51
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McDowell IC, Barrera A, D'Ippolito AM, Vockley CM, Hong LK, Leichter SM, Bartelt LC, Majoros WH, Song L, Safi A, Koçak DD, Gersbach CA, Hartemink AJ, Crawford GE, Engelhardt BE, Reddy TE. Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding. Genome Res 2018; 28:1272-1284. [PMID: 30097539 PMCID: PMC6120625 DOI: 10.1101/gr.233346.117] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 07/05/2018] [Indexed: 12/22/2022]
Abstract
Glucocorticoids are potent steroid hormones that regulate immunity and metabolism by activating the transcription factor (TF) activity of glucocorticoid receptor (GR). Previous models have proposed that DNA binding motifs and sites of chromatin accessibility predetermine GR binding and activity. However, there are vast excesses of both features relative to the number of GR binding sites. Thus, these features alone are unlikely to account for the specificity of GR binding and activity. To identify genomic and epigenetic contributions to GR binding specificity and the downstream changes resultant from GR binding, we performed hundreds of genome-wide measurements of TF binding, epigenetic state, and gene expression across a 12-h time course of glucocorticoid exposure. We found that glucocorticoid treatment induces GR to bind to nearly all pre-established enhancers within minutes. However, GR binds to only a small fraction of the set of accessible sites that lack enhancer marks. Once GR is bound to enhancers, a combination of enhancer motif composition and interactions between enhancers then determines the strength and persistence of GR binding, which consequently correlates with dramatic shifts in enhancer activation. Over the course of several hours, highly coordinated changes in TF binding and histone modification occupancy occur specifically within enhancers, and these changes correlate with changes in the expression of nearby genes. Following GR binding, changes in the binding of other TFs precede changes in chromatin accessibility, suggesting that other TFs are also sensitive to genomic features beyond that of accessibility.
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Affiliation(s)
- Ian C McDowell
- Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Alejandro Barrera
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - Anthony M D'Ippolito
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,University Program in Genetics and Genomics, Duke University, Durham, North Carolina 27708, USA
| | - Christopher M Vockley
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - Linda K Hong
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Pediatrics, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - Sarah M Leichter
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - Luke C Bartelt
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - William H Majoros
- Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA
| | - Lingyun Song
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Pediatrics, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Pediatrics, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - D Dewran Koçak
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
| | - Charles A Gersbach
- Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,University Program in Genetics and Genomics, Duke University, Durham, North Carolina 27708, USA.,Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA.,Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27708, USA
| | - Alexander J Hartemink
- Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Computer Science, Duke University, Durham, North Carolina 27708, USA.,Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Gregory E Crawford
- Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Pediatrics, Duke University Medical Center, Durham, North Carolina 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27708, USA
| | - Barbara E Engelhardt
- Department of Computer Science, Princeton University, Princeton, New Jersey 08540, USA.,Center for Statistics and Machine Learning, Princeton University, Princeton, New Jersey 08540, USA
| | - Timothy E Reddy
- Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA.,Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina 27708, USA.,University Program in Genetics and Genomics, Duke University, Durham, North Carolina 27708, USA.,Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27708, USA
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52
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Comprehensive profiling of transcriptional networks specific for lactogenic differentiation of HC11 mammary epithelial stem-like cells. Sci Rep 2018; 8:11777. [PMID: 30082875 PMCID: PMC6079013 DOI: 10.1038/s41598-018-30122-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 07/13/2018] [Indexed: 12/31/2022] Open
Abstract
The development of mammary gland as a lactogenic tissue is a highly coordinated multistep process. The epithelial cells of lactiferous tubules undergo profound changes during the developmental window of puberty, pregnancy, and lactation. Several hormones including estrogen, progesterone, glucocorticoids and prolactin act in concert, and orchestrate the development of mammary gland. Understanding the gene regulatory networks that coordinate proliferation and differentiation of HC11 Mammary Epithelial stem-like Cells (MEC) under the influence of lactogenic hormones is critical for elucidating the mechanism of lactogenesis in detail. In this study, we analyzed transcriptome profiles of undifferentiated MEC (normal) and compared them with Murine Embryonic Stem Cells (ESC) using next-generation mRNA sequencing. Further, we analyzed the transcriptome output during lactogenic differentiation of MEC following treatment with glucocorticoids (primed state) and both glucocorticoids and prolactin together (prolactin state). We established stage-specific gene regulatory networks in ESC and MEC (normal, priming and prolactin states). We validated the top up-and downregulated genes in each stage of differentiation of MEC by RT-PCR and found that they are comparable with that of RNA-seq data. HC11 MEC display decreased expression of Pou5f1 and Sox2, which is crucial for the differentiation of MEC, which otherwise ensure pluripotency to ESC. Cited4 is induced during priming and is involved in milk secretion. MEC upon exposure to both glucocorticoids and prolactin undergo terminal differentiation, which is associated with the expression of several genes, including Xbp1 and Cbp that are required for cell growth and differentiation. Our study also identified differential expression of transcription factors and epigenetic regulators in each stage of lactogenic differentiation. We also analyzed the transcriptome data for the pathways that are selectively activated during lactogenic differentiation. Further, we found that selective expression of chromatin modulators (Dnmt3l, Chd9) in response to glucocorticoids suggests a highly coordinated stage-specific lactogenic differentiation of MEC.
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53
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Jubb AW, Boyle S, Hume DA, Bickmore WA. Glucocorticoid Receptor Binding Induces Rapid and Prolonged Large-Scale Chromatin Decompaction at Multiple Target Loci. Cell Rep 2018; 21:3022-3031. [PMID: 29241532 PMCID: PMC5745231 DOI: 10.1016/j.celrep.2017.11.053] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 10/01/2017] [Accepted: 11/15/2017] [Indexed: 12/26/2022] Open
Abstract
Glucocorticoids act by binding to the glucocorticoid receptor (GR), which binds to specific motifs within enhancers of target genes to activate transcription. Previous studies have suggested that GRs can promote interactions between gene promoters and distal elements within target loci. In contrast, we demonstrate here that glucocorticoid addition to mouse bone-marrow-derived macrophages produces very rapid chromatin unfolding detectable by fluorescence in situ hybridization (FISH) at loci associated with GR binding. Rapid chromatin decompaction was generally not dependent on transcription at those loci that are known to be inducible in both mouse and human macrophages and was sustained for up to 5 days following ligand removal. Chromatin decompaction was not dependent upon persistent GR binding, which decayed fully after 24 hr. We suggest that sustained large-scale chromatin reorganization forms an important part of the response to glucocorticoid and might contribute to glucocorticoid sensitivity and resistance. Glucocorticoids can induce rapid and persistent chromatin decompaction Transcription is not essential for chromatin decompaction Large-scale chromatin organization may modulate the glucocorticoid response
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Affiliation(s)
- Alasdair W Jubb
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK; The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK; Department of Medicine, University of Cambridge, Box 93, Addenbrookes Hospital, Hills Road, Cambridge CB2 2QQ, UK
| | - Shelagh Boyle
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - David A Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK; Mater Research-University of Queensland, Translational Research Institute, 37 Kent Street, Woolloongabba, QLD 4102, Australia.
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.
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54
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Morgan MD, Marioni JC. CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness. Genome Biol 2018; 19:81. [PMID: 29945659 PMCID: PMC6020341 DOI: 10.1186/s13059-018-1461-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 06/04/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Population phenotypic variation can arise from genetic differences between individuals, or from cellular heterogeneity in an isogenic group of cells or organisms. The emergence of gene expression differences between genetically identical cells is referred to as gene expression noise, the sources of which are not well understood. RESULTS In this work, by studying gene expression noise between multiple cell lineages and mammalian species, we find consistent evidence of a role for CpG islands as sources of gene expression noise. Variation in noise among CpG island promoters can be partially attributed to differences in island size, in which short islands have noisier gene expression. Building on these findings, we investigate the potential for short CpG islands to act as fast response elements to environmental stimuli. Specifically, we find that these islands are enriched amongst primary response genes in SWI/SNF-independent stimuli, suggesting that expression noise is an indicator of promoter responsiveness. CONCLUSIONS Thus, through the integration of single-cell RNA expression profiling, chromatin landscape and temporal gene expression dynamics, we have uncovered a role for short CpG island promoters as fast response elements.
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Affiliation(s)
- Michael D Morgan
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - John C Marioni
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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55
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Shinkai Y, Kuramochi M, Doi M. Regulation of chromatin states and gene expression during HSN neuronal maturation is mediated by EOR-1/PLZF, MAU-2/cohesin loader, and SWI/SNF complex. Sci Rep 2018; 8:7942. [PMID: 29786685 PMCID: PMC5962631 DOI: 10.1038/s41598-018-26149-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 05/01/2018] [Indexed: 01/03/2023] Open
Abstract
Newborn neurons mature by distinct and sequential steps through the timely induction of specific gene expression programs in concert with epigenetic changes. However, it has been difficult to investigate the relationship between gene expression and epigenetic changes at a single-cell resolution during neuronal maturation. In this study, we investigated the maturation of hermaphrodite-specific neurons (HSNs) in C. elegans, which provided the link between chromatin dynamics, gene expression, and the degree of neuronal maturation at a single-cell resolution. Our results demonstrated that chromatin composition in the promoter region of several genes acting for neuronal terminal maturation was modulated at an early developmental stage, and is dependent on the function of the transcription factor EOR-1/PLZF and the cohesin loader MAU-2/MAU2. Components of the SWI/SNF chromatin remodeling complex were also required for the proper expression of terminal maturation genes. Epistasis analyses suggested that eor-1 functions with mau-2 and swsn-1 in the same genetic pathway to regulate the maturation of HSNs. Collectively, our study provides a novel approach to analyze neuronal maturation and proposes that predefined epigenetic modifications, mediated by EOR-1, MAU-2, and the SWI/SNF complex, are important for the preparation of future gene expression programs in neuronal terminal maturation.
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Affiliation(s)
- Yoichi Shinkai
- Molecular Neurobiology Research Group and DAI-Lab, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
| | - Masahiro Kuramochi
- Molecular Neurobiology Research Group and DAI-Lab, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8561, Japan
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Chiba, 277-8565, Japan
| | - Motomichi Doi
- Molecular Neurobiology Research Group and DAI-Lab, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1, Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
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56
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Stubbs FE, Birnie MT, Biddie SC, Lightman SL, Conway-Campbell BL. SKOV3 cells containing a truncated ARID1a protein have a restricted genome-wide response to glucocorticoids. Mol Cell Endocrinol 2018; 461:226-235. [PMID: 28942102 DOI: 10.1016/j.mce.2017.09.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 08/07/2017] [Accepted: 09/13/2017] [Indexed: 12/11/2022]
Abstract
AT-rich interacting domain subunit 1a (ARID1a) is an essential SWI/SNF component frequently mutated in human cancers. ARID1a mutations have also been associated with glucocorticoid resistance, potentially related to the well-established role of the SWI/SNF complex in glucocorticoid target gene regulation. Glucocorticoids are steroid hormones important for regulating many physiological processes through the activation of the glucocorticoid receptor (GR). As GR interacts directly with ARID1a, we hypothesized that a truncating ARID mutation would interfere with GR-dependent gene regulation. Using high throughput RNA sequencing (RNA-SEQ) we show a restricted glucocorticoid response in SKOV3 cells, which contain an inactivating ARID1a mutation. We also show a lack of GR binding at the GR-dependent regulatory site in the Period 1 gene, which has previously been shown to require chromatin remodelling. Taken together, our data suggests that ARID1a may be required for regulation of a subset of glucocorticoid responsive genes. In the case of SKOV3 cells, in which ARID1a is mutated, glucocorticoid-dependent transcriptional regulation of these genes is significantly impaired.
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Affiliation(s)
- F E Stubbs
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, School of Clinical Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol BS1 3NY, UK.
| | - M T Birnie
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, School of Clinical Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol BS1 3NY, UK.
| | - S C Biddie
- West Hertfordshire NHS Trust, Watford General Hospitals, Vicarage Road, Watford, Hertfordshire WD18 0HB, UK.
| | - S L Lightman
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, School of Clinical Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol BS1 3NY, UK.
| | - B L Conway-Campbell
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, School of Clinical Sciences, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol BS1 3NY, UK.
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57
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Quénet D. Histone Variants and Disease. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 335:1-39. [DOI: 10.1016/bs.ircmb.2017.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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58
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Liberman AC, Budziñski ML, Sokn C, Gobbini RP, Steininger A, Arzt E. Regulatory and Mechanistic Actions of Glucocorticoids on T and Inflammatory Cells. Front Endocrinol (Lausanne) 2018; 9:235. [PMID: 29867767 PMCID: PMC5964134 DOI: 10.3389/fendo.2018.00235] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/25/2018] [Indexed: 12/24/2022] Open
Abstract
Glucocorticoids (GCs) play an important role in regulating the inflammatory and immune response and have been used since decades to treat various inflammatory and autoimmune disorders. Fine-tuning the glucocorticoid receptor (GR) activity is instrumental in the search for novel therapeutic strategies aimed to reduce pathological signaling and restoring homeostasis. Despite the primary anti-inflammatory actions of GCs, there are studies suggesting that under certain conditions GCs may also exert pro-inflammatory responses. For these reasons the understanding of the GR basic mechanisms of action on different immune cells in the periphery (e.g., macrophages, dendritic cells, neutrophils, and T cells) and in the brain (microglia) contexts, that we review in this chapter, is a continuous matter of interest and may reveal novel therapeutic targets for the treatment of immune and inflammatory response.
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Affiliation(s)
- Ana C. Liberman
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) – CONICET – Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Maia L. Budziñski
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) – CONICET – Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Clara Sokn
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) – CONICET – Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Romina Paula Gobbini
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) – CONICET – Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Anja Steininger
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) – CONICET – Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Eduardo Arzt
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) – CONICET – Partner Institute of the Max Planck Society, Buenos Aires, Argentina
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- *Correspondence: Eduardo Arzt,
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59
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Weikum ER, de Vera IMS, Nwachukwu JC, Hudson WH, Nettles KW, Kojetin DJ, Ortlund EA. Tethering not required: the glucocorticoid receptor binds directly to activator protein-1 recognition motifs to repress inflammatory genes. Nucleic Acids Res 2017; 45:8596-8608. [PMID: 28591827 PMCID: PMC5737878 DOI: 10.1093/nar/gkx509] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/05/2017] [Indexed: 12/22/2022] Open
Abstract
The glucocorticoid receptor (GR) is a ligand-regulated transcription factor that controls the expression of extensive gene networks, driving both up- and down-regulation. GR utilizes multiple DNA-binding-dependent and -independent mechanisms to achieve context-specific transcriptional outcomes. The DNA-binding-independent mechanism involves tethering of GR to the pro-inflammatory transcription factor activator protein-1 (AP-1) through protein-protein interactions. This mechanism has served as the predominant model of GR-mediated transrepression of inflammatory genes. However, ChIP-seq data have consistently shown GR to occupy AP-1 response elements (TREs), even in the absence of AP-1. Therefore, the current model is insufficient to explain GR action at these sites. Here, we show that GR regulates a subset of inflammatory genes in a DNA-binding-dependent manner. Using structural biology and biochemical approaches, we show that GR binds directly to TREs via sequence-specific contacts to a GR-binding sequence (GBS) half-site found embedded within the TRE motif. Furthermore, we show that GR-mediated transrepression observed at TRE sites to be DNA-binding-dependent. This represents a paradigm shift in the field, showing that GR uses multiple mechanisms to suppress inflammatory gene expression. This work further expands our understanding of this complex multifaceted transcription factor.
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Affiliation(s)
- Emily R Weikum
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ian Mitchelle S de Vera
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jerome C Nwachukwu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - William H Hudson
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kendall W Nettles
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Douglas J Kojetin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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60
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Kelso TWR, Porter DK, Amaral ML, Shokhirev MN, Benner C, Hargreaves DC. Chromatin accessibility underlies synthetic lethality of SWI/SNF subunits in ARID1A-mutant cancers. eLife 2017; 6:30506. [PMID: 28967863 PMCID: PMC5643100 DOI: 10.7554/elife.30506] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/28/2017] [Indexed: 02/06/2023] Open
Abstract
ARID1A, a subunit of the SWI/SNF chromatin remodeling complex, is frequently mutated in cancer. Deficiency in its homolog ARID1B is synthetically lethal with ARID1A mutation. However, the functional relationship between these homologs has not been explored. Here, we use ATAC-seq, genome-wide histone modification mapping, and expression analysis to examine colorectal cancer cells lacking one or both ARID proteins. We find that ARID1A has a dominant role in maintaining chromatin accessibility at enhancers, while the contribution of ARID1B is evident only in the context of ARID1A mutation. Changes in accessibility are predictive of changes in expression and correlate with loss of H3K4me and H3K27ac marks, nucleosome spacing, and transcription factor binding, particularly at growth pathway genes including MET. We find that ARID1B knockdown in ARID1A mutant ovarian cancer cells causes similar loss of enhancer architecture, suggesting that this is a conserved function underlying the synthetic lethality between ARID1A and ARID1B.
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Affiliation(s)
- Timothy W R Kelso
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, California, United States
| | - Devin K Porter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, California, United States
| | - Maria Luisa Amaral
- The Razavi Newman Integrative Genomics and Bioinformatics Core Facility, Salk Institute for Biological Studies, California, United States
| | - Maxim N Shokhirev
- The Razavi Newman Integrative Genomics and Bioinformatics Core Facility, Salk Institute for Biological Studies, California, United States
| | - Christopher Benner
- Department of Medicine, University of California San Diego, California, United States
| | - Diana C Hargreaves
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, California, United States
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61
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Abstract
Glucocorticosteroids are the most effective anti-inflammatory therapy for asthma but are relatively ineffective in COPD. Glucocorticoids are broad-spectrum anti-inflammatory drugs that suppress inflammation via several molecular mechanisms. Glucocorticoids suppress the multiple inflammatory genes that are activated in asthma by reversing histone acetylation of activated inflammatory genes through binding of ligand-bound glucocorticoid receptors (GR) to coactivator molecules and recruitment of histone deacetylase-2 (HDAC2) to the activated inflammatory gene transcription complex (trans-repression). At higher concentrations of glucocorticoids GR homodimers interact with DNA recognition sites to activate transcription through increased histone acetylation of anti-inflammatory genes and transcription of several genes linked to glucocorticoid side effects (trans-activation). Glucocorticoids also have post-transcriptional effects and decrease stability of some proinflammatory mRNAs. Decreased glucocorticoid responsiveness is found in patients with severe asthma and asthmatics who smoke, as well as in all patients with COPD. Several molecular mechanisms of glucocorticoid resistance have now been identified which involve phosphorylation and other post-translational modifications of GR. HDAC2 is markedly reduced in activity and expression as a result of oxidative/nitrative stress and pi3 kinase-δ inhibition, so that inflammation is resistant to the anti-inflammatory actions of glucocorticoids. Dissociated glucocorticoids and selective GR modulators which show improved trans-repression over trans-activation effects have been developed to reduce side effects, but so far it has been difficult to dissociate anti-inflammatory effects from adverse effects. In patients with glucocorticoid resistance alternative anti-inflammatory treatments are being investigated as well as drugs that may reverse the molecular mechanisms of glucocorticoid resistance.
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62
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Paakinaho V, Presman DM, Ball DA, Johnson TA, Schiltz RL, Levitt P, Mazza D, Morisaki T, Karpova TS, Hager GL. Single-molecule analysis of steroid receptor and cofactor action in living cells. Nat Commun 2017. [PMID: 28635963 PMCID: PMC5482060 DOI: 10.1038/ncomms15896] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Population-based assays have been employed extensively to investigate the interactions of transcription factors (TFs) with chromatin and are often interpreted in terms of static and sequential binding. However, fluorescence microscopy techniques reveal a more dynamic binding behaviour of TFs in live cells. Here we analyse the strengths and limitations of in vivo single-molecule tracking and performed a comprehensive analysis on the intranuclear dwell times of four steroid receptors and a number of known cofactors. While the absolute residence times estimates can depend on imaging acquisition parameters due to sampling bias, our results indicate that only a small proportion of factors are specifically bound to chromatin at any given time. Interestingly, the glucocorticoid receptor and its cofactors affect each other’s dwell times in an asymmetric manner. Overall, our data indicate transient rather than stable TF-cofactors chromatin interactions at response elements at the single-molecule level. Transcription factors (TFs) are thought to regulate gene expression by stably binding to target DNA elements. Here, the authors use single-molecule tracking to analyse the dynamic behaviour of steroid receptors TFs and show that most specific interactions with chromatin are transient and dynamic.
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Affiliation(s)
- Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - David A Ball
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - R Louis Schiltz
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - Peter Levitt
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - Davide Mazza
- Istituto Scientifico Ospedale San Raffaele, Centro di Imaging Sperimentale e Università Vita-Salute San Raffaele, 20132 Milano, Italy
| | - Tatsuya Morisaki
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - Tatiana S Karpova
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Building 41, 41 Library Drive, Bethesda, Maryland 20892, USA
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Whirledge S, Cidlowski JA. Glucocorticoids and Reproduction: Traffic Control on the Road to Reproduction. Trends Endocrinol Metab 2017; 28:399-415. [PMID: 28274682 PMCID: PMC5438761 DOI: 10.1016/j.tem.2017.02.005] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/06/2017] [Accepted: 02/12/2017] [Indexed: 02/06/2023]
Abstract
Glucocorticoids are steroid hormones that regulate diverse cellular functions and are essential to facilitate normal physiology. However, stress-induced levels of glucocorticoids result in several pathologies including profound reproductive dysfunction. Compelling new evidence indicates that glucocorticoids are crucial to the establishment and maintenance of reproductive function. The fertility-promoting or -inhibiting activity of glucocorticoids depends on timing, dose, and glucocorticoid responsiveness within a given tissue, which is mediated by the glucocorticoid receptor (GR). The GR gene and protein are subject to cellular processing, contributing to signaling diversity and providing a mechanism by which both physiological and stress-induced levels of glucocorticoids function in a cell-specific manner. Understanding how glucocorticoids regulate fertility and infertility may lead to novel approaches to the regulation of reproductive function.
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Affiliation(s)
- Shannon Whirledge
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - John A Cidlowski
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC 27709, USA.
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64
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Grbesa I, Hakim O. Genomic effects of glucocorticoids. PROTOPLASMA 2017; 254:1175-1185. [PMID: 28013411 DOI: 10.1007/s00709-016-1063-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/08/2016] [Indexed: 06/06/2023]
Abstract
Glucocorticoids and their receptor (GR) have been an important area of research because of their pleiotropic physiological functions and extensive use in the clinic. In addition, the association between GR and glucocorticoids, which is highly specific, leads to rapid nuclear translocation where GR associates with chromatin to regulate gene transcription. This simplified model system has been instrumental for studying the complexity of transcription regulation processes occurring at chromatin. In this review we discuss our current understanding of GR action that has been enhanced by recent developments in genome wide measurements of chromatin accessibility, histone marks, chromatin remodeling and 3D chromatin structure in various cell types responding to glucocorticoids.
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Affiliation(s)
- Ivana Grbesa
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, 5290002, Ramat-Gan, Israel
| | - Ofir Hakim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, 5290002, Ramat-Gan, Israel.
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Pooley JR, Flynn BP, Grøntved L, Baek S, Guertin MJ, Kershaw YM, Birnie MT, Pellatt A, Rivers CA, Schiltz RL, Hager GL, Lightman SL, Conway-Campbell BL. Genome-Wide Identification of Basic Helix-Loop-Helix and NF-1 Motifs Underlying GR Binding Sites in Male Rat Hippocampus. Endocrinology 2017; 158:1486-1501. [PMID: 28200020 PMCID: PMC5460825 DOI: 10.1210/en.2016-1929] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/03/2017] [Indexed: 12/14/2022]
Abstract
Glucocorticoids regulate hippocampal function in part by modulating gene expression through the glucocorticoid receptor (GR). GR binding is highly cell type specific, directed to accessible chromatin regions established during tissue differentiation. Distinct classes of GR binding sites are dependent on the activity of additional signal-activated transcription factors that prime chromatin toward context-specific organization. We hypothesized a stress context dependency for GR binding in hippocampus as a consequence of rapidly induced stress mediators priming chromatin accessibility. Using chromatin immunoprecipitation sequencing to interrogate GR binding, we found no effect of restraint stress context on GR binding, although analysis of sequences underlying GR binding sites revealed mechanistic detail for hippocampal GR function. We note enrichment of GR binding sites proximal to genes linked to structural and organizational roles, an absence of major tethering partners for GRs, and little or no evidence for binding at negative glucocorticoid response elements. A basic helix-loop-helix motif closely resembling a NeuroD1 or Olig2 binding site was found underlying a subset of GR binding sites and is proposed as a candidate lineage-determining transcription factor directing hippocampal chromatin access for GRs. Of our GR binding sites, 54% additionally contained half-sites for nuclear factor (NF)-1 that we propose as a collaborative or general transcription factor involved in hippocampal GR function. Our findings imply a dose-dependent and context-independent action of GRs in the hippocampus. Alterations in the expression or activity of NF-1/basic helix-loop-helix factors may play an as yet undetermined role in glucocorticoid-related disease susceptibility and outcome by altering GR access to hippocampal binding sites.
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Affiliation(s)
- John R. Pooley
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - Ben P. Flynn
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - Lars Grøntved
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Songjoon Baek
- Laboratory for Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Michael J. Guertin
- University of Virginia School of Medicine, Charlottesville, Virginia 22908
| | - Yvonne M. Kershaw
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - Matthew T. Birnie
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - Annie Pellatt
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - Caroline A. Rivers
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - R. Louis Schiltz
- Laboratory for Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Gordon L. Hager
- Laboratory for Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Stafford L. Lightman
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
| | - Becky L. Conway-Campbell
- Henry Wellcome Laboratories for Integrated Neuroscience and Endocrinology, University of Bristol, Bristol BS1 3NY, United Kingdom
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66
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Epigenetic programming by stress and glucocorticoids along the human lifespan. Mol Psychiatry 2017; 22:640-646. [PMID: 28289275 DOI: 10.1038/mp.2017.35] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 01/08/2017] [Accepted: 01/17/2017] [Indexed: 12/19/2022]
Abstract
Psychosocial stress triggers a set of behavioral, neural, hormonal, and molecular responses that can be a driving force for survival when adaptive and time-limited, but may also contribute to a host of disease states if dysregulated or chronic. The beneficial or detrimental effects of stress are largely mediated by the hypothalamic-pituitary axis, a highly conserved neurohormonal cascade that culminates in systemic secretion of glucocorticoids. Glucocorticoids activate the glucocorticoid receptor, a ubiquitous nuclear receptor that not only causes widespread changes in transcriptional programs, but also induces lasting epigenetic modifications in many target tissues. While the epigenome remains sensitive to stressors throughout life, we propose two key principles that may govern the epigenetics of stress and glucocorticoids along the lifespan: first, the presence of distinct life periods, during which the epigenome shows heightened plasticity to stress exposure, such as in early development and at advanced age; and, second, the potential of stress-induced epigenetic changes to accumulate throughout life both in select chromatin regions and at the genome-wide level. These principles have important clinical and translational implications, and they show striking parallels with the existence of sensitive developmental periods and the cumulative impact of stressful experiences on the development of stress-related phenotypes. We hope that this conceptual mechanistic framework will stimulate fruitful research that aims at unraveling the molecular pathways through which our life stories sculpt genomic function to contribute to complex behavioral and somatic phenotypes.
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Love MI, Huska MR, Jurk M, Schöpflin R, Starick SR, Schwahn K, Cooper SB, Yamamoto KR, Thomas-Chollier M, Vingron M, Meijsing SH. Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation. Nucleic Acids Res 2017; 45:1805-1819. [PMID: 27903902 PMCID: PMC5389550 DOI: 10.1093/nar/gkw1163] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/03/2016] [Accepted: 11/08/2016] [Indexed: 01/18/2023] Open
Abstract
The genomic loci bound by the glucocorticoid receptor (GR), a hormone-activated transcription factor, show little overlap between cell types. To study the role of chromatin and sequence in specifying where GR binds, we used Bayesian modeling within the universe of accessible chromatin. Taken together, our results uncovered that although GR preferentially binds accessible chromatin, its binding is biased against accessible chromatin located at promoter regions. This bias can only be explained partially by the presence of fewer GR recognition sequences, arguing for the existence of additional mechanisms that interfere with GR binding at promoters. Therefore, we tested the role of H3K9ac, the chromatin feature with the strongest negative association with GR binding, but found that this correlation does not reflect a causative link. Finally, we find a higher percentage of promoter-proximal GR binding for genes regulated by GR across cell types than for cell type-specific target genes. Given that GR almost exclusively binds accessible chromatin, we propose that cell type-specific regulation by GR preferentially occurs via distal enhancers, whose chromatin accessibility is typically cell type-specific, whereas ubiquitous target gene regulation is more likely to result from binding to promoter regions, which are often accessible regardless of cell type examined.
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Affiliation(s)
- Michael I. Love
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73 14195, Berlin, Germany
- Department of Biostatistics, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Matthew R. Huska
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73 14195, Berlin, Germany
| | - Marcel Jurk
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73 14195, Berlin, Germany
| | - Robert Schöpflin
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73 14195, Berlin, Germany
| | - Stephan R. Starick
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73 14195, Berlin, Germany
| | - Kevin Schwahn
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73 14195, Berlin, Germany
| | - Samantha B. Cooper
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Keith R. Yamamoto
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA
| | - Morgane Thomas-Chollier
- Computational Systems Biology, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, Inserm, Ecole Normale Supérieure, PSL Research University, F-75005 Paris, France
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63–73 14195, Berlin, Germany
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Lakshmanan I, Salfity S, Seshacharyulu P, Rachagani S, Thomas A, Das S, Majhi PD, Nimmakayala RK, Vengoji R, Lele SM, Ponnusamy MP, Batra SK, Ganti AK. MUC16 Regulates TSPYL5 for Lung Cancer Cell Growth and Chemoresistance by Suppressing p53. Clin Cancer Res 2017; 23:3906-3917. [PMID: 28196872 DOI: 10.1158/1078-0432.ccr-16-2530] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/12/2016] [Accepted: 01/28/2017] [Indexed: 12/21/2022]
Abstract
Purpose: MUC16, a tumor biomarker and cell surface-associated mucin, is overexpressed in various cancers; however, its role in lung cancer pathogenesis is unknown. Here, we have explored the mechanistic role of MUC16 in lung cancer.Experimental Design: To identify the functional role of MUC16, stable knockdown was carried in lung cancer cells with two different shRNAs. Clinical significance of MUC16 was evaluated in lung cancer patient tissues using IHC. We have generated genetically engineered mouse model (KrasG12D; AdCre) to evaluate the preclinical significance of MUC16.Results: MUC16 was overexpressed (P = 0.03) in lung cancer as compared with normal tissues. MUC16 knockdown (KD) in lung cancer cell lines decreased the in vitro growth rate (P < 0.05), migration (P < 0.001), and in vivo tumor growth (P = 0.007), whereas overexpression of MUC16-carboxyl terminal (MUC16-Cter) resulted in increased growth rate (P < 0.001). Transcriptome analysis of MUC16 KD showed a downregulation (P = 0.005) of TSPYL5 gene, which encodes for a testis-specific Y-like protein. Rescue studies via overexpression of MUC16-Cter in MUC16 KD cells showed activation of signaling proteins, such as JAK2 (Y1007/1008), STAT3 (Y705), and glucocorticoid receptor (GR), which constitutes an important axis for the regulation of TSPYL5 for oncogenic process. Further, inhibition of STAT3 (Y705) led to decreased GR and TSPYL5, suggesting that MUC16 regulates TSPYL5 through the JAK2/STAT3/GR axis. Also, MUC16 overexpression induced cisplatin and gemcitabine resistance by downregulation of p53.Conclusions: Our findings indicate a significant role of MUC16 in tumorigenesis and metastasis of lung cancer cells possibly via regulation of TSPYL5 through the JAK2/STAT3/GR axis. Clin Cancer Res; 23(14); 3906-17. ©2017 AACR.
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Affiliation(s)
- Imayavaramban Lakshmanan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Shereen Salfity
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | | | - Satyanarayana Rachagani
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Abigail Thomas
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Srustidhar Das
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Prabin D Majhi
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Rama Krishna Nimmakayala
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Raghupathy Vengoji
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Subodh M Lele
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Moorthy P Ponnusamy
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska.,Eppley Institute for Research in Cancer and Allied Diseases Fred & Pamela Buffett Cancer Center University of Nebraska Medical Center, Omaha, Nebraska
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska. .,Eppley Institute for Research in Cancer and Allied Diseases Fred & Pamela Buffett Cancer Center University of Nebraska Medical Center, Omaha, Nebraska
| | - Apar Kishor Ganti
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska. .,Department of Internal Medicine, VA Nebraska-Western Iowa Health Care System and University of Nebraska Medical Center, Omaha, Nebraska
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Nakamoto M, Ishihara K, Watanabe T, Hirosue A, Hino S, Shinohara M, Nakayama H, Nakao M. The Glucocorticoid Receptor Regulates the ANGPTL4 Gene in a CTCF-Mediated Chromatin Context in Human Hepatic Cells. PLoS One 2017; 12:e0169225. [PMID: 28056052 PMCID: PMC5215901 DOI: 10.1371/journal.pone.0169225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/13/2016] [Indexed: 02/07/2023] Open
Abstract
Glucocorticoid signaling through the glucocorticoid receptor (GR) plays essential roles in the response to stress and in energy metabolism. This hormonal action is integrated to the transcriptional control of GR-target genes in a cell type-specific and condition-dependent manner. In the present study, we found that the GR regulates the angiopoietin-like 4 gene (ANGPTL4) in a CCCTC-binding factor (CTCF)-mediated chromatin context in the human hepatic HepG2 cells. There are at least four CTCF-enriched sites and two GR-binding sites within the ANGPTL4 locus. Among them, the major CTCF-enriched site is positioned near the ANGPTL4 enhancer that binds GR. We showed that CTCF is required for induction and subsequent silencing of ANGPTL4 expression in response to dexamethasone (Dex) and that transcription is diminished after long-term treatment with Dex. Although the ANGPTL4 locus maintains a stable higher-order chromatin conformation in the presence and absence of Dex, the Dex-bound GR activated transcription of ANGPTL4 but not that of the neighboring three genes through interactions among the ANGPTL4 enhancer, promoter, and CTCF sites. These results reveal that liganded GR spatiotemporally controls ANGPTL4 transcription in a chromosomal context.
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Affiliation(s)
- Masafumi Nakamoto
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Ko Ishihara
- Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto, Japan
- * E-mail: (MiN); (KI)
| | - Takehisa Watanabe
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Akiyuki Hirosue
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Shinjiro Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Masanori Shinohara
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hideki Nakayama
- Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
- Core Research for Evolutionary Science and Technology (CREST), Japan Agency for Medical Research and Development, Tokyo, Japan
- * E-mail: (MiN); (KI)
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Sarnowska E, Gratkowska DM, Sacharowski SP, Cwiek P, Tohge T, Fernie AR, Siedlecki JA, Koncz C, Sarnowski TJ. The Role of SWI/SNF Chromatin Remodeling Complexes in Hormone Crosstalk. TRENDS IN PLANT SCIENCE 2016; 21:594-608. [PMID: 26920655 DOI: 10.1016/j.tplants.2016.01.017] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/14/2015] [Accepted: 01/21/2016] [Indexed: 05/20/2023]
Abstract
SWI/SNF-type ATP-dependent chromatin remodeling complexes (CRCs) are evolutionarily conserved multiprotein machineries controlling DNA accessibility by regulating chromatin structure. We summarize here recent advances highlighting the role of SWI/SNF in the regulation of hormone signaling pathways and their crosstalk in Arabidopsis thaliana. We discuss the functional interdependences of SWI/SNF complexes and key elements regulating developmental and hormone signaling pathways by indicating intriguing similarities and differences in plants and humans, and summarize proposed mechanisms of SWI/SNF action on target loci. We postulate that, given their viability, several plant SWI/SNF mutants may serve as an attractive model for searching for conserved functions of SWI/SNF CRCs in hormone signaling, cell cycle control, and other regulatory pathways.
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Affiliation(s)
| | | | | | - Pawel Cwiek
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | | | - Csaba Koncz
- Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany; Institute of Plant Biology, Biological Research Center of Hungarian Academy, Temesvári Körút 62, 6724 Szeged, Hungary
| | - Tomasz J Sarnowski
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland.
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Davis MR, Daggett JJ, Pascual AS, Lam JM, Leyva KJ, Cooper KE, Hull EE. Epigenetically maintained SW13+ and SW13- subtypes have different oncogenic potential and convert with HDAC1 inhibition. BMC Cancer 2016; 16:316. [PMID: 27188282 PMCID: PMC4870788 DOI: 10.1186/s12885-016-2353-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 05/11/2016] [Indexed: 12/19/2022] Open
Abstract
Background The BRM and BRG1 tumor suppressor genes are mutually exclusive ATPase subunits of the SWI/SNF chromatin remodeling complex. The human adrenal carcinoma SW13 cell line can switch between a subtype which expresses these subunits, SW13+, and one that expresses neither subunit, SW13-. Loss of BRM expression occurs post-transcriptionally and can be restored via histone deacetylase (HDAC) inhibition. However, most previously used HDAC inhibitors are toxic and broad-spectrum, providing little insight into the mechanism of the switch between subtypes. In this work, we explore the mechanisms of HDAC inhibition in promoting subtype switching and further characterize the oncogenic potential of the two epigenetically distinct SW13 subtypes. Methods SW13 subtype morphology, chemotaxis, growth rates, and gene expression were assessed by standard immunofluorescence, transwell, growth, and qPCR assays. Metastatic potential was measured by anchorage-independent growth and MMP activity. The efficacy of HDAC inhibitors in inducing subtype switching was determined by immunofluorescence and qPCR. Histone modifications were assessed by western blot. Results Treatment of SW13- cells with HDAC1 inhibitors most effectively promotes re-expression of BRM and VIM, characteristic of the SW13+ phenotype. During treatment, hyperacetylation of histone residues and hypertrimethylation of H3K4 is pronounced. Furthermore, histone modification enzymes, including HDACs and KDM5C, are differentially expressed during treatment but several features of this differential expression pattern differs from that seen in the SW13- and SW13+ subtypes. As the SW13- subtype is more proliferative while the SW13+ subtype is more metastatic, treatment with HDACi increases the metastatic potential of SW13 cells while restoring expression of the BRM tumor suppressor. Conclusions When compared to the SW13- subtype, SW13+ cells have restored BRM expression, increased metastatic capacity, and significantly different expression of a variety of chromatin remodeling factors including those involved with histone acetylation and methylation. These data are consistent with a multistep mechanism of SW13- to SW13+ conversion and subtype stabilization: histone hypermodification results in the altered expression of chromatin remodeling factors and chromatin epigenetic enzymes and the re-expression of BRM which results in restoration of SWI/SNF complex function and leads to changes in chromatin structure and gene expression that stabilize the SW13+ phenotype. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2353-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- McKale R Davis
- Department of Biomedical Sciences, Midwestern University, Glendale, AZ, USA
| | - Juliane J Daggett
- Department of Biomedical Sciences, Midwestern University, Glendale, AZ, USA
| | - Agnes S Pascual
- Department of Biomedical Sciences, Midwestern University, Glendale, AZ, USA
| | - Jessica M Lam
- Department of Biomedical Sciences, Midwestern University, Glendale, AZ, USA
| | - Kathryn J Leyva
- Department of Microbiology and Immunology, Midwestern University, Glendale, AZ, USA
| | - Kimbal E Cooper
- Department of Biomedical Sciences, Midwestern University, Glendale, AZ, USA
| | - Elizabeth E Hull
- Department of Biomedical Sciences, Midwestern University, Glendale, AZ, USA.
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Tesikova M, Dezitter X, Nenseth HZ, Klokk TI, Mueller F, Hager GL, Saatcioglu F. Divergent Binding and Transactivation by Two Related Steroid Receptors at the Same Response Element. J Biol Chem 2016; 291:11899-910. [PMID: 27056330 DOI: 10.1074/jbc.m115.684480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Indexed: 01/19/2023] Open
Abstract
Transcription factor (TF) recruitment to chromatin is central to activation of transcription. TF-chromatin interactions are highly dynamic, which are evaluated by recovery half time (t1/2) in seconds, determined by fluorescence recovery experiments in living cells, and chromatin immunoprecipitation (ChIP) analysis, measured in minutes. These two states are related: the larger the t1/2, the longer the ChIP occupancy resulting in increased transcription. Here we present data showing that this relationship does not always hold. We found that histone deacetylase inhibitors (HDACis) significantly increased t1/2 of green fluorescent protein (GFP) fused androgen receptor (AR) on a tandem array of positive hormone response elements (HREs) in chromatin. This resulted in increased ChIP signal of GFP-AR. Unexpectedly, however, transcription was inhibited. In contrast, the GFP-fused glucocorticoid receptor (GR), acting through the same HREs, displayed a profile consistent with current models. We provide evidence that these differences are mediated, at least in part, by HDACs. Our results provide insight into TF action in living cells and show that very closely related TFs may trigger significantly divergent outcomes at the same REs.
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Affiliation(s)
- Martina Tesikova
- From the Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Xavier Dezitter
- From the Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Hatice Z Nenseth
- From the Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Tove I Klokk
- From the Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Florian Mueller
- Computational Imaging and Modeling Unit, Institut Pasteur, 75015 Paris, France
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, NCI, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Fahri Saatcioglu
- From the Department of Biosciences, University of Oslo, 0316 Oslo, Norway, Institute for Cancer Genetics and Informatics, Division of Cancer and Surgery, Oslo University Hospital, 0310 Oslo, Norway
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Kuo T, Liu PH, Chen TC, Lee RA, New J, Zhang D, Lei C, Chau A, Tang Y, Cheung E, Wang JC. Transcriptional regulation of FoxO3 gene by glucocorticoids in murine myotubes. Am J Physiol Endocrinol Metab 2016; 310:E572-85. [PMID: 26758684 PMCID: PMC4824139 DOI: 10.1152/ajpendo.00214.2015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 01/06/2016] [Indexed: 01/08/2023]
Abstract
Glucocorticoids and FoxO3 exert similar metabolic effects in skeletal muscle. FoxO3 gene expression was increased by dexamethasone (Dex), a synthetic glucocorticoid, both in vitro and in vivo. In C2C12 myotubes the increased expression is due to, at least in part, the elevated rate of FoxO3 gene transcription. In the mouse FoxO3 gene, we identified three glucocorticoid receptor (GR) binding regions (GBRs): one being upstream of the transcription start site, -17kbGBR; and two in introns, +45kbGBR and +71kbGBR. Together, these three GBRs contain four 15-bp glucocorticoid response elements (GREs). Micrococcal nuclease (MNase) assay revealed that Dex treatment increased the sensitivity to MNase in the GRE of +45kbGBR and +71kbGBR upon 30- and 60-min Dex treatment, respectively. Conversely, Dex treatment did not affect the chromatin structure near the -17kbGBR, in which the GRE is located in the linker region. Dex treatment also increased histone H3 and/or H4 acetylation in genomic regions near all three GBRs. Moreover, using chromatin conformation capture (3C) assay, we showed that Dex treatment increased the interaction between the -17kbGBR and two genomic regions: one located around +500 bp and the other around +73 kb. Finally, the transcriptional coregulator p300 was recruited to all three GBRs upon Dex treatment. The reduction of p300 expression decreased FoxO3 gene expression and Dex-stimulated interaction between distinct genomic regions of FoxO3 gene identified by 3C. Overall, our results demonstrate that glucocorticoids activated FoxO3 gene transcription through multiple GREs by chromatin structural change and DNA looping.
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Affiliation(s)
- Taiyi Kuo
- Endocrinology Graduate Program, University of California Berkeley, Berkeley, California; and Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, California
| | - Patty H Liu
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, California
| | - Tzu-Chieh Chen
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, California
| | - Rebecca A Lee
- Endocrinology Graduate Program, University of California Berkeley, Berkeley, California; and Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, California
| | - Jenny New
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, California
| | - Danyun Zhang
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, California
| | - Cassandra Lei
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, California
| | - Andy Chau
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, California
| | - Yicheng Tang
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, California
| | - Edna Cheung
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, California
| | - Jen-Chywan Wang
- Endocrinology Graduate Program, University of California Berkeley, Berkeley, California; and Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, California
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74
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Duren RP, Boudreaux SP, Conneely OM. Genome Wide Mapping of NR4A Binding Reveals Cooperativity with ETS Factors to Promote Epigenetic Activation of Distal Enhancers in Acute Myeloid Leukemia Cells. PLoS One 2016; 11:e0150450. [PMID: 26938745 PMCID: PMC4777543 DOI: 10.1371/journal.pone.0150450] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/14/2016] [Indexed: 12/25/2022] Open
Abstract
Members of the NR4A subfamily of orphan nuclear receptors regulate cell fate decisions via both genomic and non-genomic mechanisms in a cell and tissue selective manner. NR4As play a key role in maintenance of hematopoietic stem cell homeostasis and are critical tumor suppressors of acute myeloid leukemia (AML). Expression of NR4As is broadly silenced in leukemia initiating cell enriched populations from human patients relative to normal hematopoietic stem/progenitor cells. Rescue of NR4A expression in human AML cells inhibits proliferation and reprograms AML gene signatures via transcriptional mechanisms that remain to be elucidated. By intersecting an acutely regulated NR4A1 dependent transcriptional profile with genome wide NR4A binding distribution, we now identify an NR4A targetome of 685 genes that are directly regulated by NR4A1. We show that NR4As regulate gene transcription primarily through interaction with distal enhancers that are co-enriched for NR4A1 and ETS transcription factor motifs. Using a subset of NR4A activated genes, we demonstrate that the ETS factors ERG and FLI-1 are required for activation of NR4A bound enhancers and NR4A target gene induction. NR4A1 dependent recruitment of ERG and FLI-1 promotes binding of p300 histone acetyltransferase to epigenetically activate NR4A bound enhancers via acetylation at histone H3K27. These findings disclose novel epigenetic mechanisms by which NR4As and ETS factors cooperate to drive NR4A dependent gene transcription in human AML cells.
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Affiliation(s)
- Ryan P. Duren
- Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas, United States of America
| | - Seth P. Boudreaux
- Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas, United States of America
| | - Orla M. Conneely
- Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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75
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Thompson B, Varticovski L, Baek S, Hager GL. Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation. PLoS One 2016; 11:e0148619. [PMID: 26890492 PMCID: PMC4759368 DOI: 10.1371/journal.pone.0148619] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 01/20/2016] [Indexed: 12/17/2022] Open
Abstract
Bone continuously undergoes remodeling by a tightly regulated process that involves osteoblast differentiation from Mesenchymal Stem Cells (MSC). However, commitment of MSC to osteoblastic lineage is a poorly understood process. Chromatin organization functions as a molecular gatekeeper of DNA functions. Detection of sites that are hypersensitive to Dnase I has been used for detailed examination of changes in response to hormones and differentiation cues. To investigate the early steps in commitment of MSC to osteoblasts, we used a model human temperature-sensitive cell line, hFOB. When shifted to non-permissive temperature, these cells undergo "spontaneous" differentiation that takes several weeks, a process that is greatly accelerated by osteogenic induction media. We performed Dnase I hypersensitivity assays combined with deep sequencing to identify genome-wide potential regulatory events in cells undergoing early steps of commitment to osteoblasts. Massive reorganization of chromatin occurred within hours of differentiation. Whereas ~30% of unique DHS sites were located in the promoters, the majority was outside of the promoters, designated as enhancers. Many of them were at novel genomic sites and need to be confirmed experimentally. We developed a novel method for identification of cellular networks based solely on DHS enhancers signature correlated to gene expression. The analysis of enhancers that were unique to differentiating cells led to identification of bone developmental program encompassing 147 genes that directly or indirectly participate in osteogenesis. Identification of these pathways provided an unprecedented view of genomic regulation during early steps of differentiation and changes related to WNT, AP-1 and other pathways may have therapeutic implications.
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Affiliation(s)
- Bethtrice Thompson
- Laboratory of Receptor Biology and Gene Expression, NCI, NIH, Bethesda, MD, United States of America
- Center for Cancer Research and Therapeutic Development, Clark Atlanta University, Atlanta, GA, United States of America
| | - Lyuba Varticovski
- Laboratory of Receptor Biology and Gene Expression, NCI, NIH, Bethesda, MD, United States of America
- * E-mail:
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, NCI, NIH, Bethesda, MD, United States of America
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, NCI, NIH, Bethesda, MD, United States of America
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76
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Chen J, Li Q. Implication of retinoic acid receptor selective signaling in myogenic differentiation. Sci Rep 2016; 6:18856. [PMID: 26830006 PMCID: PMC4735650 DOI: 10.1038/srep18856] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 11/25/2015] [Indexed: 11/18/2022] Open
Abstract
Signaling molecules are important for committing individual cells into tissue-specific lineages during early vertebrate development. Retinoic acid (RA) is an important vertebrate morphogen, in that its concentration gradient is essential for correct patterning of the vertebrate embryo. RA signaling is mediated through the activation of retinoic acid receptors (RARs), which function as ligand-dependent transcription factors. In this study, we examined the molecular mechanisms of RAR-selective signaling in myogenic differentiation. We found that just like natural ligand RA, a RAR-selective ligand is an effective enhancer in the commitment of skeletal muscle lineage at the early stage of myogenic differentiation. Interestingly, the kinetics and molecular basis of the RAR-selective ligand in myogenic differentiation are similar to that of natural ligand RA. Also similar to natural ligand RA, the RAR-selective ligand enhances myogenic differentiation through β-catenin signaling pathway while inhibiting cardiac differentiation. Furthermore, while low concentrations of natural ligand RA or RAR-selective ligand regulate myogenic differentiation through RAR function and coactivator recruitment, high concentrations are critical to the expression of a model RA-responsive gene. Thus our data suggests that RAR-mediated gene regulation may be highly context-dependent, affected by locus-specific interaction or local chromatin environment.
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Affiliation(s)
- Jihong Chen
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Qiao Li
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
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77
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Jubb AW, Young RS, Hume DA, Bickmore WA. Enhancer Turnover Is Associated with a Divergent Transcriptional Response to Glucocorticoid in Mouse and Human Macrophages. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2016; 196:813-822. [PMID: 26663721 PMCID: PMC4707550 DOI: 10.4049/jimmunol.1502009] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/04/2015] [Indexed: 02/07/2023]
Abstract
Phenotypic differences between individuals and species are controlled in part through differences in expression of a relatively conserved set of genes. Genes expressed in the immune system are subject to especially powerful selection. We have investigated the evolution of both gene expression and candidate enhancers in human and mouse macrophages exposed to glucocorticoid (GC), a regulator of innate immunity and an important therapeutic agent. Our analyses revealed a very limited overlap in the repertoire of genes responsive to GC in human and mouse macrophages. Peaks of inducible binding of the GC receptor (GR) detected by chromatin immunoprecipitation-Seq correlated with induction, but not repression, of target genes in both species, occurred at distal regulatory sites not promoters, and were strongly enriched for the consensus GR-binding motif. Turnover of GR binding between mice and humans was associated with gain and loss of the motif. There was no detectable signal of positive selection at species-specific GR binding sites, but clear evidence of purifying selection at the small number of conserved sites. We conclude that enhancer divergence underlies the difference in transcriptional activation after GC treatment between mouse and human macrophages. Only the shared inducible loci show evidence of selection, and therefore these loci may be important for the subset of responses to GC that is shared between species.
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Affiliation(s)
- Alasdair W Jubb
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, Scotland, UK
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK
| | - Robert S Young
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, Scotland, UK
| | - David A Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, Scotland, UK
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78
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Stavreva DA, Hager GL. Chromatin structure and gene regulation: a dynamic view of enhancer function. Nucleus 2016; 6:442-8. [PMID: 26765055 DOI: 10.1080/19491034.2015.1107689] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Localized chromatin organization is now recognized as an important determinant of cell identity and developmental pathways. Recent studies have demonstrated that these epigenetic states are unexpectedly dynamic and malleable. In this Extra view we will highlight the transient nature of stimulus-induced enhancer accessibility and its importance for transcription regulation. Using glucocorticoid receptor (GR) as a model system we will discuss spatiotemporal relationships between receptor/chromatin interactions, lifetimes of the DNase I hypersensitivity sites (DHSs), long-range interactions, and gene regulation. We propose that differential temporal activation and utilization of distal regulatory elements plays a role in directing divergent stimulus-induced transcriptional programs.
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Affiliation(s)
- Diana A Stavreva
- a Laboratory of Receptor Biology and Gene Expression; National Cancer Institute; National Institutes of Health ; Bethesda , MD USA
| | - Gordon L Hager
- a Laboratory of Receptor Biology and Gene Expression; National Cancer Institute; National Institutes of Health ; Bethesda , MD USA
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79
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Wiley JW, Higgins GA, Athey BD. Stress and glucocorticoid receptor transcriptional programming in time and space: Implications for the brain-gut axis. Neurogastroenterol Motil 2016; 28:12-25. [PMID: 26690871 PMCID: PMC4688904 DOI: 10.1111/nmo.12706] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/20/2015] [Indexed: 12/25/2022]
Abstract
BACKGROUND Chronic psychological stress is associated with enhanced abdominal pain and altered intestinal barrier function that may result from a perturbation in the hypothalamic-pituitary-adrenal (HPA) axis. The glucocorticoid receptor (GR) exploits diverse mechanisms to activate or suppress congeneric gene expression, with regulatory variation associated with stress-related disorders in psychiatry and gastroenterology. PURPOSE During acute and chronic stress, corticotropin-releasing hormone drives secretion of adrenocorticotropic hormone from the pituitary, ultimately leading to the release of cortisol (human) and corticosterone (rodent) from the adrenal glands. Cortisol binds with the GR in the cytosol, translocates to the nucleus, and activates the NR3C1 (nuclear receptor subfamily 3, group C, member 1 [GR]) gene. This review focuses on the rapidly developing observations that cortisol is responsible for driving circadian and ultradian bursts of transcriptional activity in the CLOCK (clock circadian regulator) and PER (period circadian clock 1) gene families, and this rhythm is disrupted in major depressive disorder, bipolar disorder, and stress-related gastrointestinal and immune disorders. Glucocorticoid receptor regulates different sets of transcripts in a tissue-specific manner, through pulsatile waves of gene expression that includes occupancy of glucocorticoid response elements located within constitutively open spatial domains in chromatin. Emerging evidence supports a potentially pivotal role for epigenetic regulation of how GR interacts with other chromatin regulators to control the expression of its target genes. Dysregulation of the central and peripheral GR regulome has potentially significant consequences for stress-related disorders affecting the brain-gut axis.
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Affiliation(s)
- John W. Wiley
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Gerald A. Higgins
- Department of Pharmacogenomic Science, Assurex Health, Inc., 6030 South Mason Montgomery Road, Mason, OH 45040, USA,Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Brian D. Athey
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
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80
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Belikov S, Berg OG, Wrange Ö. Quantification of transcription factor-DNA binding affinity in a living cell. Nucleic Acids Res 2015; 44:3045-58. [PMID: 26657626 PMCID: PMC4838337 DOI: 10.1093/nar/gkv1350] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 11/19/2015] [Indexed: 12/17/2022] Open
Abstract
The apparent dissociation constant (Kd) for specific binding of glucocorticoid receptor (GR) and androgen receptor (AR) to DNA was determined in vivo in Xenopus oocytes. The total nuclear receptor concentration was quantified as specifically retained [3H]-hormone in manually isolated oocyte nuclei. DNA was introduced by nuclear microinjection of single stranded phagemid DNA, chromatin is then formed during second strand synthesis. The fraction of DNA sites occupied by the expressed receptor was determined by dimethylsulphate in vivo footprinting and used for calculation of the receptor-DNA binding affinity. The forkhead transcription factor FoxA1 enhanced the DNA binding by GR with an apparent Kd of ∼1 μM and dramatically stimulated DNA binding by AR with an apparent Kd of ∼0.13 μM at a composite androgen responsive DNA element containing one FoxA1 binding site and one palindromic hormone receptor binding site known to bind one receptor homodimer. FoxA1 exerted a weak constitutive- and strongly cooperative DNA binding together with AR but had a less prominent effect with GR, the difference reflecting the licensing function of FoxA1 at this androgen responsive DNA element.
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Affiliation(s)
- Sergey Belikov
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Otto G Berg
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, SE-75124 Uppsala, Sweden
| | - Örjan Wrange
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden
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81
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Wu JN, Pinello L, Yissachar E, Wischhusen JW, Yuan GC, Roberts CWM. Functionally distinct patterns of nucleosome remodeling at enhancers in glucocorticoid-treated acute lymphoblastic leukemia. Epigenetics Chromatin 2015; 8:53. [PMID: 26633995 PMCID: PMC4667523 DOI: 10.1186/s13072-015-0046-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 11/17/2015] [Indexed: 01/12/2023] Open
Abstract
Background Precise nucleosome positioning is an increasingly recognized feature of promoters and enhancers, reflecting complex contributions of DNA sequence, nucleosome positioning, histone modification and transcription factor binding to enhancer activity and regulation of gene expression. Changes in nucleosome position and occupancy, histone variants and modifications, and chromatin remodeling are also critical elements of dynamic transcriptional regulation, but poorly understood at enhancers. We investigated glucocorticoid receptor-associated (GR) nucleosome dynamics at enhancers in acute lymphoblastic leukemia. Results For the first time, we demonstrate functionally distinct modes of nucleosome remodeling upon chromatin binding by GR, which we term central, non-central, phased, and minimal. Central and non-central remodeling reflect nucleosome eviction by GR and cofactors, respectively. Phased remodeling involves nucleosome repositioning and is associated with rapidly activated enhancers and induction of gene expression. Minimal remodeling sites initially have low levels of enhancer-associated histone modification, but the majority of these regions gain H3K4me2 or H3K27Ac to become de novo enhancers. Minimal remodeling regions are associated with gene ontologies specific to decreased B cell number and mTOR inhibition and may make unique contributions to glucocorticoid-induced leukemia cell death. Conclusions Our findings form a novel framework for understanding the dynamic interplay between transcription factor binding, nucleosome remodeling, enhancer function, and gene expression in the leukemia response to glucocorticoids. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0046-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jennifer N Wu
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Luca Pinello
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T. H. Chan School of Public Heath, Boston, MA USA
| | | | | | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T. H. Chan School of Public Heath, Boston, MA USA
| | - Charles W M Roberts
- Department of Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS 281, Memphis, TN 38105 USA
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82
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Cieślik M, Bekiranov S. Genome-wide predictors of NF-κB recruitment and transcriptional activity. BioData Min 2015; 8:37. [PMID: 26617673 PMCID: PMC4661973 DOI: 10.1186/s13040-015-0071-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 11/18/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Inducible transcription factors (TFs) mediate transcriptional responses to environmental cues. In response to multiple inflammatory signals active NF-κB dimers enter the nucleus and trigger cell-type-, and stimulus-specific transcriptional programs. Although much is known about NF-κB inducing pathways and about locus-specific mechanisms of transcriptional control, it is poorly understood how the pre-existing chromatin landscape determines NF-κB target selection and activation. Specifically, it is not known which epigenetic marks and pre-bound TFs serve genome-wide as positive (negative) cues for active NF-κB. RESULTS We applied multivariate and combinatorial data mining techniques on a comprehensive dataset of DNA methylation, DNase I hypersensitivity, eight epigenetic marks, and 34 TFs to arrive at genome-wide patterns that predict NF-κB binding. Strikingly, we observed NF-κB recruitment to accessible and nucleosome-bound sites. Within nucleosomal DNA NF-κB binding was primed by H3K4me1 and H2A.Z, but also hyper-methylated DNA outside of promoters and CpG-islands. Many of these predictors showed combinatorial cooperativity and statistically significant interactions. Recruitment to pre-accessible sites was more frequent and influenced by chromatin-associated TFs. We observed that specific TF-combinations are greatly enriched for (or depleted of) NF-κB binding events. CONCLUSIONS We provide evidence of NF-κB binding within genomic regions that lack classical marks of activity. These pioneer binding events are relatively often associated with transcriptional regulation. Further, our predictive models indicate that specific combinations of epigenetic marks and transcription factors predetermine the NF-κB cistrome, supporting the feasibility of using statistical approaches to identify "histone codes".
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Affiliation(s)
- Marcin Cieślik
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia USA
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109 USA
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia USA
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83
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Wilson J, Berntsen HF, Zimmer KE, Verhaegen S, Frizzell C, Ropstad E, Connolly L. Do persistent organic pollutants interact with the stress response? Individual compounds, and their mixtures, interaction with the glucocorticoid receptor. Toxicol Lett 2015; 241:121-32. [PMID: 26599974 DOI: 10.1016/j.toxlet.2015.11.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/12/2015] [Accepted: 11/13/2015] [Indexed: 01/22/2023]
Abstract
Persistent organic pollutants (POPs) are toxic substances, highly resistant to environmental degradation, which can bio-accumulate and have long-range atmospheric transport potential (UNEP, 2001). The majority of studies on endocrine disruption have focused on interferences on the sexual steroid hormones and so have overlooked disruption to glucocorticoid hormones. Here the endocrine disrupting potential of individual POPs and their mixtures has been investigated in vitro to identify any disruption to glucocorticoid nuclear receptor transcriptional activity. POP mixtures were screened for glucocorticoid receptor (GR) translocation using a GR redistribution assay (RA) on a CellInsight™ NXT high content screening (HCS) platform. A mammalian reporter gene assay (RGA) was then used to assess the individual POPs, and their mixtures, for effects on glucocorticoid nuclear receptor transactivation. POP mixtures did not induce GR translocation in the GR RA or produce an agonist response in the GR RGA. However, in the antagonist test, in the presence of cortisol, an individual POP, p,p'-dichlorodiphenyldichloroethylene (p,p'-DDE), was found to decrease glucocorticoid nuclear receptor transcriptional activity to 72.5% (in comparison to the positive cortisol control). Enhanced nuclear transcriptional activity, in the presence of cortisol, was evident for the two lowest concentrations of perfluorodecanoic acid (PFOS) potassium salt (0.0147mg/ml and 0.0294mg/ml), the two highest concentrations of perfluorodecanoic acid (PFDA) (0.0025mg/ml and 0.005mg/ml) and the highest concentration of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) (0.0000858mg/ml). It is important to gain a better understanding of how POPs can interact with GRs as the disruption of glucocorticoid action is thought to contribute to complex diseases.
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Affiliation(s)
- Jodie Wilson
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Northern Ireland, United Kingdom
| | | | | | | | - Caroline Frizzell
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Northern Ireland, United Kingdom
| | - Erik Ropstad
- Norwegian University of Life Sciences, Oslo, Norway
| | - Lisa Connolly
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Northern Ireland, United Kingdom.
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84
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Brunelle M, Nordell Markovits A, Rodrigue S, Lupien M, Jacques PÉ, Gévry N. The histone variant H2A.Z is an important regulator of enhancer activity. Nucleic Acids Res 2015; 43:9742-56. [PMID: 26319018 PMCID: PMC4787790 DOI: 10.1093/nar/gkv825] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 07/15/2015] [Accepted: 08/03/2015] [Indexed: 12/11/2022] Open
Abstract
Gene regulatory programs in different cell types are largely defined through cell-specific enhancers activity. The histone variant H2A.Z has been shown to play important roles in transcription mainly by controlling proximal promoters, but its effect on enhancer functions remains unclear. Here, we demonstrate by genome-wide approaches that H2A.Z is present at a subset of active enhancers bound by the estrogen receptor alpha (ERα). We also determine that H2A.Z does not influence the local nucleosome positioning around ERα enhancers using ChIP sequencing at nucleosomal resolution and unsupervised pattern discovery. We further highlight that H2A.Z-enriched enhancers are associated with chromatin accessibility, H3K122ac enrichment and hypomethylated DNA. Moreover, upon estrogen stimulation, the enhancers occupied by H2A.Z produce enhancer RNAs (eRNAs), and recruit RNA polymerase II as well as RAD21, a member of the cohesin complex involved in chromatin interactions between enhancers and promoters. Importantly, their recruitment and eRNAs production are abolished by H2A.Z depletion, thereby revealing a novel functional link between H2A.Z occupancy and enhancer activity. Taken together, our findings suggest that H2A.Z acts as an important player for enhancer functions by establishing and maintaining a chromatin environment required for RNA polymerase II recruitment, eRNAs transcription and enhancer-promoters interactions, all essential attributes of enhancer activity.
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Affiliation(s)
- Mylène Brunelle
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'Université, J1K 2R1, Sherbrooke, Québec, Canada
| | - Alexei Nordell Markovits
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'Université, J1K 2R1, Sherbrooke, Québec, Canada Ontario Cancer Institute, Princess Margaret Cancer Centre/University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Sébastien Rodrigue
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'Université, J1K 2R1, Sherbrooke, Québec, Canada
| | - Mathieu Lupien
- Département d'informatique, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'Université, J1K 2R1, Sherbrooke, Québec, Canada
| | - Pierre-Étienne Jacques
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'Université, J1K 2R1, Sherbrooke, Québec, Canada Ontario Cancer Institute, Princess Margaret Cancer Centre/University Health Network and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada Centre de recherche du Centre hospitalier universitaire de Sherbrooke, 12e Avenue Nord, Sherbrooke, Québec, J1H 5N4, Canada
| | - Nicolas Gévry
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'Université, J1K 2R1, Sherbrooke, Québec, Canada
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85
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Pihlajamaa P, Sahu B, Jänne OA. Determinants of Receptor- and Tissue-Specific Actions in Androgen Signaling. Endocr Rev 2015; 36:357-84. [PMID: 26052734 DOI: 10.1210/er.2015-1034] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The physiological androgens testosterone and 5α-dihydrotestosterone regulate the development and maintenance of primary and secondary male sexual characteristics through binding to the androgen receptor (AR), a ligand-dependent transcription factor. In addition, a number of nonreproductive tissues of both genders are subject to androgen regulation. AR is also a central target in the treatment of prostate cancer. A large number of studies over the last decade have characterized many regulatory aspects of the AR pathway, such as androgen-dependent transcription programs, AR cistromes, and coregulatory proteins, mostly in cultured cells of prostate cancer origin. Moreover, recent work has revealed the presence of pioneer/licensing factors and chromatin modifications that are important to guide receptor recruitment onto appropriate chromatin loci in cell lines and in tissues under physiological conditions. Despite these advances, current knowledge related to the mechanisms responsible for receptor- and tissue-specific actions of androgens is still relatively limited. Here, we review topics that pertain to these specificity issues at different levels, both in cultured cells and tissues in vivo, with a particular emphasis on the nature of the steroid, the response element sequence, the AR cistromes, pioneer/licensing factors, and coregulatory proteins. We conclude that liganded AR and its DNA-response elements are required but are not sufficient for establishment of tissue-specific transcription programs in vivo, and that AR-selective actions over other steroid receptors rely on relaxed rather than increased stringency of cis-elements on chromatin.
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Affiliation(s)
- Päivi Pihlajamaa
- Department of Physiology (P.P., B.S., O.A.J.), and Research Programs Unit, Genome-Scale Biology (P.P., B.S.), Biomedicum Helsinki, University of Helsinki, FI-00014 Helsinki, Finland
| | - Biswajyoti Sahu
- Department of Physiology (P.P., B.S., O.A.J.), and Research Programs Unit, Genome-Scale Biology (P.P., B.S.), Biomedicum Helsinki, University of Helsinki, FI-00014 Helsinki, Finland
| | - Olli A Jänne
- Department of Physiology (P.P., B.S., O.A.J.), and Research Programs Unit, Genome-Scale Biology (P.P., B.S.), Biomedicum Helsinki, University of Helsinki, FI-00014 Helsinki, Finland
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86
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Dror I, Golan T, Levy C, Rohs R, Mandel-Gutfreund Y. A widespread role of the motif environment in transcription factor binding across diverse protein families. Genome Res 2015; 25:1268-80. [PMID: 26160164 PMCID: PMC4561487 DOI: 10.1101/gr.184671.114] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 07/08/2015] [Indexed: 12/12/2022]
Abstract
Transcriptional regulation requires the binding of transcription factors (TFs) to short sequence-specific DNA motifs, usually located at the gene regulatory regions. Interestingly, based on a vast amount of data accumulated from genomic assays, it has been shown that only a small fraction of all potential binding sites containing the consensus motif of a given TF actually bind the protein. Recent in vitro binding assays, which exclude the effects of the cellular environment, also demonstrate selective TF binding. An intriguing conjecture is that the surroundings of cognate binding sites have unique characteristics that distinguish them from other sequences containing a similar motif that are not bound by the TF. To test this hypothesis, we conducted a comprehensive analysis of the sequence and DNA shape features surrounding the core-binding sites of 239 and 56 TFs extracted from in vitro HT-SELEX binding assays and in vivo ChIP-seq data, respectively. Comparing the nucleotide content of the regions around the TF-bound sites to the counterpart unbound regions containing the same consensus motifs revealed significant differences that extend far beyond the core-binding site. Specifically, the environment of the bound motifs demonstrated unique sequence compositions, DNA shape features, and overall high similarity to the core-binding motif. Notably, the regions around the binding sites of TFs that belong to the same TF families exhibited similar features, with high agreement between the in vitro and in vivo data sets. We propose that these unique features assist in guiding TFs to their cognate binding sites.
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Affiliation(s)
- Iris Dror
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel; Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, California 90089, USA
| | - Tamar Golan
- Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Carmit Levy
- Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Remo Rohs
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, California 90089, USA
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
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87
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Stavreva DA, Coulon A, Baek S, Sung MH, John S, Stixova L, Tesikova M, Hakim O, Miranda T, Hawkins M, Stamatoyannopoulos JA, Chow CC, Hager GL. Dynamics of chromatin accessibility and long-range interactions in response to glucocorticoid pulsing. Genome Res 2015; 25:845-57. [PMID: 25677181 PMCID: PMC4448681 DOI: 10.1101/gr.184168.114] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/05/2015] [Indexed: 12/20/2022]
Abstract
Although physiological steroid levels are often pulsatile (ultradian), the genomic effects of this pulsatility are poorly understood. By utilizing glucocorticoid receptor (GR) signaling as a model system, we uncovered striking spatiotemporal relationships between receptor loading, lifetimes of the DNase I hypersensitivity sites (DHSs), long-range interactions, and gene regulation. We found that hormone-induced DHSs were enriched within ± 50 kb of GR-responsive genes and displayed a broad spectrum of lifetimes upon hormone withdrawal. These lifetimes dictate the strength of the DHS interactions with gene targets and contribute to gene regulation from a distance. Our results demonstrate that pulsatile and constant hormone stimulations induce unique, treatment-specific patterns of gene and regulatory element activation. These modes of activation have implications for corticosteroid function in vivo and for steroid therapies in various clinical settings.
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Affiliation(s)
- Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Antoine Coulon
- Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Sam John
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Lenka Stixova
- Department of Molecular Cytology and Cytometry, Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 65 Brno, Czech Republic
| | - Martina Tesikova
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Ofir Hakim
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Tina Miranda
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Mary Hawkins
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | | | - Carson C Chow
- Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland 20892, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
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88
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Chatzopoulou A, Roy U, Meijer AH, Alia A, Spaink HP, Schaaf MJM. Transcriptional and metabolic effects of glucocorticoid receptor α and β signaling in zebrafish. Endocrinology 2015; 156:1757-69. [PMID: 25756310 DOI: 10.1210/en.2014-1941] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In humans and zebrafish, 2 glucocorticoid (GC) receptor (GR) splice variants exist: the canonical GR α-isoform (GRα), and the GRβ. In the present study, we have used the zebrafish model system in order to reveal genes affected by each of these 2 receptor isoforms. By injecting zebrafish embryos with different splice-blocking morpholinos, we could knock down both GR isoforms or could target the alternative splicing of the GR pre-mRNA in favor of the GRβ. In addition, specific GRβ overexpression was achieved by injecting mRNA. Embryos were treated with the synthetic GC dexamethasone, and transcriptome analysis was performed. Two distinct gene clusters were found that were regulated by GRα: one that was regulated by GRα under basal conditions (presence of endogenous cortisol only), and one that was regulated upon increased activation of GRα (using a pharmacological dose of dexamathasone). GRβ may act as a dominant-negative inhibitor of GRα when GRβ is overexpressed and the GRα expression level is knocked down simultaneously. However, without GRα knockdown, no evidence for this activity was found. In addition, the data indicate regulation of gene transcription through other mechanisms of action by GRβ. We also investigated the concentrations of several metabolites using nuclear magnetic resonance spectroscopy. We found that dexamethasone treatment and knockdown of GRα together with overexpression of GRβ had opposite effects on glucose, amino acid, and fatty acid levels. Thus, we have shed new light on the molecular mechanisms of GC-induced effects on metabolism, which are known to increase the risk of obesity, hyperglycemia, and diabetes.
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Affiliation(s)
- Antonia Chatzopoulou
- Department of Animal Sciences and Health (A.C., A.H.M., H.P.S., M.J.M.S.), Institute of Biology, Leiden University, 2333CC Leiden, The Netherlands; Department of Biophysical Organic Chemistry/Solid State NMR (U.R., A.A.), Leiden Institute of Chemistry, Leiden University, 2333CC Leiden, The Netherlands; and Institute of Medical Physics and Biophysics (A.A.), University of Leipzig, D-04107 Leipzig, Germany
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89
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Glucocorticoid receptor regulates accurate chromosome segregation and is associated with malignancy. Proc Natl Acad Sci U S A 2015; 112:5479-84. [PMID: 25847991 DOI: 10.1073/pnas.1411356112] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The glucocorticoid receptor (GR) is a member of the nuclear receptor superfamily, which controls programs regulating cell proliferation, differentiation, and apoptosis. We have identified an unexpected role for GR in mitosis. We discovered that specifically modified GR species accumulate at the mitotic spindle during mitosis in a distribution that overlaps with Aurora kinases. We found that Aurora A was required to mediate mitosis-driven GR phosphorylation, but not recruitment of GR to the spindle. GR was necessary for mitotic progression, with increased time to complete mitosis, frequency of mitotic aberrations, and death in mitosis observed following GR knockdown. Complementation studies revealed an essential role for the GR ligand-binding domain, but no clear requirement for ligand binding in regulating chromosome segregation. The GR N-terminal domain, and specifically phosphosites S203 and S211, were not required. Reduced GR expression results in a cell cycle phenotype, with isolated cells from mouse and human subjects showing changes in chromosome content over prolonged passage. Furthermore, GR haploinsufficient mice have an increased incidence of tumor formation, and, strikingly, these tumors are further depleted for GR, implying additional GR loss as a consequence of cell transformation. We identified reduced GR expression in a panel of human liver, lung, prostate, colon, and breast cancers. We therefore reveal an unexpected role for the GR in promoting accurate chromosome segregation during mitosis, which is causally linked to tumorigenesis, making GR an authentic tumor suppressor gene.
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90
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Athwal RK, Walkiewicz MP, Baek S, Fu S, Bui M, Camps J, Ried T, Sung MH, Dalal Y. CENP-A nucleosomes localize to transcription factor hotspots and subtelomeric sites in human cancer cells. Epigenetics Chromatin 2015; 8:2. [PMID: 25788983 PMCID: PMC4363203 DOI: 10.1186/1756-8935-8-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 12/21/2022] Open
Abstract
Background The histone H3 variant CENP-A is normally tightly regulated to ensure only one centromere exists per chromosome. Native CENP-A is often found overexpressed in human cancer cells and a range of human tumors. Consequently, CENP-A misregulation is thought to contribute to genome instability in human cancers. However, the consequences of such overexpression have not been directly elucidated in human cancer cells. Results To investigate native CENP-A overexpression, we sought to uncover CENP-A-associated defects in human cells. We confirm that CENP-A is innately overexpressed in several colorectal cancer cell lines. In such cells, we report that a subset of structurally distinct CENP-A-containing nucleosomes associate with canonical histone H3, and with the transcription-coupled chaperones ATRX and DAXX. Furthermore, such hybrid CENP-A nucleosomes localize to DNase I hypersensitive and transcription factor binding sites, including at promoters of genes across the human genome. A distinct class of CENP-A hotspots also accumulates at subtelomeric chromosomal locations, including at the 8q24/Myc region long-associated with genomic instability. We show this 8q24 accumulation of CENP-A can also be seen in early stage primary colorectal tumors. Conclusions Our data demonstrate that excess CENP-A accumulates at noncentromeric locations in the human cancer genome. These findings suggest that ectopic CENP-A nucleosomes could alter the state of the chromatin fiber, potentially impacting gene regulation and chromosome fragility. Electronic supplementary material The online version of this article (doi:10.1186/1756-8935-8-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rajbir K Athwal
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA ; Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
| | - Marcin P Walkiewicz
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA ; Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
| | - Song Fu
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA ; Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
| | - Minh Bui
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA ; Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
| | - Jordi Camps
- Genetics Branch, Center for Cancer Research, National Cancer Institute National Institutes of Health, 50 South Drive, Bethesda, MD 20892 USA
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute National Institutes of Health, 50 South Drive, Bethesda, MD 20892 USA
| | - Myong-Hee Sung
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
| | - Yamini Dalal
- Chromatin Structure and Epigenetics Mechanisms Unit, Center for Cancer Research, National Cancer Institute National Institutes of Health, 41 Center Drive, Bethesda, MD 20892 USA
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91
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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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92
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Knutson SK, Warholic NM, Johnston LD, Klaus CR, Wigle TJ, Iwanowicz D, Littlefield BA, Porter-Scott M, Smith JJ, Moyer MP, Copeland RA, Pollock RM, Kuntz KW, Raimondi A, Keilhack H. Synergistic Anti-Tumor Activity of EZH2 Inhibitors and Glucocorticoid Receptor Agonists in Models of Germinal Center Non-Hodgkin Lymphomas. PLoS One 2014; 9:e111840. [PMID: 25493630 PMCID: PMC4262195 DOI: 10.1371/journal.pone.0111840] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 10/01/2014] [Indexed: 01/07/2023] Open
Abstract
Patients with non-Hodgkin lymphoma (NHL) are treated today with a cocktail of drugs referred to as CHOP (Cyclophosphamide, Hydroxyldaunorubicin, Oncovin, and Prednisone). Subsets of patients with NHL of germinal center origin bear oncogenic mutations in the EZH2 histone methyltransferase. Clinical testing of the EZH2 inhibitor EPZ-6438 has recently begun in patients. We report here that combining EPZ-6438 with CHOP in preclinical cell culture and mouse models results in dramatic synergy for cell killing in EZH2 mutant germinal center NHL cells. Surprisingly, we observe that much of this synergy is due to Prednisolone - a glucocorticoid receptor agonist (GRag) component of CHOP. Dramatic synergy was observed when EPZ-6438 is combined with Prednisolone alone, and a similar effect was observed with Dexamethasone, another GRag. Remarkably, the anti-proliferative effect of the EPZ-6438+GRag combination extends beyond EZH2 mutant-bearing cells to more generally impact germinal center NHL. These preclinical data reveal an unanticipated biological intersection between GR-mediated gene regulation and EZH2-mediated chromatin remodeling. The data also suggest the possibility of a significant and practical benefit of combining EZH2 inhibitors and GRag that warrants further investigation in a clinical setting.
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Affiliation(s)
- Sarah K. Knutson
- Research and Development, Epizyme Inc., Cambridge, Massachusetts, United States of America
| | - Natalie M. Warholic
- Research and Development, Epizyme Inc., Cambridge, Massachusetts, United States of America
| | - L. Danielle Johnston
- Research and Development, Epizyme Inc., Cambridge, Massachusetts, United States of America
| | - Christine R. Klaus
- Research and Development, Epizyme Inc., Cambridge, Massachusetts, United States of America
| | - Tim J. Wigle
- Research and Development, Epizyme Inc., Cambridge, Massachusetts, United States of America
| | - Dorothy Iwanowicz
- Research and Development, Epizyme Inc., Cambridge, Massachusetts, United States of America
| | | | - Margaret Porter-Scott
- Research and Development, Epizyme Inc., Cambridge, Massachusetts, United States of America
| | - Jesse J. Smith
- Research and Development, Epizyme Inc., Cambridge, Massachusetts, United States of America
| | - Mikel P. Moyer
- Research and Development, Epizyme Inc., Cambridge, Massachusetts, United States of America
| | - Robert A. Copeland
- Research and Development, Epizyme Inc., Cambridge, Massachusetts, United States of America
| | - Roy M. Pollock
- Research and Development, Epizyme Inc., Cambridge, Massachusetts, United States of America
| | - Kevin W. Kuntz
- Research and Development, Epizyme Inc., Cambridge, Massachusetts, United States of America
| | - Alejandra Raimondi
- Research and Development, Epizyme Inc., Cambridge, Massachusetts, United States of America
| | - Heike Keilhack
- Research and Development, Epizyme Inc., Cambridge, Massachusetts, United States of America
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93
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Lim MS, Jeong KW. Role of Flightless-I (Drosophila) homolog in the transcription activation of type I collagen gene mediated by transforming growth factor beta. Biochem Biophys Res Commun 2014; 454:393-8. [PMID: 25451260 DOI: 10.1016/j.bbrc.2014.10.100] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 10/20/2014] [Indexed: 11/15/2022]
Abstract
Flightless-I (Drosophila) homolog (FLII) is a nuclear receptor coactivator that is known to interact with other transcriptional regulators such as the SWI/SNF complex, an ATP-dependent chromatin-remodeling complex, at the promoter or enhancer region of estrogen receptor (ER)-α target genes. However, little is known about the role of FLII during transcription initiation in the transforming growth factor beta (TGFβ)/SMAD-dependent signaling pathway. Here, we demonstrate that FLII functions as a coactivator in the expression of type I collagen gene induced by TGFβ in A549 cells. FLII activates the reporter gene driven by COL1A2 promoter in a dose-dependent manner. Co-expression of GRIP1, CARM1, or p300 did not show any synergistic activation of transcription. Furthermore, the level of COL1A2 expression correlated with the endogenous level of FLII mRNA level. Depletion of FLII resulted in a reduction of TGFβ-induced expression of COL1A2 gene. In contrast, over-expression of FLII caused an increase in the endogenous expression of COL1A2. We also showed that FLII is associated with Brahma-related gene 1 (BRG1) as well as SMAD in A549 cells. Notably, the recruitment of BRG1 to the COL1A2 promoter region was decreased in FLII-depleted A549 cells, suggesting that FLII is required for TGFβ-induced chromatin remodeling, which is carried out by the SWI/SNF complex. Furthermore, formaldehyde-assisted isolation of regulatory elements (FAIRE)-quantitative polymerase chain reaction (qPCR) experiments revealed that depletion of FLII caused a reduction in chromatin accessibility at the COL1A2 promoter. These results suggest that FLII plays a critical role in TGFβ/SMAD-mediated transcription of the COL1A2 gene through its role in recruiting the SWI/SNF complex to facilitate chromatin accessibility.
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Affiliation(s)
- Mi-Sun Lim
- Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University, 7-45 Songdo-dong, Yeonsu-gu, Incheon 406-840, Republic of Korea
| | - Kwang Won Jeong
- Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University, 7-45 Songdo-dong, Yeonsu-gu, Incheon 406-840, Republic of Korea.
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94
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Opposing regulation of BIM and BCL2 controls glucocorticoid-induced apoptosis of pediatric acute lymphoblastic leukemia cells. Blood 2014; 125:273-83. [PMID: 25336632 DOI: 10.1182/blood-2014-05-576470] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glucocorticoids are critical components of combination chemotherapy regimens in pediatric acute lymphoblastic leukemia (ALL). The proapoptotic BIM protein is an important mediator of glucocorticoid-induced apoptosis in normal and malignant lymphocytes, whereas the antiapoptotic BCL2 confers resistance. The signaling pathways regulating BIM and BCL2 expression in glucocorticoid-treated lymphoid cells remain unclear. In this study, pediatric ALL patient-derived xenografts (PDXs) inherently sensitive or resistant to glucocorticoids were exposed to dexamethasone in vivo. Microarray analysis showed that KLF13 and MYB gene expression changes were significantly greater in dexamethasone-sensitive than -resistant PDXs. Chromatin immunoprecipitation (ChIP) analysis detected glucocorticoid receptor (GR) binding at the KLF13 promoter to trigger KLF13 expression only in sensitive PDXs. Next, KLF13 bound to the MYB promoter, deactivating MYB expression only in sensitive PDXs. Sustained MYB expression in resistant PDXs resulted in maintenance of BCL2 expression and inhibition of apoptosis. ChIP sequencing analysis revealed a novel GR binding site in a BIM intronic region (IGR) that was engaged only in dexamethasone-sensitive PDXs. The absence of GR binding at the BIM IGR was associated with BIM silencing and dexamethasone resistance. This study has identified novel mechanisms of opposing BCL2 and BIM gene regulation that control glucocorticoid-induced apoptosis in pediatric ALL cells in vivo.
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95
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Liberman AC, Antunica-Noguerol M, Arzt E. Modulation of the Glucocorticoid Receptor Activity by Post-Translational Modifications. NUCLEAR RECEPTOR RESEARCH 2014. [DOI: 10.11131/2014/101086] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Ana Clara Liberman
- Instituto de Investigación en Biomedicina de Buenos Aires - CONICET - Partner Institute of the Max Planck Society
| | - María Antunica-Noguerol
- Instituto de Investigación en Biomedicina de Buenos Aires - CONICET - Partner Institute of the Max Planck Society
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires
| | - Eduardo Arzt
- Instituto de Investigación en Biomedicina de Buenos Aires - CONICET - Partner Institute of the Max Planck Society
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires
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96
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Ayroldi E, Macchiarulo A, Riccardi C. Targeting glucocorticoid side effects: selective glucocorticoid receptor modulator or glucocorticoid-induced leucine zipper? A perspective. FASEB J 2014; 28:5055-70. [PMID: 25205742 DOI: 10.1096/fj.14-254755] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Glucocorticoids (GCs) are steroid hormones that are necessary for life and important in health and disease. They regulate crucial homeostatic functions, including metabolism, cell growth, and development. Although GCs are regulated by circadian rhythm, increased production is associated with stress. Synthetic GCs are a valuable resource for anti-inflammatory and immunosuppressive therapy. Natural and synthetic GCs transduce signals mainly through GC receptor (GR) activation. Extensive research has explored the downstream targets of the GR, and optimization of GC therapy has required collaborative efforts. One highly promising approach involves new dissociative GR modulators. Because transrepression and transactivation of GR genes induce beneficial and adverse effects, respectively, this approach favors transrepression. Another approach involves the use of GC-dependent genes to generate proteins to mediate therapeutic GC effects. In a third approach, drug discovery is used to identify agents that selectively target GR isoforms to obtain differential gene transcription and effects. In this review, we focus on mechanisms of GR function compatible with the use of dissociative drugs. We highlight GC-induced leucine zipper (GILZ), a gene cloned in our laboratory, as a mediator of GC anti-inflammatory and immunosuppressive effects, to outline our perspective on the future of GC therapy.
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Affiliation(s)
- Emira Ayroldi
- Department of Medicine, Section of Pharmacology, and
| | - Antonio Macchiarulo
- Department of Chemistry and Drug Technology, University of Perugia, Perugia, Italy
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Genome-wide binding and transcriptome analysis of human farnesoid X receptor in primary human hepatocytes. PLoS One 2014; 9:e105930. [PMID: 25198545 PMCID: PMC4157742 DOI: 10.1371/journal.pone.0105930] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 07/20/2014] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND & AIMS Farnesoid X receptor (FXR, NR1H4) is a ligand-activated transcription factor, belonging to the nuclear receptor superfamily. FXR is highly expressed in the liver and is essential in regulating bile acid homeostasis. FXR deficiency is implicated in numerous liver diseases and mice with modulation of FXR have been used as animal models to study liver physiology and pathology. We have reported genome-wide binding of FXR in mice by chromatin immunoprecipitation - deep sequencing (ChIP-seq), with results indicating that FXR may be involved in regulating diverse pathways in liver. However, limited information exists for the functions of human FXR and the suitability of using murine models to study human FXR functions. METHODS In the current study, we performed ChIP-seq in primary human hepatocytes (PHHs) treated with a synthetic FXR agonist, GW4064 or DMSO control. In parallel, RNA deep sequencing (RNA-seq) and RNA microarray were performed for GW4064 or control treated PHHs and wild type mouse livers, respectively. RESULTS ChIP-seq showed similar profiles of genome-wide FXR binding in humans and mice in terms of motif analysis and pathway prediction. However, RNA-seq and microarray showed more different transcriptome profiles between PHHs and mouse livers upon GW4064 treatment. CONCLUSIONS In summary, we have established genome-wide human FXR binding and transcriptome profiles. These results will aid in determining the human FXR functions, as well as judging to what level the mouse models could be used to study human FXR functions.
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Gibbs J, Ince L, Matthews L, Mei J, Bell T, Yang N, Saer B, Begley N, Poolman T, Pariollaud M, Farrow S, DeMayo F, Hussell T, Worthen GS, Ray D, Loudon A. An epithelial circadian clock controls pulmonary inflammation and glucocorticoid action. Nat Med 2014; 20:919-26. [PMID: 25064128 PMCID: PMC4268501 DOI: 10.1038/nm.3599] [Citation(s) in RCA: 311] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 05/16/2014] [Indexed: 12/12/2022]
Abstract
The circadian system is an important regulator of immune function. Human inflammatory lung diseases frequently show time-of-day variation in symptom severity and lung function, but the mechanisms and cell types underlying these effects remain unclear. We show that pulmonary antibacterial responses are modulated by a circadian clock within epithelial club (Clara) cells. These drive circadian neutrophil recruitment to the lung via the chemokine CXCL5. Genetic ablation of the clock gene Bmal1 (also called Arntl or MOP3) in bronchiolar cells disrupts rhythmic Cxcl5 expression, resulting in exaggerated inflammatory responses to lipopolysaccharide and an impaired host response to Streptococcus pneumoniae infection. Adrenalectomy blocks rhythmic inflammatory responses and the circadian regulation of CXCL5, suggesting a key role for the adrenal axis in driving CXCL5 expression and pulmonary neutrophil recruitment. Glucocorticoid receptor occupancy at the Cxcl5 locus shows circadian oscillations, but this is disrupted in mice with bronchiole-specific ablation of Bmal1, leading to enhanced CXCL5 expression despite normal corticosteroid secretion. The therapeutic effects of the synthetic glucocorticoid dexamethasone depend on intact clock function in the airway. We now define a regulatory mechanism that links the circadian clock and glucocorticoid hormones to control both time-of-day variation and the magnitude of pulmonary inflammation and responses to bacterial infection.
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Affiliation(s)
- Julie Gibbs
- Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Louise Ince
- Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Laura Matthews
- Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Junjie Mei
- Division of Neonatology, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Thomas Bell
- Manchester Collaborative Centre for Inflammation Research, Core Technology Facility, University of Manchester, Manchester, UK
| | - Nan Yang
- Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Ben Saer
- Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Nicola Begley
- Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Toryn Poolman
- Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Marie Pariollaud
- Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Stuart Farrow
- 1] Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, UK. [2] Respiratory Therapy Area, GlaxoSmithKline, Stevenage, UK
| | - Francesco DeMayo
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, USA
| | - Tracy Hussell
- Manchester Collaborative Centre for Inflammation Research, Core Technology Facility, University of Manchester, Manchester, UK
| | - G Scott Worthen
- Division of Neonatology, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David Ray
- Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Andrew Loudon
- Faculty of Life Sciences, University of Manchester, Manchester, UK
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Abstract
Acute kidney injury (AKI) is a risk factor for chronic kidney disease and death. Despite progress made in understanding the cellular and molecular basis of AKI pathogenesis there has been no improvement in the high mortality rate from this disease in decades. Epigenetics is one of the most intensively studied fields of biology today and represents a new paradigm for understanding the pathophysiology of disease. Although epigenetics of AKI is a nascent field, the available information already is providing compelling evidence that chromatin biology plays a critical role in this disease. In this article we explore what is known about the contribution of epigenetic mechanisms to the pathophysiology of AKI and how this knowledge already is guiding the development of new diagnostic tools and epigenetic therapies.
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Marsh DJ, Shah JS, Cole AJ. Histones and their modifications in ovarian cancer - drivers of disease and therapeutic targets. Front Oncol 2014; 4:144. [PMID: 24971229 PMCID: PMC4053763 DOI: 10.3389/fonc.2014.00144] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Accepted: 05/27/2014] [Indexed: 01/08/2023] Open
Abstract
Epithelial ovarian cancer has the highest mortality of the gynecological malignancies. High grade serous epithelial ovarian cancer (SEOC) is the most common subtype, with the majority of women presenting with advanced disease where 5-year survival is around 25%. Platinum-based chemotherapy in combination with paclitaxel remains the most effective treatment despite platinum therapies being introduced almost 40 years ago. Advances in molecular medicine are underpinning new strategies for the treatment of cancer. Major advances have been made by international initiatives to sequence cancer genomes. For SEOC, with the exception of TP53 that is mutated in virtually 100% of these tumors, there is no other gene mutated at high frequency. There is extensive copy number variation, as well as changes in methylation patterns that will influence gene expression. To date, the role of histones and their post-translational modifications in ovarian cancer is a relatively understudied field. Post-translational histone modifications play major roles in gene expression as they direct the configuration of chromatin and so access by transcription factors. Histone modifications include methylation, acetylation, and monoubiquitination, with involvement of enzymes including histone methyltransferases, histone acetyltransferases/deacetylases, and ubiquitin ligases/deubiquitinases, respectively. Complexes such as the Polycomb repressive complex also play roles in the control of histone modifications and more recently roles for long non-coding RNA and microRNAs are emerging. Epigenomic-based therapies targeting histone modifications are being developed and offer new approaches for the treatment of ovarian cancer. Here, we discuss histone modifications and their aberrant regulation in malignancy and specifically in ovarian cancer. We review current and upcoming histone-based therapies that have the potential to inform and improve treatment strategies for women with ovarian cancer.
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Affiliation(s)
- Deborah J Marsh
- Hormones and Cancer Group, Kolling Institute of Medical Research, Royal North Shore Hospital, The University of Sydney , Sydney, NSW , Australia
| | - Jaynish S Shah
- Hormones and Cancer Group, Kolling Institute of Medical Research, Royal North Shore Hospital, The University of Sydney , Sydney, NSW , Australia
| | - Alexander J Cole
- Hormones and Cancer Group, Kolling Institute of Medical Research, Royal North Shore Hospital, The University of Sydney , Sydney, NSW , Australia
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