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Kulikowski E, Rakai BD, Wong NCW. Inhibitors of bromodomain and extra-terminal proteins for treating multiple human diseases. Med Res Rev 2020; 41:223-245. [PMID: 32926459 PMCID: PMC7756446 DOI: 10.1002/med.21730] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/17/2022]
Abstract
Clinical development of bromodomain and extra‐terminal (BET) protein inhibitors differs from the traditional course of drug development. These drugs are simultaneously being evaluated for treating a wide spectrum of human diseases due to their novel mechanism of action. BET proteins are epigenetic “readers,” which play a primary role in transcription. Here, we briefly describe the BET family of proteins, of which BRD4 has been studied most extensively. We discuss BRD4 activity at latent enhancers as an example of BET protein function. We examine BRD4 redistribution and enhancer reprogramming in embryonic development, cancer, cardiovascular, autoimmune, and metabolic diseases, presenting hallmark studies that highlight BET proteins as attractive targets for therapeutic intervention. We review the currently available approaches to targeting BET proteins, methods of selectively targeting individual bromodomains, and review studies that compare the effects of selective BET inhibition to those of pan‐BET inhibition. Lastly, we examine the current clinical landscape of BET inhibitor development.
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Sasse SK, Gruca M, Allen MA, Kadiyala V, Song T, Gally F, Gupta A, Pufall MA, Dowell RD, Gerber AN. Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression. Genome Res 2019; 29:1753-1765. [PMID: 31519741 PMCID: PMC6836729 DOI: 10.1101/gr.248187.119] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 09/06/2019] [Indexed: 12/16/2022]
Abstract
The glucocorticoid receptor (NR3C1, also known as GR) binds to specific DNA sequences and directly induces transcription of anti-inflammatory genes that contribute to cytokine repression, frequently in cooperation with NF-kB. Whether inflammatory repression also occurs through local interactions between GR and inflammatory gene regulatory elements has been controversial. Here, using global run-on sequencing (GRO-seq) in human airway epithelial cells, we show that glucocorticoid signaling represses transcription within 10 min. Many repressed regulatory regions reside within “hyper-ChIPable” genomic regions that are subject to dynamic, yet nonspecific, interactions with some antibodies. When this artifact was accounted for, we determined that transcriptional repression does not require local GR occupancy. Instead, widespread transcriptional induction through canonical GR binding sites is associated with reciprocal repression of distal TNF-regulated enhancers through a chromatin-dependent process, as evidenced by chromatin accessibility and motif displacement analysis. Simultaneously, transcriptional induction of key anti-inflammatory effectors is decoupled from primary repression through cooperation between GR and NF-kB at a subset of regulatory regions. Thus, glucocorticoids exert bimodal restraints on inflammation characterized by rapid primary transcriptional repression without local GR occupancy and secondary anti-inflammatory effects resulting from transcriptional cooperation between GR and NF-kB.
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Affiliation(s)
- Sarah K Sasse
- Department of Medicine, National Jewish Health, Denver, Colorado 80206, USA
| | - Margaret Gruca
- BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
| | - Mary A Allen
- BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
| | - Vineela Kadiyala
- Department of Medicine, National Jewish Health, Denver, Colorado 80206, USA
| | - Tengyao Song
- Department of Medicine, National Jewish Health, Denver, Colorado 80206, USA
| | - Fabienne Gally
- Department of Biomedical Research, National Jewish Health, Denver, Colorado 80206, USA
| | - Arnav Gupta
- Department of Medicine, University of Colorado, Aurora, Colorado 80045, USA
| | - Miles A Pufall
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Robin D Dowell
- BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA.,Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA.,Computer Science, University of Colorado, Boulder, Colorado 80309, USA
| | - Anthony N Gerber
- Department of Medicine, National Jewish Health, Denver, Colorado 80206, USA.,Department of Biomedical Research, National Jewish Health, Denver, Colorado 80206, USA.,Department of Medicine, University of Colorado, Aurora, Colorado 80045, USA
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Salinas-Rubio D, Tovar AR, Noriega LG. Emerging perspectives on branched-chain amino acid metabolism during adipocyte differentiation. Curr Opin Clin Nutr Metab Care 2018; 21:49-57. [PMID: 29035970 DOI: 10.1097/mco.0000000000000429] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
PURPOSE OF REVIEW Adipogenesis has been extensively studied in the context of carbohydrate and lipid metabolism. However, little information exists on the role of amino acid metabolism during adipocyte differentiation. Here, we review how branched-chain amino acid (BCAA) metabolism is modified during adipogenesis and, due to the limited information in the area, address questions that remain to be answered with further research. RECENT FINDINGS BCAAs are rapidly consumed during adipocyte differentiation and are indispensable for this process. Furthermore, we describe how BCAA catabolic enzymes and the metabolic fate of BCAAs are modified during adipogenesis. SUMMARY Obesity is a chronic disease characterized by increased adipose tissue due to either an increase in the size (hypertrophy) and/or number of adipocytes (hyperplasia). Hyperplasia is determined by the rate of adipogenesis. Therefore, understanding the mechanism that modulates adipogenesis in the context of amino acid metabolism will help to establish pharmacological and dietary interventions involving the type and amount of dietary protein for the treatment of obesity and its associated comorbidities.Video abstract http://links.lww.com/COCN/A11.
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Affiliation(s)
- Daniela Salinas-Rubio
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México, México
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Pradhan RN, Zachara M, Deplancke B. A systems perspective on brown adipogenesis and metabolic activation. Obes Rev 2017; 18 Suppl 1:65-81. [PMID: 28164456 DOI: 10.1111/obr.12512] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 12/12/2016] [Indexed: 12/31/2022]
Abstract
Brown adipocytes regulate energy expenditure via mitochondrial uncoupling. This makes these fat cells attractive therapeutic targets to tackle the burgeoning issue of obesity, which itself is coupled to insulin resistance, type 2 diabetes, cardiovascular and fatty liver disease. Recent research has revealed a complex network underlying brown fat cell differentiation and thermogenic activation, involving secreted factors, signal transduction, metabolic pathways and gene regulatory components. Given that brown fat is now reported to be present in adult humans, it is desirable to harness the knowledge from each network module to design effective therapeutic strategies. In this review, we will present a systems perspective on brown adipogenesis and the subsequent metabolic activation of brown adipocytes by integrating signaling, metabolic and gene regulatory modules with a specific focus on known 'druggable' targets within each module.
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Affiliation(s)
- R N Pradhan
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - M Zachara
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - B Deplancke
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Loft A, Forss I, Mandrup S. Genome-Wide Insights into the Development and Function of Thermogenic Adipocytes. Trends Endocrinol Metab 2017; 28:104-120. [PMID: 27979331 DOI: 10.1016/j.tem.2016.11.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 11/01/2016] [Accepted: 11/07/2016] [Indexed: 12/31/2022]
Abstract
Brown and brown-like adipocytes are specialized adipocytes with a high capacity to convert metabolic energy to heat. This function is not only eminent in supporting organismal thermogenesis, but may also have potential in the fight against obesity. The latter has spurred a massive interest in understanding the development and regulation of these thermogenic adipocytes. Here, we review how genome-wide studies based on next-generation sequencing have provided insight into how the chromatin and transcriptional landscapes are established in thermogenic adipocytes and how thermogenic signals can change the genomic programming of white adipocytes. Furthermore, we discuss how the integration of genomic data can be used to discover novel transcriptional pathways that may be modulated as part of therapeutic strategies for the treatment of obesity.
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Affiliation(s)
- Anne Loft
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark; Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich, 85764 Neuherberg, Germany; Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Isabel Forss
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.
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Abstract
Cofactor squelching is the term used to describe competition between transcription factors (TFs) for a limited amount of cofactors in a cell with the functional consequence that TFs in a given cell interfere with the activity of each other. Since cofactor squelching was proposed based primarily on reporter assays some 30 years ago, it has remained controversial, and the idea that it could be a physiologically relevant mechanism for transcriptional repression has not received much support. However, recent genome-wide studies have demonstrated that signal-dependent TFs are very often absent from the enhancers that are acutely repressed by those signals, which is consistent with an indirect mechanism of repression such as squelching. Here we review these recent studies in the light of the classical studies of cofactor squelching, and we discuss how TF cooperativity in so-called hotspots and super-enhancers may sensitize these to cofactor squelching.
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Affiliation(s)
- Søren Fisker Schmidt
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Bjørk Ditlev Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Anne Loft
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230, Odense M, Denmark
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