1
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Yang YH, Yan F, Yuan W, Shi PS, Wu SM, Cui DJ. High-altitude hypoxia promotes BRD4-mediated activation of the Wnt/β-catenin pathway and disruption of intestinal barrier. Cell Signal 2024; 120:111187. [PMID: 38648894 DOI: 10.1016/j.cellsig.2024.111187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 04/03/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
Hypobaric hypoxia, commonly experienced at elevated altitudes, presents significant physiological challenges. Our investigation is centered on the impact of the bromodomain protein 4 (BRD4) under these conditions, especially its interaction with the Wnt/β-Catenin pathway and resultant effects on glycolytic inflammation and intestinal barrier stability. By combining transcriptome sequencing with bioinformatics, we identified BRD4's key role in hypoxia-related intestinal anomalies. Clinical parameters of altitude sickness patients, including serum BRD4 levels, inflammatory markers, and barrier integrity metrics, were scrutinized. In vitro studies using CCD 841 CoN cells depicted expression changes in BRD4, Interleukin (IL)-1β, IL-6, and β-Catenin. Transepithelial electrical resistance (TEER) and FD4 analyses assessed barrier resilience. Hypoxia-induced mouse models, analyzed via H&E staining and Western blot, provided insights into barrier and protein alterations. Under hypoxic conditions, marked BRD4 expression variations emerged. Elevated serum BRD4 in patients coincided with intensified Wnt signaling, inflammation, and barrier deterioration. In vitro, findings showed hypoxia-induced upregulation of BRD4 and inflammatory markers but a decline in Occludin and ZO1, affecting barrier strength-effects mitigated by BRD4 inhibition. Mouse models echoed these patterns, linking BRD4 upregulation in hypoxia to barrier perturbations. Hypobaric hypoxia-induced BRD4 upregulation disrupts the Wnt/β-Catenin signaling, sparking glycolysis-fueled inflammation and weakening intestinal tight junctions and barrier degradation.
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Affiliation(s)
- Yun-Han Yang
- Department of Gastroenterology, National Institution of Drug Clinical Trial, Guizhou Provincial People's Hospital, Guiyang 550002, China
| | - Fang Yan
- Department of Gastroenterology, National Institution of Drug Clinical Trial, Guizhou Provincial People's Hospital, Guiyang 550002, China
| | - Wenqiang Yuan
- Department of Gastroenterology, National Institution of Drug Clinical Trial, Guizhou Provincial People's Hospital, Guiyang 550002, China
| | - Peng-Shuang Shi
- Department of Gastroenterology, National Institution of Drug Clinical Trial, Guizhou Provincial People's Hospital, Guiyang 550002, China
| | - Shi-Min Wu
- Graduate School, Zunyi Medical University, Zunyi, China
| | - De-Jun Cui
- Department of Gastroenterology, Guizhou Provincial People's Hospital, No. 83, Zhongshan East Road, Guiyang 550002, Guizhou Province, China.
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2
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Cozzolino K, Sanford L, Hunter S, Molison K, Erickson B, Jones T, Courvan MCS, Ajit D, Galbraith MD, Espinosa JM, Bentley DL, Allen MA, Dowell RD, Taatjes DJ. Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.05.547813. [PMID: 37461585 PMCID: PMC10349994 DOI: 10.1101/2023.07.05.547813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Hyperactive interferon (IFN) signaling is a hallmark of Down syndrome (DS), a condition caused by trisomy 21 (T21); strategies that normalize IFN signaling could benefit this population. Mediator-associated kinases CDK8 and CDK19 drive inflammatory responses through incompletely understood mechanisms. Using sibling-matched cell lines with/without T21, we investigated Mediator kinase function in the context of hyperactive IFN in DS over a 45min - 24h timeframe. Activation of IFN-response genes was suppressed in cells treated with the CDK8/CDK19 inhibitor cortistatin A (CA), and this occurred through rapid suppression of IFN-responsive transcription factor activity. Moreover, we discovered that CDK8/CDK19 affect splicing, a novel means by which Mediator kinases control gene expression. To further probe Mediator kinase function, we completed cytokine screens and untargeted metabolomics experiments. Cytokines are master regulators of inflammatory responses; by screening 105 different cytokine proteins, we show that Mediator kinases help drive IFN-dependent cytokine responses at least in part through transcriptional regulation of cytokine genes and receptors. Metabolomics revealed that Mediator kinase inhibition altered core metabolic pathways, including broad up-regulation of anti-inflammatory lipid mediators, whose levels were elevated during hyperactive IFN signaling. A subset of these lipid mediators (e.g. oleamide, desmosterol) serve as ligands for nuclear receptors PPAR and LXR, and activation of these receptors occurred specifically during hyperactive IFN signaling in CA-treated cells, revealing a mechanistic link between Mediator kinase activity and nuclear receptor function. Collectively, our results identify new mechanisms by which CDK8/CDK19 regulate gene expression, and establish that Mediator kinase inhibition antagonizes IFN signaling through transcriptional, metabolic, and cytokine responses, with implications for DS and other chronic inflammatory conditions.
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Affiliation(s)
- Kira Cozzolino
- Dept. of Biochemistry, University of Colorado, Boulder, CO, 80303, USA
| | - Lynn Sanford
- Dept. of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, 80303, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80303, USA
| | - Samuel Hunter
- Dept. of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, 80303, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80303, USA
| | - Kayla Molison
- Dept. of Biochemistry, University of Colorado, Boulder, CO, 80303, USA
| | - Benjamin Erickson
- Dept. Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- UC-Denver RNA Bioscience Initiative
| | - Taylor Jones
- Dept. of Biochemistry, University of Colorado, Boulder, CO, 80303, USA
| | - Meaghan C S Courvan
- Dept. of Biochemistry, University of Colorado, Boulder, CO, 80303, USA
- Dept. of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, 80303, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80303, USA
- Crnic Institute Boulder Branch
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Deepa Ajit
- Metabolon, Inc., Durham, North Carolina, USA
| | - Matthew D Galbraith
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Dept. of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joaquin M Espinosa
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Dept. of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - David L Bentley
- Dept. Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- UC-Denver RNA Bioscience Initiative
| | - Mary A Allen
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80303, USA
| | - Robin D Dowell
- Dept. of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, 80303, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80303, USA
| | - Dylan J Taatjes
- Dept. of Biochemistry, University of Colorado, Boulder, CO, 80303, USA
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3
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Wang D, Ritz C, Pierce A, Brunt B, Luo Y, Dahl N, Venkataraman S, Danis E, Kuś K, Mazan M, Rzymski T, Veo B, Vibhakar R. Transcriptional Regulation of Protein Synthesis by Mediator Kinase in MYC-driven Medulloblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584103. [PMID: 38559100 PMCID: PMC10979852 DOI: 10.1101/2024.03.08.584103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
MYC-driven medulloblastoma (MB) is a highly aggressive cancer type with poor prognosis and limited treatment options. Through CRISPR-Cas9 screening across MB cell lines, we identified the Mediator-associated kinase CDK8 as the top dependence for MYC-driven MB. Loss of CDK8 markedly reduces MYC expression and impedes MB growth. Mechanistically, we demonstrate that CDK8 depletion suppresses ribosome biogenesis and mRNA translation. CDK8 regulates occupancy of phospho-Polymerase II at specific chromatin loci facilitating an epigenetic alteration that promotes transcriptional regulation of ribosome biogenesis. Additionally, CDK8-mediated phosphorylation of 4EBP1 plays a crucial role in initiating eIF4E-dependent translation. Targeting CDK8 effectively suppresses cancer stem and progenitor cells, characterized by increased ribosome biogenesis activity. We also report the synergistic inhibition of CDK8 and mTOR in vivo and in vitro . Overall, our findings establish a connection between transcription and translation regulation, suggesting a promising therapeutic approach targets multiple points in the protein synthesis network for MYC-driven MB.
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4
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Sun L, Zhou J, Xu X, Liu Y, Ma N, Liu Y, Nie W, Zou L, Deng XW, He H. Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL. Nat Commun 2024; 15:35. [PMID: 38167349 PMCID: PMC10762229 DOI: 10.1038/s41467-023-44347-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 12/10/2023] [Indexed: 01/05/2024] Open
Abstract
Although chromatin organizations in plants have been dissected at the scales of compartments and topologically associating domain (TAD)-like domains, there remains a gap in resolving fine-scale structures. Here, we use Micro-C-XL, a high-throughput chromosome conformation capture (Hi-C)-based technology that involves micrococcal nuclease (instead of restriction enzymes) and long cross-linkers, to dissect single nucleosome-resolution chromatin organization in Arabidopsis. Insulation analysis reveals more than 14,000 boundaries, which mostly include chromatin accessibility, epigenetic modifications, and transcription factors. Micro-C-XL reveals associations between RNA Pols and local chromatin organizations, suggesting that gene transcription substantially contributes to the establishment of local chromatin domains. By perturbing Pol II both genetically and chemically at the gene level, we confirm its function in regulating chromatin organization. Visible loops and stripes are assigned to super-enhancers and their targeted genes, thus providing direct insights for the identification and mechanistic analysis of distal CREs and their working modes in plants. We further investigate possible factors regulating these chromatin loops. Subsequently, we expand Micro-C-XL to soybean and rice. In summary, we use Micro-C-XL for analyses of plants, which reveal fine-scale chromatin organization and enhancer-promoter loops and provide insights regarding three-dimensional genomes in plants.
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Affiliation(s)
- Linhua Sun
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Jingru Zhou
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
| | - Xiao Xu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
| | - Yi Liu
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Ni Ma
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
- PKU-Tsinghua-NIBS Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Yutong Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
| | - Wenchao Nie
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, 430075, China
| | - Ling Zou
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, 430075, China
| | - Xing Wang Deng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China.
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China.
| | - Hang He
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China.
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China.
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5
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Abstract
Enhancers are cis-regulatory elements that can stimulate gene expression from distance, and drive precise spatiotemporal gene expression profiles during development. Functional enhancers display specific features including an open chromatin conformation, Histone H3 lysine 27 acetylation, Histone H3 lysine 4 mono-methylation enrichment, and enhancer RNAs production. These features are modified upon developmental cues which impacts their activity. In this review, we describe the current state of knowledge about enhancer functions and the diverse chromatin signatures found on enhancers. We also discuss the dynamic changes of enhancer chromatin signatures, and their impact on lineage specific gene expression profiles, during development or cellular differentiation.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,CONTACT Amandine Barral Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. 3400 Civic Blvd, Philadelphia, Pennsylvania19104, USA
| | - Jérôme Déjardin
- Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, Montpellier, France,Jérôme Déjardin Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier34000, France
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6
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Duan B, Zhou X, Zhang X, Qiu F, Zhang S, Chen Y, Yang J, Wang J, Tan W. BRD4-binding enhancer promotes CRC progression by interacting with YY1 to activate the Wnt pathway through upregulation of TCF7L2. Biochem Pharmacol 2023; 218:115877. [PMID: 37879498 DOI: 10.1016/j.bcp.2023.115877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/15/2023] [Accepted: 10/20/2023] [Indexed: 10/27/2023]
Abstract
Colorectal carcinoma (CRC), one of the most life-threatening cancer types, is associated with aberrant expression of epigenetic modifiers and activation of the Wnt pathway. However, the role of epigenetic regulators in driving cancer cell proliferation and their potential as therapeutic targets affecting the Wnt pathway remain unclear. In this study, BRD4 was found to promote the progression of CRC both in vitro and in vivo. The expression of BRD4 correlated with shortened CRC patient survival. In addition, BRD4 function was strongly correlated with the Wnt pathway, but rather through regulation of TCF7L2 at transcriptional levels. BRD4 and H3K27ac have overlapping occupancies in the cis-regulatory elements of TCF7L2, suggesting enhancer-based epigenetic regulation. Numerous YY1 binding sites were found in the abovementioned region. YY1 recruited BRD4 to bind to cis-regulatory elements of TCF7L2, thereby regulating the expression of TCF7L2. Altogether, this study validates that BRD4 performs a canonical epigenetic regulatory function in CRC and can be used in the treatment of Wnt pathway-dependent CRC or other malignancies with clinically available bromodomain inhibitors.
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Affiliation(s)
- Biao Duan
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China.
| | - Xuwei Zhou
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Xiaoyi Zhang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Fenglan Qiu
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Shaoqing Zhang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yue Chen
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Jun Yang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Juan Wang
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Wenfu Tan
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China.
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7
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Talukdar PD, Chatterji U. Transcriptional co-activators: emerging roles in signaling pathways and potential therapeutic targets for diseases. Signal Transduct Target Ther 2023; 8:427. [PMID: 37953273 PMCID: PMC10641101 DOI: 10.1038/s41392-023-01651-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/27/2023] [Accepted: 09/10/2023] [Indexed: 11/14/2023] Open
Abstract
Specific cell states in metazoans are established by the symphony of gene expression programs that necessitate intricate synergic interactions between transcription factors and the co-activators. Deregulation of these regulatory molecules is associated with cell state transitions, which in turn is accountable for diverse maladies, including developmental disorders, metabolic disorders, and most significantly, cancer. A decade back most transcription factors, the key enablers of disease development, were historically viewed as 'undruggable'; however, in the intervening years, a wealth of literature validated that they can be targeted indirectly through transcriptional co-activators, their confederates in various physiological and molecular processes. These co-activators, along with transcription factors, have the ability to initiate and modulate transcription of diverse genes necessary for normal physiological functions, whereby, deregulation of such interactions may foster tissue-specific disease phenotype. Hence, it is essential to analyze how these co-activators modulate specific multilateral processes in coordination with other factors. The proposed review attempts to elaborate an in-depth account of the transcription co-activators, their involvement in transcription regulation, and context-specific contributions to pathophysiological conditions. This review also addresses an issue that has not been dealt with in a comprehensive manner and hopes to direct attention towards future research that will encompass patient-friendly therapeutic strategies, where drugs targeting co-activators will have enhanced benefits and reduced side effects. Additional insights into currently available therapeutic interventions and the associated constraints will eventually reveal multitudes of advanced therapeutic targets aiming for disease amelioration and good patient prognosis.
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Affiliation(s)
- Priyanka Dey Talukdar
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Urmi Chatterji
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
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8
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Chen M, Li J, Zhang L, Wang L, Cheng C, Ji H, Altilia S, Ding X, Cai G, Altomare D, Shtutman M, Byrum SD, Mackintosh SG, Feoktistov A, Soshnikova N, Mogila VA, Tatarskiy V, Erokhin M, Chetverina D, Prawira A, Ni Y, Urban S, McInnes C, Broude EV, Roninson IB. CDK8 and CDK19: positive regulators of signal-induced transcription and negative regulators of Mediator complex proteins. Nucleic Acids Res 2023; 51:7288-7313. [PMID: 37378433 PMCID: PMC10415139 DOI: 10.1093/nar/gkad538] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
We have conducted a detailed transcriptomic, proteomic and phosphoproteomic analysis of CDK8 and its paralog CDK19, alternative enzymatic components of the kinase module associated with transcriptional Mediator complex and implicated in development and diseases. This analysis was performed using genetic modifications of CDK8 and CDK19, selective CDK8/19 small molecule kinase inhibitors and a potent CDK8/19 PROTAC degrader. CDK8/19 inhibition in cells exposed to serum or to agonists of NFκB or protein kinase C (PKC) reduced the induction of signal-responsive genes, indicating a pleiotropic role of Mediator kinases in signal-induced transcriptional reprogramming. CDK8/19 inhibition under basal conditions initially downregulated a small group of genes, most of which were inducible by serum or PKC stimulation. Prolonged CDK8/19 inhibition or mutagenesis upregulated a larger gene set, along with a post-transcriptional increase in the proteins comprising the core Mediator complex and its kinase module. Regulation of both RNA and protein expression required CDK8/19 kinase activities but both enzymes protected their binding partner cyclin C from proteolytic degradation in a kinase-independent manner. Analysis of isogenic cell populations expressing CDK8, CDK19 or their kinase-inactive mutants revealed that CDK8 and CDK19 have the same qualitative effects on protein phosphorylation and gene expression at the RNA and protein levels, whereas differential effects of CDK8 versus CDK19 knockouts were attributable to quantitative differences in their expression and activity rather than different functions.
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Affiliation(s)
- Mengqian Chen
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
- Senex Biotechnology, Inc. Columbia, SC 29208, USA
| | - Jing Li
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Li Zhang
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Lili Wang
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Chen Cheng
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Hao Ji
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Serena Altilia
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Xiaokai Ding
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Guoshuai Cai
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Diego Altomare
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Michael Shtutman
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Alexey Feoktistov
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Nataliya Soshnikova
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Vladislav A Mogila
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Victor Tatarskiy
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Maksim Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Darya Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russian Federation
| | - Angga Prawira
- Department of Infectious Diseases, University Hospital of Heidelberg, Heidelberg, Germany
| | - Yi Ni
- Department of Infectious Diseases, University Hospital of Heidelberg, Heidelberg, Germany
| | - Stephan Urban
- Department of Infectious Diseases, University Hospital of Heidelberg, Heidelberg, Germany
| | - Campbell McInnes
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Eugenia V Broude
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
| | - Igor B Roninson
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA
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9
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Liu H, Jiang M, Ma F, Qin J, Zhou X, Xu L, Yan X, Jiang T. JMJD6 functions as an oncogene and is associated with poor prognosis in esophageal squamous cell carcinoma. BMC Cancer 2023; 23:696. [PMID: 37488513 PMCID: PMC10367331 DOI: 10.1186/s12885-023-11171-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 07/11/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is one of the most common malignant tumors with a high prevalence and poor prognosis. It is an urgent problem to deeply understand the molecular mechanism of ESCC and develop effective diagnostic and prognostic methods. METHODS Using tumor tissue and corresponding paracancerous samples from 141 resected ESCC patients, we assessed Jumonji domain-containing protein 6 (JMJD6) expression using Immunohistochemical (IHC) staining. Kaplan-Meier survival analysis and univariate or multivariate analysis were used to investigate the relationship between JMJD6 expression and clinicopathological features. The expression status and prognostic value of JMJD6 were analyzed by bioinformatics and enrichment analysis. RESULTS The expression of JMJD6 in ESCC samples was higher than that in the corresponding paracancerous samples, and high expression of JMJD6 was positively associated with poor prognosis of ESCC patients. In addition, bioinformatics analysis of the expression and prognosis of JMJD6 in a variety of tumors showed that high expression of JMJD6 was significantly associated with poor overall survival (OS) in ESCC patients. Enrichment analysis indicated that the high expression of genes similar to JMJD6, such as Conserved oligomeric Golgi 1(COG1), Major facilitator superfamily domain 11 (MFSD11) and Death Effector Domain Containing 2 (DEDD2), was associated with poor prognosis of ESCC, suggesting that JMJD6 might be involved in the occurrence and prognosis of ESCC. CONCLUSION Our study found that JMJD6 expression was significantly increased in ESCC patients and positively correlated with prognosis, indicating that targeting JMJD6 might be an attractive prognostic biomarker and provides a potential treatment strategy for ESCC. TRIAL REGISTRATION The study was approved by Tangdu Hospital ethics committee (No. TDLL-202110-02).
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Affiliation(s)
- Honggang Liu
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, 1 Xinsi Road, Xi'an, 710038, China
| | - Menglong Jiang
- Department of Thoracic Surgery, 1st Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Fenghui Ma
- Medical Examination Center, Tangdu Hospital, Air Force Medical University, 1 Xinsi Road, Xi'an, 710038, China
| | - Jiapei Qin
- Department of Medical Oncology, Senior Department of Oncology, The Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xin Zhou
- Department of Medical Oncology, Senior Department of Oncology, The Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Liqun Xu
- Department of Aerospace Medicine, Air Force Medical University, 169 Changle West Road, Xi'an, 710032, China.
| | - Xiaolong Yan
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, 1 Xinsi Road, Xi'an, 710038, China.
| | - Tao Jiang
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, 1 Xinsi Road, Xi'an, 710038, China.
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10
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Thieme E, Bruss N, Sun D, Dominguez EC, Coleman D, Liu T, Roleder C, Martinez M, Garcia-Mansfield K, Ball B, Pirrotte P, Wang L, Xia Z, Danilov AV. CDK9 inhibition induces epigenetic reprogramming revealing strategies to circumvent resistance in lymphoma. Mol Cancer 2023; 22:64. [PMID: 36998071 PMCID: PMC10061728 DOI: 10.1186/s12943-023-01762-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) exhibits significant genetic heterogeneity which contributes to drug resistance, necessitating development of novel therapeutic approaches. Pharmacological inhibitors of cyclin-dependent kinases (CDK) demonstrated pre-clinical activity in DLBCL, however many stalled in clinical development. Here we show that AZD4573, a selective inhibitor of CDK9, restricted growth of DLBCL cells. CDK9 inhibition (CDK9i) resulted in rapid changes in the transcriptome and proteome, with downmodulation of multiple oncoproteins (eg, MYC, Mcl-1, JunB, PIM3) and deregulation of phosphoinotiside-3 kinase (PI3K) and senescence pathways. Following initial transcriptional repression due to RNAPII pausing, we observed transcriptional recovery of several oncogenes, including MYC and PIM3. ATAC-Seq and ChIP-Seq experiments revealed that CDK9i induced epigenetic remodeling with bi-directional changes in chromatin accessibility, suppressed promoter activation and led to sustained reprograming of the super-enhancer landscape. A CRISPR library screen suggested that SE-associated genes in the Mediator complex, as well as AKT1, confer resistance to CDK9i. Consistent with this, sgRNA-mediated knockout of MED12 sensitized cells to CDK9i. Informed by our mechanistic findings, we combined AZD4573 with either PIM kinase or PI3K inhibitors. Both combinations decreased proliferation and induced apoptosis in DLBCL and primary lymphoma cells in vitro as well as resulted in delayed tumor progression and extended survival of mice xenografted with DLBCL in vivo. Thus, CDK9i induces reprogramming of the epigenetic landscape, and super-enhancer driven recovery of select oncogenes may contribute to resistance to CDK9i. PIM and PI3K represent potential targets to circumvent resistance to CDK9i in the heterogeneous landscape of DLBCL.
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Affiliation(s)
- Elana Thieme
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Nur Bruss
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Duanchen Sun
- grid.516136.6Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
- grid.5288.70000 0000 9758 5690Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR USA
- grid.27255.370000 0004 1761 1174Present address: School of Mathematics, Shandong University, Jinan, 250100 Shandong China
| | - Edward C. Dominguez
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Daniel Coleman
- grid.516136.6Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
| | - Tingting Liu
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Carly Roleder
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Melissa Martinez
- grid.250942.80000 0004 0507 3225Translational Genomics Research Institute, Phoenix, AZ 85004 USA
- grid.410425.60000 0004 0421 8357Integrated Mass Spectrometry Shared Resource, City of Hope National Medical Center, Duarte, CA USA
| | - Krystine Garcia-Mansfield
- grid.250942.80000 0004 0507 3225Translational Genomics Research Institute, Phoenix, AZ 85004 USA
- grid.410425.60000 0004 0421 8357Integrated Mass Spectrometry Shared Resource, City of Hope National Medical Center, Duarte, CA USA
| | - Brian Ball
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Patrick Pirrotte
- grid.250942.80000 0004 0507 3225Translational Genomics Research Institute, Phoenix, AZ 85004 USA
- grid.410425.60000 0004 0421 8357Integrated Mass Spectrometry Shared Resource, City of Hope National Medical Center, Duarte, CA USA
| | - Lili Wang
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
| | - Zheng Xia
- grid.516136.6Knight Cancer Institute, Oregon Health & Science University, Portland, OR USA
- grid.5288.70000 0000 9758 5690Biomedical Engineering Department, Oregon Health & Science University, Portland, OR USA
| | - Alexey V. Danilov
- grid.410425.60000 0004 0421 8357City of Hope National Medical Center, 1500 E Duarte Road, Duarte, CA 91010 USA
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11
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Richter WF, Nayak S, Iwasa J, Taatjes DJ. The Mediator complex as a master regulator of transcription by RNA polymerase II. Nat Rev Mol Cell Biol 2022; 23:732-749. [PMID: 35725906 PMCID: PMC9207880 DOI: 10.1038/s41580-022-00498-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2022] [Indexed: 02/08/2023]
Abstract
The Mediator complex, which in humans is 1.4 MDa in size and includes 26 subunits, controls many aspects of RNA polymerase II (Pol II) function. Apart from its size, a defining feature of Mediator is its intrinsic disorder and conformational flexibility, which contributes to its ability to undergo phase separation and to interact with a myriad of regulatory factors. In this Review, we discuss Mediator structure and function, with emphasis on recent cryogenic electron microscopy data of the 4.0-MDa transcription preinitiation complex. We further discuss how Mediator and sequence-specific DNA-binding transcription factors enable enhancer-dependent regulation of Pol II function at distal gene promoters, through the formation of molecular condensates (or transcription hubs) and chromatin loops. Mediator regulation of Pol II reinitiation is also discussed, in the context of transcription bursting. We propose a working model for Mediator function that combines experimental results and theoretical considerations related to enhancer-promoter interactions, which reconciles contradictory data regarding whether enhancer-promoter communication is direct or indirect. We conclude with a discussion of Mediator's potential as a therapeutic target and of future research directions.
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Affiliation(s)
- William F Richter
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Shraddha Nayak
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Janet Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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12
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Dannappel MV, Zhu D, Sun X, Chua HK, Poppelaars M, Suehiro M, Khadka S, Lim Kam Sian TC, Sooraj D, Loi M, Gao H, Croagh D, Daly RJ, Faridi P, Boyer TG, Firestein R. CDK8 and CDK19 regulate intestinal differentiation and homeostasis via the chromatin remodeling complex SWI/SNF. J Clin Invest 2022; 132:158593. [PMID: 36006697 PMCID: PMC9566890 DOI: 10.1172/jci158593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Initiation and maintenance of transcriptional states are critical for controlling normal tissue homeostasis and differentiation. The cyclin dependent kinases CDK8 and CDK19 (Mediator kinases) are regulatory components of Mediator, a highly conserved complex that orchestrates enhancer-mediated transcriptional output. While Mediator kinases have been implicated in the transcription of genes necessary for development and growth, its function in mammals has not been well defined. Using genetically defined models and pharmacological inhibitors, we showed that CDK8 and CDK19 function in a redundant manner to regulate intestinal lineage specification in humans and mice. The Mediator kinase module bound and phosphorylated key components of the chromatin remodeling complex switch/sucrose non-fermentable (SWI/SNF) in intestinal epithelial cells. Concomitantly, SWI/SNF and MED12-Mediator colocalized at distinct lineage-specifying enhancers in a CDK8/19-dependent manner. Thus, these studies reveal a transcriptional mechanism of intestinal cell specification, coordinated by the interaction between the chromatin remodeling complex SWI/SNF and Mediator kinase.
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Affiliation(s)
- Marius V Dannappel
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science and
| | - Danxi Zhu
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Xin Sun
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science and
| | - Hui Kheng Chua
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science and
| | - Marle Poppelaars
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science and
| | - Monica Suehiro
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science and
| | - Subash Khadka
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Terry Cc Lim Kam Sian
- Cancer Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology
| | - Dhanya Sooraj
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science and
| | - Melissa Loi
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science and
| | - Hugh Gao
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Molecular and Translational Science, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | | | - Roger J Daly
- Cancer Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology
| | - Pouya Faridi
- Department of Medicine, School of Clinical Sciences at Monash Health, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Thomas G Boyer
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Ron Firestein
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Molecular and Translational Science and
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13
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van der Noord VE, van de Water B, Le Dévédec SE. Targeting the Heterogeneous Genomic Landscape in Triple-Negative Breast Cancer through Inhibitors of the Transcriptional Machinery. Cancers (Basel) 2022; 14:4353. [PMID: 36139513 PMCID: PMC9496798 DOI: 10.3390/cancers14184353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer defined by lack of the estrogen, progesterone and human epidermal growth factor receptor 2. Although TNBC tumors contain a wide variety of oncogenic mutations and copy number alterations, the direct targeting of these alterations has failed to substantially improve therapeutic efficacy. This efficacy is strongly limited by interpatient and intratumor heterogeneity, and thereby a lack in uniformity of targetable drivers. Most of these genetic abnormalities eventually drive specific transcriptional programs, which may be a general underlying vulnerability. Currently, there are multiple selective inhibitors, which target the transcriptional machinery through transcriptional cyclin-dependent kinases (CDKs) 7, 8, 9, 12 and 13 and bromodomain extra-terminal motif (BET) proteins, including BRD4. In this review, we discuss how inhibitors of the transcriptional machinery can effectively target genetic abnormalities in TNBC, and how these abnormalities can influence sensitivity to these inhibitors. These inhibitors target the genomic landscape in TNBC by specifically suppressing MYC-driven transcription, inducing further DNA damage, improving anti-cancer immunity, and preventing drug resistance against MAPK and PI3K-targeted therapies. Because the transcriptional machinery enables transcription and propagation of multiple cancer drivers, it may be a promising target for (combination) treatment, especially of heterogeneous malignancies, including TNBC.
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Affiliation(s)
| | | | - Sylvia E. Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
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14
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Xiao Q, Xiao Y, Li LY, Chen MK, Wu M. Multifaceted regulation of enhancers in cancer. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194839. [PMID: 35750313 DOI: 10.1016/j.bbagrm.2022.194839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/24/2022] [Accepted: 06/14/2022] [Indexed: 12/12/2022]
Abstract
Enhancer is one kind of cis-elements regulating gene transcription, whose activity is tightly controlled by epigenetic enzymes and histone modifications. Active enhancers are classified into typical enhancers, super-enhancers and over-active enhancers, according to the enrichment and location of histone modifications. Epigenetic factors control the level of histone modifications on enhancers to determine their activity, such as histone methyltransferases and acetylases. Transcription factors, cofactors and mediators co-operate together and are required for enhancer functions. In turn, abnormalities in these trans-acting factors affect enhancer activity. Recent studies have revealed enhancer dysregulation as one of the important features for cancer. Variations in enhancer regions and mutations of enhancer regulatory genes are frequently observed in cancer cells, and altering the activity of onco-enhancers is able to repress oncogene expression, and suppress tumorigenesis and metastasis. Here we summarize the recent discoveries about enhancer regulation in cancer and discuss their potential application in diagnosis and treatment.
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Affiliation(s)
- Qiong Xiao
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China
| | - Yong Xiao
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China
| | - Lian-Yun Li
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China
| | - Ming-Kai Chen
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China.
| | - Min Wu
- Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, Hubei 430072, China.
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15
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The Mediator kinase module: an interface between cell signaling and transcription. Trends Biochem Sci 2022; 47:314-327. [DOI: 10.1016/j.tibs.2022.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 12/14/2022]
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