1007/978-1-4939-2895-8_1] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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32
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Morange M. What history tells us XXXV. Enhancers: their existence and characteristics have raised puzzling issues since their discovery. J Biosci 2014; 39:741-5. [PMID: 25431403 DOI: 10.1007/s12038-014-9482-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michel Morange
- Centre Cavailles, Republique des Savoirs USR 3608, Ecole Normale Superieure, 29 rue d'Ulm, 75230 Paris Cedex 05, France,
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33
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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 329] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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34
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Abstract
The discovery of retinoic acid receptors arose from research into how vitamins are essential for life. Early studies indicated that Vitamin A was metabolized into an active factor, retinoic acid (RA), which regulates RNA and protein expression in cells. Each step forward in our understanding of retinoic acid in human health was accomplished by the development and application of new technologies. Development cDNA cloning techniques and discovery of nuclear receptors for steroid hormones provided the basis for identification of two classes of retinoic acid receptors, RARs and RXRs, each of which has three isoforms, α, β and ɣ. DNA manipulation and crystallographic studies revealed that the receptors contain discrete functional domains responsible for binding to DNA, ligands and cofactors. Ligand binding was shown to induce conformational changes in the receptors that cause release of corepressors and recruitment of coactivators to create functional complexes that are bound to consensus promoter DNA sequences called retinoic acid response elements (RAREs) and that cause opening of chromatin and transcription of adjacent genes. Homologous recombination technology allowed the development of mice lacking expression of retinoic acid receptors, individually or in various combinations, which demonstrated that the receptors exhibit vital, but redundant, functions in fetal development and in vision, reproduction, and other functions required for maintenance of adult life. More recent advancements in sequencing and proteomic technologies reveal the complexity of retinoic acid receptor involvement in cellular function through regulation of gene expression and kinase activity. Future directions will require systems biology approaches to decipher how these integrated networks affect human stem cells, health, and disease.
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35
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Rousseau GG. Fifty years ago: the quest for steroid hormone receptors. Mol Cell Endocrinol 2013; 375:10-3. [PMID: 23684885 DOI: 10.1016/j.mce.2013.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 04/29/2013] [Accepted: 05/07/2013] [Indexed: 01/18/2023]
Abstract
In 1963 Peter Karlson put forward the revolutionary "hormone-gene" hypothesis, which would change drastically the way in which steroid hormones were thought to act at the time. From a historical perspective, this review relates the acceptance of this initially controversial idea, the discovery of the steroid receptors and the key experiments that have led to the current understanding of the mechanism of steroid hormone action. It shows how, over 50years, the field has widened beyond all expectation and has contributed to major advances not only in endocrinology, but also in molecular biology, pharmacology and therapeutics.
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Affiliation(s)
- Guy G Rousseau
- de Duve Institute and Université Catholique de Louvain, Brussels, Belgium.
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36
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Ziv L, Muto A, Schoonheim PJ, Meijsing SH, Strasser D, Ingraham HA, Schaaf MJ, Yamamoto KR, Baier H. An affective disorder in zebrafish with mutation of the glucocorticoid receptor. Mol Psychiatry 2013; 18:681-91. [PMID: 22641177 PMCID: PMC4065652 DOI: 10.1038/mp.2012.64] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 03/26/2012] [Accepted: 04/03/2012] [Indexed: 11/25/2022]
Abstract
Upon binding of cortisol, the glucocorticoid receptor (GR) regulates the transcription of specific target genes, including those that encode the stress hormones corticotropin-releasing hormone (CRH) and adrenocorticotropic hormone. Dysregulation of the stress axis is a hallmark of major depression in human patients. However, it is still unclear how glucocorticoid signaling is linked to affective disorders. We identified an adult-viable zebrafish mutant in which the negative feedback on the stress response is disrupted, due to abolition of all transcriptional activity of GR. As a consequence, cortisol is elevated, but unable to signal through GR. When placed into an unfamiliar aquarium ('novel tank'), mutant fish become immobile ('freeze'), show reduced exploratory behavior and do not habituate to this stressor upon repeated exposure. Addition of the antidepressant fluoxetine to the holding water and social interactions restore normal behavior, followed by a delayed correction of cortisol levels. Fluoxetine does not affect the overall transcription of CRH, the mineralocorticoid receptor (MR), the serotonin transporter (Serta) or GR itself. Fluoxetine, however, suppresses the stress-induced upregulation of MR and Serta in both wild-type fish and mutants. Our studies show a conserved, protective function of glucocorticoid signaling in the regulation of emotional behavior and reveal novel molecular aspects of how chronic stress impacts vertebrate brain physiology and behavior. Importantly, the zebrafish model opens up the possibility of high-throughput drug screens in search of new classes of antidepressants.
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Affiliation(s)
- Limor Ziv
- Department of Physiology, Programs in Neuroscience, Genetics and Developmental & Stem Cell biology, University of California, San Francisco, USA
- Cancer Research Center, Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Akira Muto
- Department of Physiology, Programs in Neuroscience, Genetics and Developmental & Stem Cell biology, University of California, San Francisco, USA
| | - Peter J. Schoonheim
- Department of Physiology, Programs in Neuroscience, Genetics and Developmental & Stem Cell biology, University of California, San Francisco, USA
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Sebastiaan H. Meijsing
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, USA
| | - Daniel Strasser
- Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Holly A. Ingraham
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, USA
| | | | - Keith R. Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, USA
| | - Herwig Baier
- Department of Physiology, Programs in Neuroscience, Genetics and Developmental & Stem Cell biology, University of California, San Francisco, USA
- Max Planck Institute of Neurobiology, Department Genes – Circuits – Behavior, Martinsried, Germany
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37
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Man XY, Li W, Chen JQ, Zhou J, Landeck L, Zhang KH, Mu Z, Li CM, Cai SQ, Zheng M. Impaired nuclear translocation of glucocorticoid receptors: novel findings from psoriatic epidermal keratinocytes. Cell Mol Life Sci 2013; 70:2205-20. [PMID: 23334186 PMCID: PMC11113139 DOI: 10.1007/s00018-012-1255-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 12/19/2012] [Accepted: 12/27/2012] [Indexed: 01/21/2023]
Abstract
Psoriasis is a chronic proliferative skin disease and is usually treated with topical glucocorticoids, which act through the glucocorticoid receptor (GR), a component of the physiological systems essential for immune responses, differentiation, and homeostasis. To investigate the possible role of GR in the pathogenesis of psoriasis, normal and psoriatic lesional skin were recruited. Firstly, the immunolocalization of GR in the skin and cultured epidermal keratinocytes were determined by immunofluorescence. In normal skin and cultured human epidermal keratinocytes, intracellular GR is localized in the nuclei, while in psoriatic skin and cultured keratinocytes, GR is in the cytoplasm. Next, we investigated possible factors associated with the cytoplasmic distribution. We found that VEGF and IFN-γ led to impaired nuclear translocation of GR through p53 and microtubule-inhibitor, vincristine, and inhibited nuclear uptake of GR in normal keratinocytes. In addition to dexamethasone, interleukin (IL)-13 was also able to transfer GR into nuclei of psoriatic keratinocytes. Furthermore, discontinuation of dexamethasone induced cytoplasmic retention of GR in normal keratinocytes. In contrast, energy depletion of normal epidermal keratinocytes did not change the nuclear distribution of GR. To confirm our findings in vivo, an imiquimod-induced psoriasis-like skin mouse model was included. IL-13 ameliorated (but vincristine exacerbated) the skin lesions on the mouse. Taken together, our findings define that impaired nuclear translocation of GR is associated with VEGF, IFN-γ, p53, and microtubule. Therapeutic strategies designed to accumulate GR in the nucleus, such as IL-13, may be beneficial for the therapy of psoriasis.
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Affiliation(s)
- Xiao-Yong Man
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009 China
| | - Wei Li
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009 China
| | - Jia-Qi Chen
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009 China
| | - Jiong Zhou
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009 China
| | - Lilla Landeck
- Department of Dermatology, University of Osnabrueck, Osnabrueck, Germany
| | - Kai-Hong Zhang
- Department of Dermatology, Affiliated Hospital, Taishan Medical College, Taishan, China
| | - Zhen Mu
- Department of Dermatology, Affiliated Hospital, Taishan Medical College, Taishan, China
| | - Chun-Ming Li
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009 China
| | - Sui-Qing Cai
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009 China
| | - Min Zheng
- Department of Dermatology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009 China
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38
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Polman JAE, de Kloet ER, Datson NA. Two populations of glucocorticoid receptor-binding sites in the male rat hippocampal genome. Endocrinology 2013; 154:1832-44. [PMID: 23525215 DOI: 10.1210/en.2012-2187] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In the present study, genomic binding sites of glucocorticoid receptors (GR) were identified in vivo in the rat hippocampus applying chromatin immunoprecipitation followed by next-generation sequencing. We identified 2470 significant GR-binding sites (GBS) and were able to confirm GR binding to a random selection of these GBS covering a wide range of P values. Analysis of the genomic distribution of the significant GBS revealed a high prevalence of intragenic GBS. Gene ontology clusters involved in neuronal plasticity and other essential neuronal processes were overrepresented among the genes harboring a GBS or located in the vicinity of a GBS. Male adrenalectomized rats were challenged with increasing doses of the GR agonist corticosterone (CORT) ranging from 3 to 3000 μg/kg, resulting in clear differences in the GR-binding profile to individual GBS. Two groups of GBS could be distinguished: a low-CORT group that displayed GR binding across the full range of CORT concentrations, and a second high-CORT group that displayed significant GR binding only after administering the highest concentration of CORT. All validated GBS, in both the low-CORT and high-CORT groups, displayed mineralocorticoid receptor binding, which remained relatively constant from 30 μg/kg CORT upward. Motif analysis revealed that almost all GBS contained a glucocorticoid response element resembling the consensus motif in literature. In addition, motifs corresponding with new potential GR-interacting proteins were identified, such as zinc finger and BTB domain containing 3 (Zbtb3) and CUP (CG11181 gene product from transcript CG11181-RB), which may be involved in GR-dependent transactivation and transrepression, respectively. In conclusion, our results highlight the existence of 2 populations of GBS in the rat hippocampal genome.
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Affiliation(s)
- J Annelies E Polman
- Division of Medical Pharmacology, Leiden/Amsterdam Center for Drug Research, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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Lotter H, Helk E, Bernin H, Jacobs T, Prehn C, Adamski J, González-Roldán N, Holst O, Tannich E. Testosterone increases susceptibility to amebic liver abscess in mice and mediates inhibition of IFNγ secretion in natural killer T cells. PLoS One 2013; 8:e55694. [PMID: 23424637 PMCID: PMC3570563 DOI: 10.1371/journal.pone.0055694] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/02/2013] [Indexed: 11/18/2022] Open
Abstract
Amebic liver abscess (ALA), a parasitic disease due to infection with the protozoan Entamoeba histolytica, occurs age and gender dependent with strong preferences for adult males. Using a mouse model for ALA with a similar male bias for the disease, we have investigated the role of female and male sexual hormones and provide evidence for a strong contribution of testosterone. Removal of testosterone by orchiectomy significantly reduced sizes of abscesses in male mice, while substitution of testosterone increased development of ALA in female mice. Activation of natural killer T (NKT) cells, which are known to be important for the control of ALA, is influenced by testosterone. Specifically activated NKT cells isolated from female mice produce more IFNγ compared to NKT cells derived from male mice. This high level production of IFNγ in female derived NKT cells was inhibited by testosterone substitution, while the IFNγ production in male derived NKT cells was increased by orchiectomy. Gender dependent differences were not a result of differences in the total number of NKT cells, but a result of a higher activation potential for the CD4(-) NKT cell subpopulation in female mice. Taken together, we conclude that the hormone status of the host, in particular the testosterone level, determines susceptibility to ALA at least in a mouse model of the disease.
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Affiliation(s)
- Hannelore Lotter
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
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Yuan H, Upadhyay G, Lu J, Kopelovich L, Glazer RI. The chemopreventive effect of mifepristone on mammary tumorigenesis is associated with an anti-invasive and anti-inflammatory gene signature. Cancer Prev Res (Phila) 2012; 5:754-64. [PMID: 22427346 PMCID: PMC3437618 DOI: 10.1158/1940-6207.capr-11-0526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Progesterone receptor (PR) antagonists are potent antitumor agents in carcinogen and progestin-dependent mammary tumorigenesis models through both PR- and non-PR-mediated mechanisms. The PR antagonist mifepristone/RU486 has been used primarily as an abortifacient possessing high affinity for both the PR and glucocorticoid receptors (GR). To determine whether mifepristone would be effective as a chemopreventive agent, we assessed its effect on progestin/7,12-dimethylbenz(a)anthracene (DMBA)-induced mammary carcinogenesis in wild-type (WT) and estrogen receptor-α-positive (ER(+)) transgenic mice expressing the dominant-negative Pax8PPARγ (Pax8) fusion protein. Mifepristone administered at a dose of 2.5 mg significantly delayed mammary tumorigenesis in WT, but not in Pax8 mice, whereas, a three-fold higher dose almost completely blocked tumorigenesis in both WT and Pax8 mice. The sensitivity of WT mice to 2.5 mg mifepristone correlated with an expression profile of 79 genes in tumors, 52 of which exhibited the opposite response in Pax8 mice, and corresponded primarily to the downregulation of genes associated with metabolism, inflammation, and invasion. These results suggest that the chemopreventive activity of mifepristone in WT mice correlates with a specific gene expression signature that is associated with multiple nuclear receptor signaling pathways.
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MESH Headings
- 9,10-Dimethyl-1,2-benzanthracene
- Animals
- Antineoplastic Agents, Hormonal/pharmacology
- Antineoplastic Agents, Hormonal/therapeutic use
- Carcinogens
- Carcinoma/chemically induced
- Carcinoma/genetics
- Carcinoma/pathology
- Carcinoma/prevention & control
- Chemoprevention/methods
- Drug Evaluation, Preclinical
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/drug effects
- Hormone Antagonists/pharmacology
- Hormone Antagonists/therapeutic use
- Inflammation/genetics
- Mammary Neoplasms, Experimental/chemically induced
- Mammary Neoplasms, Experimental/genetics
- Mammary Neoplasms, Experimental/pathology
- Mammary Neoplasms, Experimental/prevention & control
- Mice
- Mice, Transgenic
- Microarray Analysis
- Mifepristone/pharmacology
- Mifepristone/therapeutic use
- Neoplasm Invasiveness/genetics
- PAX8 Transcription Factor
- Paired Box Transcription Factors/genetics
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Affiliation(s)
- Hongyan Yuan
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Geeta Upadhyay
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Jin Lu
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Levy Kopelovich
- Chemoprevention Agent Development Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland
| | - Robert I. Glazer
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
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41
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Winkler R, Benz V, Clemenz M, Bloch M, Foryst-Ludwig A, Wardat S, Witte N, Trappiel M, Namsolleck P, Mai K, Spranger J, Matthias G, Roloff T, Truee O, Kappert K, Schupp M, Matthias P, Kintscher U. Histone deacetylase 6 (HDAC6) is an essential modifier of glucocorticoid-induced hepatic gluconeogenesis. Diabetes 2012; 61:513-23. [PMID: 22210316 PMCID: PMC3266407 DOI: 10.2337/db11-0313] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In the current study, we investigated the importance of histone deacetylase (HDAC)6 for glucocorticoid receptor-mediated effects on glucose metabolism and its potential as a therapeutic target for the prevention of glucocorticoid-induced diabetes. Dexamethasone-induced hepatic glucose output and glucocorticoid receptor translocation were analyzed in wild-type (wt) and HDAC6-deficient (HDAC6KO) mice. The effect of the specific HDAC6 inhibitor tubacin was analyzed in vitro. wt and HDAC6KO mice were subjected to 3 weeks' dexamethasone treatment before analysis of glucose and insulin tolerance. HDAC6KO mice showed impaired dexamethasone-induced hepatic glucocorticoid receptor translocation. Accordingly, dexamethasone-induced expression of a large number of hepatic genes was significantly attenuated in mice lacking HDAC6 and by tubacin in vitro. Glucose output of primary hepatocytes from HDAC6KO mice was diminished. A significant improvement of dexamethasone-induced whole-body glucose intolerance as well as insulin resistance in HDAC6KO mice compared with wt littermates was observed. This study demonstrates that HDAC6 is an essential regulator of hepatic glucocorticoid-stimulated gluconeogenesis and impairment of whole-body glucose metabolism through modification of glucocorticoid receptor nuclear translocation. Selective pharmacological inhibition of HDAC6 may provide a future therapeutic option against the prodiabetogenic actions of glucocorticoids.
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Affiliation(s)
- Robin Winkler
- Institute of Pharmacology, Charité Medical University, Center for Cardiovascular Research, Berlin, Germany
| | - Verena Benz
- Institute of Pharmacology, Charité Medical University, Center for Cardiovascular Research, Berlin, Germany
| | - Markus Clemenz
- Institute of Pharmacology, Charité Medical University, Center for Cardiovascular Research, Berlin, Germany
| | - Mandy Bloch
- Institute of Pharmacology, Charité Medical University, Center for Cardiovascular Research, Berlin, Germany
| | - Anna Foryst-Ludwig
- Institute of Pharmacology, Charité Medical University, Center for Cardiovascular Research, Berlin, Germany
| | - Sami Wardat
- Institute of Pharmacology, Charité Medical University, Center for Cardiovascular Research, Berlin, Germany
| | - Nicole Witte
- Department of Endocrinology, Diabetes and Nutrition, Charité Medical University, Center for Cardiovascular Research, Berlin, Germany
| | - Manuela Trappiel
- Institute of Laboratory Medicine, Charité Medical University, Center for Cardiovascular Research, Berlin, Germany
| | - Pawel Namsolleck
- Institute of Pharmacology, Charité Medical University, Center for Cardiovascular Research, Berlin, Germany
| | - Knut Mai
- Department of Endocrinology, Diabetes and Nutrition, Charité Medical University, Center for Cardiovascular Research, Berlin, Germany
| | - Joachim Spranger
- Department of Endocrinology, Diabetes and Nutrition, Charité Medical University, Center for Cardiovascular Research, Berlin, Germany
| | - Gabriele Matthias
- Friedrich-Miescher-Institute for Biomedical Research, Basel, Switzerland
| | - Tim Roloff
- Friedrich-Miescher-Institute for Biomedical Research, Basel, Switzerland
| | - Oliver Truee
- Friedrich-Miescher-Institute for Biomedical Research, Basel, Switzerland
| | - Kai Kappert
- Institute of Laboratory Medicine, Charité Medical University, Center for Cardiovascular Research, Berlin, Germany
| | - Michael Schupp
- Department of Endocrinology, Diabetes and Nutrition, Charité Medical University, Center for Cardiovascular Research, Berlin, Germany
| | - Patrick Matthias
- Institute of Laboratory Medicine, Charité Medical University, Center for Cardiovascular Research, Berlin, Germany
| | - Ulrich Kintscher
- Institute of Pharmacology, Charité Medical University, Center for Cardiovascular Research, Berlin, Germany
- Corresponding author: Ulrich Kintscher,
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42
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Simian virus 40 strains with novel properties generated by replacing the viral enhancer with synthetic oligonucleotides. J Virol 2012; 86:3135-42. [PMID: 22238322 DOI: 10.1128/jvi.06293-11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Typical enhancers of viral or cellular genes are approximately 100 to 400 bp long and contain several transcription factor binding sites. Previously, we have shown that simian virus 40 (SV40) genomic DNA that lacks its own enhancer can be used as an "enhancer trap" since it reacquires infectivity upon incorporation of heterologous enhancers. Here, we show that SV40 infectivity can be restored with synthetic enhancers that are assembled by the host cell. We found that several oligonucleotides, cotransfected with enhancerless SV40 DNA into host cells, were incorporated into the viral genome via cellular DNA end joining. The oligonucleotides tested included metal response elements (MREs), the binding sites for the transcription factor MTF-1, which induces gene activity in response to heavy metals. These recombinant SV40 strains showed preferential growth on cells overloaded with zinc or cadmium. We also cotransfected enhancerless SV40 DNA with oligonucleotides corresponding to enhancer motifs of human and mouse cytomegalovirus (HCMV and MCMV, respectively). In contrast to SV40 wild type, the viruses with cytomegalovirus-derived patchwork enhancers strongly expressed T-antigen in human HEK293 cells, accompanied by viral DNA replication. Occasionally, we also observed the assembly of functional viral genomes by incorporation of fragments of bovine DNA, an ingredient of the fetal calf serum in the medium. These fragments contained, among other sites, binding sites for AP-1 and CREB transcription factors. Taken together, our studies show that viruses with novel properties can be generated by intracellular incorporation of synthetic enhancer DNA motifs.
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43
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Schweingruber N, Reichardt SD, Lühder F, Reichardt HM. Mechanisms of glucocorticoids in the control of neuroinflammation. J Neuroendocrinol 2012; 24:174-82. [PMID: 21615563 DOI: 10.1111/j.1365-2826.2011.02161.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Glucocorticoids (GCs) are widely used to treat inflammatory diseases such as multiple sclerosis (MS). They predominantly act through the GC receptor, a member of the nuclear receptor superfamily that controls transcription by several different mechanisms. Owing to its ubiquitous expression, there are a variety of cell types that could serve as GC targets in the pathogenesis and treatment of MS. This brings about a great diversity of mechanisms potentially involved in the modulation of neuroinflammation by GCs, including the induction of apoptosis, repression of pro-inflammatory mediators and the expansion of myeloid-derived suppressor cells. Nevertheless, it is not well understood which of these mechanisms are essential for therapeutic efficacy. In this review, we summarise findings made concerning the actions of GCs in MS and its animal model experimental autoimmune encephalomyelitis, and also elucidate current concepts and developments that pertain to this clinically highly relevant treatment regimen.
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Affiliation(s)
- N Schweingruber
- Department of Cellular and Molecular Immunology, University of Göttingen Medical School, Germany
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44
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Hidalgo AA, Deeb KK, Pike JW, Johnson CS, Trump DL. Dexamethasone enhances 1alpha,25-dihydroxyvitamin D3 effects by increasing vitamin D receptor transcription. J Biol Chem 2011; 286:36228-37. [PMID: 21868377 DOI: 10.1074/jbc.m111.244061] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Calcitriol, the active form of vitamin D, in combination with the glucocorticoid dexamethasone (Dex) has been shown to increase the antitumor effects of calcitriol in squamous cell carcinoma. In this study we found that pretreatment with Dex potentiates calcitriol effects by inhibiting cell growth and increasing vitamin D receptor (VDR) and VDR-mediated transcription. Treatment with actinomycin D inhibits Vdr mRNA synthesis, indicating that Dex regulates VDR expression at transcriptional level. Real time PCR shows that treatment with Dex increases Vdr transcripts in a time- and a dose-dependent manner, indicating that Dex directly regulates expression of Vdr. RU486, an inhibitor of glucocorticoids, inhibits Dex-induced Vdr expression. In addition, the silencing of glucocorticoid receptor (GR) abolishes the induction of Vdr by Dex, indicating that Dex increases Vdr transcripts in a GR-dependent manner. A fragment located 5.2 kb upstream of Vdr transcription start site containing two putative glucocorticoid response elements (GREs) was evaluated using a luciferase-based reporter assay. Treatment with 100 nm Dex induces transcription of luciferase driven by the fragment. Deletion of the GRE distal to transcription start site was sufficient to abolish Dex induction of luciferase. Also, chromatin immunoprecipitation reveals recruitment of GR to distal GRE with Dex treatment. We conclude that Dex increases VDR and vitamin D effects by increasing Vdr de novo transcription in a GR-dependent manner.
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Affiliation(s)
- Alejandro A Hidalgo
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, New York 14214, USA
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45
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Fluhr R, Kuhlemeier C, Nagy F, Chua NH. Organ-specific and light-induced expression of plant genes. Science 2010; 232:1106-12. [PMID: 17754498 DOI: 10.1126/science.232.4754.1106] [Citation(s) in RCA: 159] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Light plays a pivotal role in the development of plants. The photoregulation of plant genes involves recognition of light quality and quantity by phytochrome and other light receptors. Two gene families, rbcS and Cab, which code for abundant proteins active in photosynthesis, the small subunit of ribulose bisphosphate carboxylase and the chlorophyll a/b binding protein, show a 20-to 50-fold increase in transcript abundance in the light. Analyses in calli and transgenic plants of deletions of the rbcS gene and of chimeric constructions has allowed localization of two regions involved in light-induced transcription. One element is confined to a 33-base pair region surrounding the TATA box. In addition, an enhancer-like element contained within a 240-base pair fragment can confer phytochrome-induced transcription and organ specificity on nonregulated promoters.
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46
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Newton R, Leigh R, Giembycz MA. Pharmacological strategies for improving the efficacy and therapeutic ratio of glucocorticoids in inflammatory lung diseases. Pharmacol Ther 2009; 125:286-327. [PMID: 19932713 DOI: 10.1016/j.pharmthera.2009.11.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Accepted: 11/02/2009] [Indexed: 10/20/2022]
Abstract
Glucocorticoids are widely used to treat various inflammatory lung diseases. Acting via the glucocorticoid receptor (GR), they exert clinical effects predominantly by modulating gene transcription. This may be to either induce (transactivate) or repress (transrepress) gene transcription. However, certain individuals, including those who smoke, have certain asthma phenotypes, chronic obstructive pulmonary disease (COPD) or some interstitial diseases may respond poorly to the beneficial effects of glucocorticoids. In these cases, high dose, often oral or parental, glucocorticoids are typically prescribed. This generally leads to adverse effects that compromise clinical utility. There is, therefore, a need to enhance the clinical efficacy of glucocorticoids while minimizing adverse effects. In this context, a long-acting beta(2)-adrenoceptor agonist (LABA) can enhance the clinical efficacy of an inhaled corticosteroid (ICS) in asthma and COPD. Furthermore, LABAs can augment glucocorticoid-dependent gene expression and this action may account for some of the benefits of LABA/ICS combination therapies when compared to ICS given as a monotherapy. In addition to metabolic genes and other adverse effects that are induced by glucocorticoids, there are many other glucocorticoid-inducible genes that have significant anti-inflammatory potential. We therefore advocate a move away from the search for ligands of GR that dissociate transactivation from transrepression. Instead, we submit that ligands should be functionally screened by virtue of their ability to induce or repress biologically-relevant genes in target tissues. In this review, we discuss pharmacological methods by which selective GR modulators and "add-on" therapies may be exploited to improve the clinical efficacy of glucocorticoids while reducing potential adverse effects.
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Affiliation(s)
- Robert Newton
- Department of Cell Biology and Anatomy, Airway Inflammation Group, Institute of Infection, Immunity and Inflammation, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada.
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47
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Xie J. Control of alternative pre-mRNA splicing by Ca(++) signals. BIOCHIMICA ET BIOPHYSICA ACTA 2008; 1779:438-52. [PMID: 18258215 PMCID: PMC3500379 DOI: 10.1016/j.bbagrm.2008.01.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2007] [Revised: 12/18/2007] [Accepted: 01/08/2008] [Indexed: 02/06/2023]
Abstract
Alternative pre-mRNA splicing is a common way of gene expression regulation in metazoans. The selective use of specific exons can be modulated in response to various manipulations that alter Ca(++) signals, particularly in neurons. A number of splicing factors have also been found to be controlled by Ca(++) signals. Moreover, pre-mRNA elements have been identified that are essential and sufficient to mediate Ca(++)-regulated splicing, providing model systems for dissecting the involved molecular components. In neurons, this regulation likely contributes to the fine-tuning of neuronal properties.
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Affiliation(s)
- Jiuyong Xie
- Department of Physiology, Faculty of Medicine, University of Manitoba, 730 William Avenue, Winnipeg, Canada MB R3E 3J7.
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48
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van der Laan S, Meijer OC. Pharmacology of glucocorticoids: Beyond receptors. Eur J Pharmacol 2008; 585:483-91. [DOI: 10.1016/j.ejphar.2008.01.060] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 01/11/2008] [Accepted: 01/24/2008] [Indexed: 11/28/2022]
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49
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So AYL, Chaivorapol C, Bolton EC, Li H, Yamamoto KR. Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor. PLoS Genet 2007; 3:e94. [PMID: 17559307 PMCID: PMC1904358 DOI: 10.1371/journal.pgen.0030094] [Citation(s) in RCA: 240] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Accepted: 04/23/2007] [Indexed: 11/19/2022] Open
Abstract
The glucocorticoid receptor (GR) associates with glucocorticoid response elements (GREs) and regulates selective gene transcription in a cell-specific manner. Native GREs are typically thought to be composite elements that recruit GR as well as other regulatory factors into functional complexes. We assessed whether GR occupancy is commonly a limiting determinant of GRE function as well as the extent to which core GR binding sequences and GRE architecture are conserved at functional loci. We surveyed 100-kb regions surrounding each of 548 known or potentially glucocorticoid-responsive genes in A549 human lung cells for GR-occupied GREs. We found that GR was bound in A549 cells predominately near genes responsive to glucocorticoids in those cells and not at genes regulated by GR in other cells. The GREs were positionally conserved at each responsive gene but across the set of responsive genes were distributed equally upstream and downstream of the transcription start sites, with 63% of them >10 kb from those sites. Strikingly, although the core GR binding sequences across the set of GREs varied extensively around a consensus, the precise sequence at an individual GRE was conserved across four mammalian species. Similarly, sequences flanking the core GR binding sites also varied among GREs but were conserved at individual GREs. We conclude that GR occupancy is a primary determinant of glucocorticoid responsiveness in A549 cells and that core GR binding sequences as well as GRE architecture likely harbor gene-specific regulatory information. The glucocorticoid receptor (GR) regulates a myriad of physiological functions, such as cell differentiation and metabolism, achieved through modulating transcription in a cell- and gene-specific manner. However, the determinants that specify cell- and gene-specific GR transcriptional regulation are not well established. We describe three properties that contribute to this specificity: (1) GR occupancy at genomic glucocorticoid response elements (GREs) appears to be a primary determinant of glucocorticoid responsiveness; (2) the DNA sequences bound by GR vary widely around a consensus, but the precise sequences of individual GREs are highly conserved, suggesting a role for these sequences in gene-specific GR transcriptional regulation; and (3) native chromosomal GREs were generally found to be composite elements, comprised of multiple factor binding sites that were highly variable in composition, but as with the GR binding sequences, highly conserved at individual GREs. In addition, we discovered that most GREs were positioned far from their GR target genes and that they were equally distributed upstream and downstream of the target genes. These findings, which may be applicable to other regulatory factors, provide fundamental insights for understanding cell- and gene-specific transcriptional regulation.
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Affiliation(s)
- Alex Yick-Lun So
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, California, United States of America
| | - Christina Chaivorapol
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
- Graduate Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California, United States of America
| | - Eric C Bolton
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
| | - Hao Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
- Graduate Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California, United States of America
| | - Keith R Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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50
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Bhure S, Sharma B. Cloning and characterization of ovine alphaS1-casein gene promoter: a transfection study in rat mammary gland cell line. ACTA ACUST UNITED AC 2007; 18:39-46. [PMID: 17364812 DOI: 10.1080/10425170601017145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Promoter regions of milk protein genes are frequently used to produce pharmaceutically and medically important proteins in the mammary gland of transgenic animals and also can be used for the construction of an inducible eukaryotic expression vector. The aim of the present study was to clone, sequence and characterize the regulatory elements in ovine alphaS1-CSNGP. For the first time we have cloned and sequenced region extending from - 2136 to +49 bp containing 5'-flanking region and exon I. Computational analysis of the sequence showed presence of core promoter elements viz., TATA box, CAAT box and initiator sequence. Mammary gland specific sequences included MGF/STAT 5, MPBF, Yu Lee 2, 4 and 5, Oka box C and hormone responsive elements (HRE) viz., GRE, PRE, PRL, IRE and also Polyoma enhancer 3 sequences. Computational analysis data is validated by following the reporter gene expression studies in rat breast cell line. Six reporter gene constructs under the control of full length, proximal, distal, minimal and proximal-distal fused promoter segments were constructed to assess the effect of presence or absence of few selected regulatory elements on expression ability of the promoter. Based on qualitative evaluation of fluorescence, the pGFP-F/VspI showed highest fluorescence followed by pGFP-P, pGFP-F/SpeI, pGFPminimal and pGFP-D.
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Affiliation(s)
- Sanjeevkumar Bhure
- Project Directorate on Animal Disease Monitoring Surveillance (PD_ADMAS). Hebbal, Bangalore, Karnataka, 560 024. India.
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