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Boye C, Nirmalan S, Ranjbaran A, Luca F. Genotype × environment interactions in gene regulation and complex traits. Nat Genet 2024; 56:1057-1068. [PMID: 38858456 DOI: 10.1038/s41588-024-01776-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 04/25/2024] [Indexed: 06/12/2024]
Abstract
Genotype × environment interactions (GxE) have long been recognized as a key mechanism underlying human phenotypic variation. Technological developments over the past 15 years have dramatically expanded our appreciation of the role of GxE in both gene regulation and complex traits. The richness and complexity of these datasets also required parallel efforts to develop robust and sensitive statistical and computational approaches. Although our understanding of the genetic architecture of molecular and complex traits has been maturing, a large proportion of complex trait heritability remains unexplained. Furthermore, there are increasing efforts to characterize the effect of environmental exposure on human health. We therefore review GxE in human gene regulation and complex traits, advocating for a comprehensive approach that jointly considers genetic and environmental factors in human health and disease.
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Affiliation(s)
- Carly Boye
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US
| | - Shreya Nirmalan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US
| | - Ali Ranjbaran
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US.
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, US.
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy.
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2
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Portuguez AS, Grbesa I, Tal M, Deitch R, Raz D, Kliker L, Weismann R, Schwartz M, Loza O, Cohen L, Marchenkov-Flam L, Sung MH, Kaplan T, Hakim O. Ep300 sequestration to functionally distinct glucocorticoid receptor binding loci underlie rapid gene activation and repression. Nucleic Acids Res 2022; 50:6702-6714. [PMID: 35713523 PMCID: PMC9262608 DOI: 10.1093/nar/gkac488] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 05/18/2022] [Accepted: 05/26/2022] [Indexed: 12/24/2022] Open
Abstract
The rapid transcriptional response to the transcription factor, glucocorticoid receptor (GR), including gene activation or repression, is mediated by the spatial association of genes with multiple GR binding sites (GBSs) over large genomic distances. However, only a minority of the GBSs have independent GR-mediated activating capacity, and GBSs with independent repressive activity were rarely reported. To understand the positive and negative effects of GR we mapped the regulatory environment of its gene targets. We show that the chromatin interaction networks of GR-activated and repressed genes are spatially separated and vary in the features and configuration of their GBS and other non-GBS regulatory elements. The convergence of the KLF4 pathway in GR-activated domains and the STAT6 pathway in GR-repressed domains, impose opposite transcriptional effects to GR, independent of hormone application. Moreover, the ROR and Rev-erb transcription factors serve as positive and negative regulators, respectively, of GR-mediated gene activation. We found that the spatial crosstalk between GBSs and non-GBSs provides a physical platform for sequestering the Ep300 co-activator from non-GR regulatory loci in both GR-activated and -repressed gene compartments. While this allows rapid gene repression, Ep300 recruitment to GBSs is productive specifically in the activated compartments, thus providing the basis for gene induction.
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Affiliation(s)
| | | | - Moran Tal
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Rachel Deitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Dana Raz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Limor Kliker
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Ran Weismann
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Michal Schwartz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Olga Loza
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Leslie Cohen
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Libi Marchenkov-Flam
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, NIA, National Institutes of Health, Baltimore, MD 21224, USA
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel,Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel
| | - Ofir Hakim
- To whom correspondence should be addressed. Tel: +972 3 738 4295; Fax: +972 3 738 4296;
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3
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Liu C, Ding J, Gao X, Du C, Hou C, Wu X, Shen W, Zhu J. Effects of acute low temperature stress on the hormones and gene expression of glucocorticoid receptor of large yellow croaker Larimichthys crocea. J Therm Biol 2021; 99:103018. [PMID: 34420651 DOI: 10.1016/j.jtherbio.2021.103018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/12/2021] [Accepted: 05/30/2021] [Indexed: 11/28/2022]
Abstract
The neuroendocrine system of fish responds to low temperature via regulating hormones. To explore the adaptability of Larimichthys crocea to low temperature, the levels of the plasma cortisol, thyroid stimulating hormone (TSH), triiodothyronine (T3), thyroxine (T4), total cholesterol (TC), and glucose were determined after exposure to low temperature and during subsequent rewarming. Furthermore, the mRNA expression of the glucocorticoid receptor (GR) gene was analyzed under the stress. We found that the levels of the plasma cortisol, TSH, T3, glucose, and TC increased under the low temperature stress, suggesting that elevated hormones may be conducive to promoting the mobilization of the glucose and lipid in L. crocea exposed to low temperature. During the rewarming period, the plasma cortisol level decreased, whereas the T3 level was still significantly higher than that in the control group. Notably, the plasma T4 level was unaffected by the temperature changes. Furthermore, the sequence alignment and phylogenetic tree analysis revealed that the GR protein of L. crocea had high homology and a similar protein structure with those from other teleosts. Under the low temperature stress, the GR mRNA expression increased in the brain and head kidney, whereas it basically returned to the control level following rewarming. These findings revealed the changes of the hormones and the potential function of the GR gene in L. crocea following exposure to low temperature, providing some insights into breeding low temperature-resistant varieties of L. crocea.
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Affiliation(s)
- Cheng Liu
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China; Ningbo Academy of Oceanology and Fishery, Ningbo, 315012, Zhejiang, China
| | - Jie Ding
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China; Ningbo Academy of Oceanology and Fishery, Ningbo, 315012, Zhejiang, China
| | - Xinming Gao
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Chen Du
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Congcong Hou
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Xiongfei Wu
- Ningbo Academy of Oceanology and Fishery, Ningbo, 315012, Zhejiang, China
| | - Weiliang Shen
- Ningbo Academy of Oceanology and Fishery, Ningbo, 315012, Zhejiang, China.
| | - Junquan Zhu
- Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China.
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4
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Diwadkar AR, Kan M, Himes BE. Facilitating Analysis of Publicly Available ChIP-Seq Data for Integrative Studies. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2020; 2019:371-379. [PMID: 32308830 PMCID: PMC7153109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
ChIP-Seq, a technique that allows for quantification of DNA sequences bound by transcription factors or histones, has been widely used to characterize genome-wide DNA-protein binding at baseline and induced by specific exposures. Integrating results of multiple ChIP-Seq datasets is a convenient approach to identify robust DNA- protein binding sites and determine their cell-type specificity. We developed brocade, a computational pipeline for reproducible analysis of publicly available ChIP-Seq data that creates R markdown reports containing information on datasets downloaded, quality control metrics, and differential binding results. Glucocorticoids are commonly used anti-inflammatory drugs with tissue-specific effects that are not fully understood. We demonstrate the utility of brocade via the analysis of five ChIP-Seq datasets involving glucocorticoid receptor (GR), a transcription factor that mediates glucocorticoid response, to identify cell type-specific and shared GR binding sites across the five cell types. Our results show that brocade facilitates analysis of individual ChIP-Seq datasets and comparative studies involving multiple datasets.
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Affiliation(s)
- Avantika R Diwadkar
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, US
| | - Mengyuan Kan
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, US
| | - Blanca E Himes
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, US
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Rosiglitazone, a Ligand to PPAR γ, Improves Blood Pressure and Vascular Function through Renin-Angiotensin System Regulation. PPAR Res 2019; 2019:1371758. [PMID: 30863432 PMCID: PMC6378057 DOI: 10.1155/2019/1371758] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 01/20/2019] [Indexed: 12/16/2022] Open
Abstract
Rosiglitazone (RGZ), a peroxisome proliferator-activated receptor gamma (PPARγ) ligand, has been reported to act as insulin sensitizer and exert cardiovascular actions. In this work, we hypothesized that RGZ exerts a PPARγ–dependent regulation of blood pressure through modulation of angiotensin-converting enzyme (ACE)-type 2 (ACE2)/angiotensin-(1-7)/angiotensin II type-2 receptor (AT2R) axis in an experimental model of high blood pressure. We carried on experiments in normotensive (Sham) and aortic coarctation (AoCo)-induced hypertensive male Wistar rats. Both sham and AoCo rats were treated 7 days with vehicle (V), RGZ (5 mg/kg/day), or RGZ+BADGE (120 mg/kg/day) post-coarctation. We measured blood pressure and vascular reactivity on aortic rings, as well as the expression of renin-angiotensin system (RAS) proteins. We found that RGZ treatment in AoCo group decreases blood pressure values and improves vascular response to acetylcholine, both parameters dependent on PPARγ-stimulation. RGZ lowered serum angiotensin II (AngII) but increased Ang-(1-7) levels. It also decreased 8-hydroxy-2′-deoxyguanosine (8-OH-2dG), malondialdehyde (MDA), and improved the antioxidant capacity. Regarding protein expression of RAS, RGZ decreases ACE and angiotensin II type 1 receptor (AT1R) and improved ACE2, AT2R, and Mas receptor in AoCo rats. Additionally, an in silico analysis revealed that 5′UTR regions of RAS and PPARγ share motifs with a transcriptional regulatory role. We conclude that RGZ lowers blood pressure values by increasing the expression of RAS axis proteins ACE2 and AT2R, decreasing the levels of AngII and increasing levels of Ang-(1-7) in a PPARγ-dependent manner. The in silico analysis is a valuable tool to predict the interaction between PPARγ and RAS.
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Béracochéa D, Mons N, David V. Targeting the Glucocorticoid Receptors During Alcohol Withdrawal to Reduce Protracted Neurocognitive Disorders. Front Psychiatry 2019; 10:580. [PMID: 31620025 PMCID: PMC6759466 DOI: 10.3389/fpsyt.2019.00580] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 07/23/2019] [Indexed: 11/13/2022] Open
Abstract
Persistent regional glucocorticoid (GC) dysregulation in alcohol-withdrawn subjects emerges as a key factor responsible for protracted molecular and neural alterations associated with long-term cognitive dysfunction. Regional brain concentrations of corticosterone vary independently from plasma concentrations in alcohol-withdrawn subjects, which may account for the treatment of alcohol withdrawal-induced persistent pathology. Thus, from a pharmacological point of view, a main issue remains to determine the relative efficacy of compounds targeting the GC receptors to attenuate or suppress the long-lasting persistence of brain regional GC dysfunctions in abstinent alcoholics, as well as persistent changes of neural plasticity. Data from animal research show that acting directly on GC receptors during the withdrawal period, via selective antagonists, can significantly counteract the development and persistence of cognitive and neural plasticity disorders during protracted abstinence. A critical remaining issue is to better assess the relative long-term efficacy of GC antagonists and other compounds targeting the corticotropic axis activity such as gamma-aminobutyric acid A (GABAA) and GABAB agonists. Indeed, benzodiazepines (acting indirectly on GABAA receptors) and baclofen (agonist of the GABAB receptor) are the compounds most widely used to reduce alcohol dependence. Clinical and preclinical data suggest that baclofen exerts an effective and more powerful counteracting action on such persistent cognitive and endocrine dysfunctions as compared to diazepam, even though its potential negative effects on memory processes, particularly at high doses, should be better taken into account.
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Affiliation(s)
- Daniel Béracochéa
- Université de Bordeaux, Institut de Neurosciences Cognitives et Intégratives d'Aquitaine, Pessac, France.,CNRS UMR 5287, Institut de Neurosciences Cognitives et Intégratives d'Aquitaine, Pessac, France
| | - Nicole Mons
- Université de Bordeaux, Institut de Neurosciences Cognitives et Intégratives d'Aquitaine, Pessac, France.,CNRS UMR 5287, Institut de Neurosciences Cognitives et Intégratives d'Aquitaine, Pessac, France
| | - Vincent David
- Université de Bordeaux, Institut de Neurosciences Cognitives et Intégratives d'Aquitaine, Pessac, France.,CNRS UMR 5287, Institut de Neurosciences Cognitives et Intégratives d'Aquitaine, Pessac, France
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7
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Social status alters chromatin accessibility and the gene regulatory response to glucocorticoid stimulation in rhesus macaques. Proc Natl Acad Sci U S A 2018; 116:1219-1228. [PMID: 30538209 PMCID: PMC6347725 DOI: 10.1073/pnas.1811758115] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Low social status is an important predictor of disease susceptibility and mortality risk in humans and other social mammals. These effects are thought to stem in part from dysregulation of the glucocorticoid (GC)-mediated stress response. However, the molecular mechanisms that connect low social status and GC dysregulation to downstream health outcomes remain elusive. Here, we used an in vitro GC challenge to investigate the consequences of experimentally manipulated social status (i.e., dominance rank) for immune cell gene regulation in female rhesus macaques, using paired control and GC-treated peripheral blood mononuclear cell samples. We show that social status not only influences immune cell gene expression but also chromatin accessibility at hundreds of regions in the genome. Social status effects on gene expression were less pronounced following GC treatment than under control conditions. In contrast, social status effects on chromatin accessibility were stable across conditions, resulting in an attenuated relationship between social status, chromatin accessibility, and gene expression after GC exposure. Regions that were more accessible in high-status animals and regions that become more accessible following GC treatment were enriched for a highly concordant set of transcription factor binding motifs, including motifs for the GC receptor cofactor AP-1. Together, our findings support the hypothesis that social status alters the dynamics of GC-mediated gene regulation and identify chromatin accessibility as a mechanism involved in social stress-driven GC resistance. More broadly, they emphasize the context-dependent nature of social status effects on gene regulation and implicate epigenetic remodeling of chromatin accessibility as a contributing factor.
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8
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Siahpirani AF, Roy S. A prior-based integrative framework for functional transcriptional regulatory network inference. Nucleic Acids Res 2018; 45:e21. [PMID: 27794550 PMCID: PMC5389674 DOI: 10.1093/nar/gkw963] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 10/12/2016] [Indexed: 12/16/2022] Open
Abstract
Transcriptional regulatory networks specify regulatory proteins controlling the context-specific expression levels of genes. Inference of genome-wide regulatory networks is central to understanding gene regulation, but remains an open challenge. Expression-based network inference is among the most popular methods to infer regulatory networks, however, networks inferred from such methods have low overlap with experimentally derived (e.g. ChIP-chip and transcription factor (TF) knockouts) networks. Currently we have a limited understanding of this discrepancy. To address this gap, we first develop a regulatory network inference algorithm, based on probabilistic graphical models, to integrate expression with auxiliary datasets supporting a regulatory edge. Second, we comprehensively analyze our and other state-of-the-art methods on different expression perturbation datasets. Networks inferred by integrating sequence-specific motifs with expression have substantially greater agreement with experimentally derived networks, while remaining more predictive of expression than motif-based networks. Our analysis suggests natural genetic variation as the most informative perturbation for network inference, and, identifies core TFs whose targets are predictable from expression. Multiple reasons make the identification of targets of other TFs difficult, including network architecture and insufficient variation of TF mRNA level. Finally, we demonstrate the utility of our inference algorithm to infer stress-specific regulatory networks and for regulator prioritization.
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Affiliation(s)
- Alireza F Siahpirani
- Department of Computer Sciences, University of Wisconsin-Madison, 1210 W. Dayton St. Madison, WI 53706-1613, USA
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Discovery Building 330 North Orchard St. Madison, WI 53715, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, K6/446 Clinical Sciences Center 600 Highland Avenue Madison, WI 53792-4675, USA
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Abstract
Resistance to steroid hormones presents a serious problem with respect to their mass use in therapy. It may be caused genetically by mutation of genes involved in hormonal signaling, not only steroid receptors, but also other players in the signaling cascade as co-regulators and other nuclear factors, mediating the hormone-born signal. Another possibility is acquired resistance which may develop under long-term steroid treatment, of which a particular case is down regulation of the receptors. In the review recent knowledge is summarized on the mechanism of main steroid hormone action, pointing to already proven or potential sites causing steroid resistance. We have attempted to address following questions: 1) What does stay behind differences among patients as to their response to the (anti)steroid treatment? 2) Why do various tissues/cells respond differently to the same steroid hormone though they contain the same receptors? 3) Are such differences genetically dependent? The main attention was devoted to glucocorticoids as the most frequently used steroid therapeutics. Further, androgen insensitivity is discussed with a particular attention to acquired resistance to androgen deprivation therapy of prostate cancer. Finally the potential causes are outlined of breast and related cancer(s) resistance to antiestrogen therapy.
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Affiliation(s)
- R Hampl
- Institute of Endocrinology, Prague, Czech Republic.
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10
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Wu J, Wang Q, Dai W, Wang W, Yue M, Wang J. Massive GGAAs in genomic repetitive sequences serve as a nuclear reservoir of NF-κB. J Genet Genomics 2018; 45:193-203. [PMID: PMID : 29748061 DOI: 10.1016/j.jgg.2018.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 04/05/2018] [Accepted: 04/09/2018] [Indexed: 12/01/2022]
Abstract
Nuclear factor κB (NF-κB) is a DNA-binding transcription factor. Characterizing its genomic binding sites is crucial for understanding its gene regulatory function and mechanism in cells. This study characterized the binding sites of NF-κB RelA/p65 in the tumor neurosis factor-α (TNFα) stimulated HeLa cells by a precise chromatin immunoprecipitation-sequencing (ChIP-seq). The results revealed that NF-κB binds nontraditional motifs (nt-motifs) containing conserved GGAA quadruplet. Moreover, nt-motifs mainly distribute in the peaks nearby centromeres that contain a larger number of repetitive elements such as satellite, simple repeats and short interspersed nuclear elements (SINEs). This intracellular binding pattern was then confirmed by the in vitro detection, indicating that NF-κB dimers can bind the nontraditional κB (nt-κB) sites with low affinity. However, this binding hardly activates transcription. This study thus deduced that NF-κB binding nt-motifs may realize functions other than gene regulation as NF-κB binding traditional motifs (t-motifs). To testify the deduction, many ChIP-seq data of other cell lines were then analyzed. The results indicate that NF-κB binding nt-motifs is also widely present in other cells. The ChIP-seq data analysis also revealed that nt-motifs more widely distribute in the peaks with low-fold enrichment. Importantly, it was also found that NF-κB binding nt-motifs is mainly present in the resting cells, whereas NF-κB binding t-motifs is mainly present in the stimulated cells. Astonishingly, no known function was enriched by the gene annotation of nt-motif peaks. Based on these results, this study proposed that the nt-κB sites that extensively distribute in larger numbers of repeat elements function as a nuclear reservoir of NF-κB. The nuclear NF-κB proteins stored at nt-κB sites in the resting cells may be recruited to the t-κB sites for regulating its target genes upon stimulation.
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Affiliation(s)
- Jian Wu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Qiao Wang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Wei Dai
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Wei Wang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Ming Yue
- Department of Infectious Diseases, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210002, China
| | - Jinke Wang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China.
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11
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García-Sánchez A, Marqués-García F. Review of Methods to Study Gene Expression Regulation Applied to Asthma. Methods Mol Biol 2017; 1434:71-89. [PMID: 27300532 DOI: 10.1007/978-1-4939-3652-6_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Gene expression regulation is the cellular process that controls, increasing or decreasing, the expression of gene products (RNA or protein). A complex set of interactions between genes, RNA molecules, protein, and other components determined when and where specific genes are activated and the amount of protein or RNA produced. Here, we focus on several methods to study gene regulation applied to asthma and allergic research such as: Western Blot to identify and quantify proteins, electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) to study protein interactions with nucleic acids, and RNA interference (RNAi) by which gene expression could be silenced.
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Affiliation(s)
- Asunción García-Sánchez
- Department of Biomedical and Diagnostic Sciences, University of Salamanca, Salamanca, Spain. .,Salamanca Institute for Biomedical Research (IBSAL), UniversityHospital of Salamanca, Salamanca, Spain.
| | - Fernando Marqués-García
- Salamanca Institute for Biomedical Research (IBSAL), Salamanca, Spain.,Department of Clinical Biochemistry, University Hospital of Salamanca, Salamanca, Spain
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12
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Yang F, Ma Q, Liu Z, Li W, Tan Y, Jin C, Ma W, Hu Y, Shen J, Ohgi KA, Telese F, Liu W, Rosenfeld MG. Glucocorticoid Receptor:MegaTrans Switching Mediates the Repression of an ERα-Regulated Transcriptional Program. Mol Cell 2017; 66:321-331.e6. [PMID: 28475868 PMCID: PMC5510478 DOI: 10.1016/j.molcel.2017.03.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 11/01/2016] [Accepted: 03/31/2017] [Indexed: 12/17/2022]
Abstract
The molecular mechanisms underlying the opposing functions of glucocorticoid receptors (GRs) and estrogen receptor α (ERα) in breast cancer development remain poorly understood. Here we report that, in breast cancer cells, liganded GR represses a large ERα-activated transcriptional program by binding, in trans, to ERα-occupied enhancers. This abolishes effective activation of these enhancers and their cognate target genes, and it leads to the inhibition of ERα-dependent binding of components of the MegaTrans complex. Consistent with the effects of SUMOylation on other classes of nuclear receptors, dexamethasone (Dex)-induced trans-repression of the estrogen E2 program appears to depend on GR SUMOylation, which leads to stable trans-recruitment of the GR-N-CoR/SMRT-HDAC3 corepressor complex on these enhancers. Together, these results uncover a mechanism by which competitive recruitment of DNA-binding nuclear receptors/transcription factors in trans to hot spot enhancers serves as an effective biological strategy for trans-repression, with clear implications for breast cancer and other diseases.
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Affiliation(s)
- Feng Yang
- Howard Hughes Medical Institute, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Qi Ma
- Howard Hughes Medical Institute, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhijie Liu
- Department of Molecular Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, University of Texas McGovern Medical School, Houston, TX 77030, USA
| | - Yuliang Tan
- Howard Hughes Medical Institute, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chunyu Jin
- Howard Hughes Medical Institute, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wubin Ma
- Howard Hughes Medical Institute, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yiren Hu
- Howard Hughes Medical Institute, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jia Shen
- Howard Hughes Medical Institute, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kenneth A Ohgi
- Howard Hughes Medical Institute, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Francesca Telese
- Howard Hughes Medical Institute, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wen Liu
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, Fujian 361102, China
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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13
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Genes directly regulated by NF-κB in human hepatocellular carcinoma HepG2. Int J Biochem Cell Biol 2017; 89:157-170. [PMID: 28579529 DOI: 10.1016/j.biocel.2017.05.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/25/2017] [Accepted: 05/29/2017] [Indexed: 12/14/2022]
Abstract
It has been well-known that over activation of NF-κB has close relationship with hepatitis and hepatocellular carcinoma (HCC). However, the complete and exact underlying molecular pathways and mechanisms still remain not fully understood. By manipulating NF-κB activity with its recognized activator TNFα and using ChIP-seq and RNA-seq techniques, this study identified 699 NF-κB direct target genes (DTGs) in a widely used HCC cell line, HepG2, including 399 activated and 300 repressed genes. In these NF-κB DTGs, 216 genes (126 activated and 90 repressed genes) are among the current HCC gene signature. In comparison with NF-κB target genes identified in LPS-induced THP-1 and TNFα-induced HeLa cells, only limited numbers (24-46) of genes were shared by the two cell lines, indicating the HCC specificity of identified genes. Functional annotation revealed that NF-κB DTGs in HepG2 cell are mainly related with many typical NF-κB-related biological processes including immune system process, response to stress, response to stimulus, defense response, and cell death, and signaling pathways of MAPK, TNF, TGF-beta, Chemokine, NF-kappa B, and Toll-like receptor. Some NF-κB DTGs are also involved in Hepatitis C and B pathways. It was found that 82 NF-κB DTGs code secretory proteins, which include CCL2 and DKK1 that have already been used as HCC markers. Finally, the NF-κB DTGs were further confirmed by detecting the NF-κB binding and expression of 14 genes with ChIP-PCR and RT-PCR. This study thus provides a useful NF-κB DTG list for future studies of NF-κB-related molecular mechanisms and theranostic biomarkers of HCC.
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14
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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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15
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Moyerbrailean GA, Richards AL, Kurtz D, Kalita CA, Davis GO, Harvey CT, Alazizi A, Watza D, Sorokin Y, Hauff N, Zhou X, Wen X, Pique-Regi R, Luca F. High-throughput allele-specific expression across 250 environmental conditions. Genome Res 2016; 26:1627-1638. [PMID: 27934696 PMCID: PMC5131815 DOI: 10.1101/gr.209759.116] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/13/2016] [Indexed: 11/24/2022]
Abstract
Gene-by-environment (GxE) interactions determine common disease risk factors and biomedically relevant complex traits. However, quantifying how the environment modulates genetic effects on human quantitative phenotypes presents unique challenges. Environmental covariates are complex and difficult to measure and control at the organismal level, as found in GWAS and epidemiological studies. An alternative approach focuses on the cellular environment using in vitro treatments as a proxy for the organismal environment. These cellular environments simplify the organism-level environmental exposures to provide a tractable influence on subcellular phenotypes, such as gene expression. Expression quantitative trait loci (eQTL) mapping studies identified GxE interactions in response to drug treatment and pathogen exposure. However, eQTL mapping approaches are infeasible for large-scale analysis of multiple cellular environments. Recently, allele-specific expression (ASE) analysis emerged as a powerful tool to identify GxE interactions in gene expression patterns by exploiting naturally occurring environmental exposures. Here we characterized genetic effects on the transcriptional response to 50 treatments in five cell types. We discovered 1455 genes with ASE (FDR < 10%) and 215 genes with GxE interactions. We demonstrated a major role for GxE interactions in complex traits. Genes with a transcriptional response to environmental perturbations showed sevenfold higher odds of being found in GWAS. Additionally, 105 genes that indicated GxE interactions (49%) were identified by GWAS as associated with complex traits. Examples include GIPR–caffeine interaction and obesity and include LAMP3–selenium interaction and Parkinson disease. Our results demonstrate that comprehensive catalogs of GxE interactions are indispensable to thoroughly annotate genes and bridge epidemiological and genome-wide association studies.
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Affiliation(s)
- Gregory A Moyerbrailean
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Allison L Richards
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Daniel Kurtz
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Cynthia A Kalita
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Gordon O Davis
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Chris T Harvey
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Donovan Watza
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Yoram Sorokin
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
| | - Nancy Hauff
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
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16
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Moyerbrailean GA, Davis GO, Harvey CT, Watza D, Wen X, Pique-Regi R, Luca F. A high-throughput RNA-seq approach to profile transcriptional responses. Sci Rep 2015; 5:14976. [PMID: 26510397 PMCID: PMC4625130 DOI: 10.1038/srep14976] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/01/2015] [Indexed: 12/12/2022] Open
Abstract
In recent years RNA-seq protocols have been developed to investigate a variety of biological problems by measuring the abundance of different RNAs. Many study designs involve performing expensive preliminary studies to screen or optimize experimental conditions. Testing a large number of conditions in parallel may be more cost effective. For example, analyzing tissue/environment-specific gene expression generally implies screening a large number of cellular conditions and samples, without prior knowledge of which conditions are most informative (e.g., some cell types may not respond to certain treatments). To circumvent these challenges, we have established a new two-step high-throughput RNA-seq approach: the first step consists of gene expression screening of a large number of conditions, while the second step focuses on deep sequencing of the most relevant conditions (e.g., largest number of differentially expressed genes). This study design allows for a fast and economical screen in step one, with a more efficient allocation of resources for the deep sequencing of the most biologically relevant libraries in step two. We have applied this approach to study the response to 23 treatments in three lymphoblastoid cell lines demonstrating that it should also be useful for other high-throughput transcriptome profiling applications requiring iterative refinement or screening.
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Affiliation(s)
- G A Moyerbrailean
- Wayne State University, Center for Molecular Medicine and Genetics, Detroit, 48201, USA
| | - G O Davis
- Wayne State University, Center for Molecular Medicine and Genetics, Detroit, 48201, USA
| | - C T Harvey
- Wayne State University, Center for Molecular Medicine and Genetics, Detroit, 48201, USA
| | - D Watza
- Wayne State University, Center for Molecular Medicine and Genetics, Detroit, 48201, USA
| | - X Wen
- University of Michigan, Department of Biostatistics, Ann Arbor, postcode, USA
| | - R Pique-Regi
- Wayne State University, Center for Molecular Medicine and Genetics, Detroit, 48201, USA.,Wayne State University, Department of Obstetrics and Gynecology, Detroit, 48201, USA
| | - F Luca
- Wayne State University, Center for Molecular Medicine and Genetics, Detroit, 48201, USA.,Wayne State University, Department of Obstetrics and Gynecology, Detroit, 48201, USA
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Bileck A, Kreutz D, Muqaku B, Slany A, Gerner C. Comprehensive assessment of proteins regulated by dexamethasone reveals novel effects in primary human peripheral blood mononuclear cells. J Proteome Res 2014; 13:5989-6000. [PMID: 25347463 DOI: 10.1021/pr5008625] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Inflammation is a physiological process involved in many diseases. Monitoring proteins involved in regulatory effects may help to improve our understanding of inflammation. We have analyzed proteome alterations induced in peripheral blood mononuclear cells (PBMCs) upon inflammatory activation in great detail using high-resolution mass spectrometry. Moreover, the activated cells were treated with dexamethasone to investigate their response to this antiphlogistic drug. From a total of 6886 identified proteins, 469 proteins were significantly regulated upon inflammatory activation. Data are available via ProteomeXchange with identifiers PXD001415-23. Most of these proteins were counter-regulated by dexamethasone, with some exceptions concerning members of the interferon-induced protein family. To confirm some of these results, we performed targeted MRM analyses of selected peptides. The inflammation-induced upregulation of proteins such as IL-1β, IL-6, CXCL2, and GROα was confirmed, however, with strong quantitative interindividual differences. Furthermore, the inability of dexamethasone to downregulate inflammation-induced proteins such as PTX3 and TSG6 was clearly demonstrated. In conclusion, the relation of cell function as well as drug-induced modulation thereof was successfully mapped to proteomes, suggesting targeted analysis as a novel and powerful drug evaluation method. Although most consequences of dexamethasone were found to be compatible with the expected mode of action, some unexpected but significant observations may be related to adverse effects.
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Affiliation(s)
- Andrea Bileck
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna , Vienna 1090, Austria
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18
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Schäfer ST, Gessner S, Scherag A, Rump K, Frey UH, Siffert W, Westendorf AM, Steinmann J, Peters J, Adamzik M. Hydrocortisone fails to abolish NF-κB1 protein nuclear translocation in deletion allele carriers of the NFKB1 promoter polymorphism (-94ins/delATTG) and is associated with increased 30-day mortality in septic shock. PLoS One 2014; 9:e104953. [PMID: 25133403 PMCID: PMC4136840 DOI: 10.1371/journal.pone.0104953] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 07/11/2014] [Indexed: 12/28/2022] Open
Abstract
Background Previous investigations and meta-analyses on the effect of glucocorticoids on mortality in septic shock revealed mixed results. This heterogeneity might be evoked by genetic variations. Such candidate is a promoter polymorphism (-94ins/delATTG) of the gene encoding the ubiquitous transcription-factor nuclear-factor-κB (NF-κB) which binds to recognition elements in the promoter of several genes encoding for the innate immune-system. In turn, hydrocortisone inhibits NF-κB nuclear translocation and thus transcription of key immune-response regulators. Accordingly, we tested the hypotheses that hydrocortisone has a NFKB1 genotype dependent effect on 1) NF-κB1 nuclear translocation evoked by lipopolysaccharide (LPS) in monocytes in vitro, and 2) mortality in septic shock. Methods Monocytes of volunteers with the homozygous insertion (II; n = 5) or deletion (DD; n = 6) NFKB1 genotype were incubated with 10 µgml-1 LPS ± hydrocortisone (10-5M), and NF-κB1 nuclear translocation was assessed (immunofluorescence). Furthermore, we analyzed 30-day-mortality in 160 patients with septic shock stratified for both genotype and hydrocortisone therapy. Results Hydrocortisone inhibited LPS induced nuclear translocation of NF-κB1 in II (25%±11;p = 0.0001) but not in DD genotypes (51%±15;p = n.s.). Onehundredandfour of 160 patients with septic shock received hydrocortisone, at the discretion of the intensivist. NFKB1 deletion allele carriers (ID/DD) receiving hydrocortisone had a much greater 30-day-mortality (57.6%) than II genotypes (24.4%; HR:3.18, 95%-CI:1.61-6.28;p = 0.001). In contrast, 30-day mortality was 22.2% in ID/DD and 25.0% in II genotypes without hydrocortisone therapy. Results were similar when using propensity score matching to account for possible bias in the intensivists' decision to administer hydrocortisone. Conclusion Hydrocortisone fails to inhibit LPS induced nuclear NF-κB1 translocation in deletion allele carriers of the NFKB1 promoter polymorphism (-94ins/delATTG). In septic shock, hydrocortisone treatment is associated with markedly increased 30-day-mortality only in such carriers. Accordingly, previous heterogeneous results regarding the benefit of hydrocortisone in septic shock may be reconciled by genetic variation of the NFKB1 promoter polymorphism.
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Affiliation(s)
- Simon T. Schäfer
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Essen, Germany
- * E-mail:
| | - Sophia Gessner
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Essen, Germany
| | - André Scherag
- Klinische Epidemiologie, Integriertes Forschungs- und Behandlungszentrum (IFB) Sepsis und Sepsisfolgen - Center for Sepsis Control and Care (CSCC), Universitätsklinikum Jena, Jena, Germany
| | - Katharina Rump
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Essen, Germany
- Universität Duisburg-Essen and Universitätsklinikum Essen, Essen Germany; Klinik für Anästhesiologie und Intensivmedizin, Knappschaftskrankenhaus Bochum and Ruhruniversität Bochum, Bochum, Germany
| | - Ulrich H. Frey
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Essen, Germany
| | - Winfried Siffert
- Institut für Pharmakogenetik, Universität Duisburg-Essen and Universitätsklinikum Essen, Essen, Germany
| | | | - Jörg Steinmann
- Institut für Medizinische Mikrobiologie. Zurich, Switzerland
| | - Jürgen Peters
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Essen, Germany
| | - Michael Adamzik
- Klinik für Anästhesiologie & Intensivmedizin, Universität Duisburg-Essen and Universitätsklinikum Essen, Essen, Germany
- Universität Duisburg-Essen and Universitätsklinikum Essen, Essen Germany; Klinik für Anästhesiologie und Intensivmedizin, Knappschaftskrankenhaus Bochum and Ruhruniversität Bochum, Bochum, Germany
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19
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Dominance of the strongest: inflammatory cytokines versus glucocorticoids. Cytokine Growth Factor Rev 2013; 25:21-33. [PMID: 24412262 DOI: 10.1016/j.cytogfr.2013.12.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 12/15/2013] [Indexed: 02/08/2023]
Abstract
Pro-inflammatory cytokines are involved in the pathogenesis of many inflammatory diseases, and the excessive expression of many of them is normally counteracted by glucocorticoids (GCs), which are steroids that bind to the glucocorticoid receptor (GR). Hence, GCs are potent inhibitors of inflammation, and they are widely used to treat inflammatory diseases, such as asthma, rheumatoid arthritis and inflammatory bowel disease. However, despite the success of GC therapy, many patients show some degree of GC unresponsiveness, called GC resistance (GCR). This is a serious problem because it limits the full therapeutic exploitation of the anti-inflammatory power of GCs. Patients with reduced GC responses often have higher cytokine levels, and there is a complex interplay between GCs and cytokines: GCs downregulate pro-inflammatory cytokines while cytokines limit GC action. Treatment of inflammatory diseases with GCs is successful when GCs dominate. But when cytokines overrule the anti-inflammatory actions of GCs, patients become GC insensitive. New insights into the molecular mechanisms of GR-mediated actions and GCR are needed for the design of more effective GC-based therapies.
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Luo M, Lu X, Zhu R, Zhang Z, Chow CC, Li R, Simons SS. A conserved protein motif is required for full modulatory activity of negative elongation factor subunits NELF-A and NELF-B in modifying glucocorticoid receptor-regulated gene induction properties. J Biol Chem 2013; 288:34055-34072. [PMID: 24097989 DOI: 10.1074/jbc.m113.512426] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
NELF-B is a BRCA1-interacting protein and subunit (with NELF-A, -C/D, and -E) of the human negative elongation factor (NELF) complex, which participates in RNA polymerase II pausing shortly after transcription initiation, especially for synchronized gene expression. We now report new activities of NELF-B and other NELF complex subunits, which are to attenuate glucocorticoid receptor (GR)-mediated gene induction, reduce the partial agonist activity of an antagonist, and increase the EC50 of an agonist during nonsynchronized expression of exogenous and endogenous reporters. Stable knockdown of endogenous NELF-B has the opposite effects on an exogenous gene. The GR ligand-binding domain suffices for these biological responses. ChIP assays reveal that NELF-B diminishes GR recruitment to promoter regions of two endogenous genes. Using a new competition assay, NELF-A and NELF-B are each shown to act independently as competitive decelerators at two steps after the site of GR action and before or at the site of reporter gene activity. A common motif in each NELF was identified that is required for full activity of both NELF-A and NELF-B. These studies allow us to position the actions of two new modulators of GR-regulated transactivation, NELF-A and NELF-B, relative to other factors in the overall gene induction sequence.
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Affiliation(s)
- Min Luo
- Steroid Hormones Section, NIDDK/Laboratory of Endocrinology and Receptor Biology (LERB), National Institutes of Health, Bethesda, Maryland 20892
| | - Xinping Lu
- Steroid Hormones Section, NIDDK/Laboratory of Endocrinology and Receptor Biology (LERB), National Institutes of Health, Bethesda, Maryland 20892
| | - Rong Zhu
- Steroid Hormones Section, NIDDK/Laboratory of Endocrinology and Receptor Biology (LERB), National Institutes of Health, Bethesda, Maryland 20892
| | - Zhenhuan Zhang
- Steroid Hormones Section, NIDDK/Laboratory of Endocrinology and Receptor Biology (LERB), National Institutes of Health, Bethesda, Maryland 20892
| | - Carson C Chow
- Laboratory of Biological Modeling, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Rong Li
- Cancer Therapy and Research Center, University of Texas Health Science Center, San Antonio, Texas 78229
| | - S Stoney Simons
- Steroid Hormones Section, NIDDK/Laboratory of Endocrinology and Receptor Biology (LERB), National Institutes of Health, Bethesda, Maryland 20892.
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