51
|
Her YR, Wang L, Chepelev I, Manterola M, Berkovits B, Cui K, Zhao K, Wolgemuth DJ. Genome-wide chromatin occupancy of BRDT and gene expression analysis suggest transcriptional partners and specific epigenetic landscapes that regulate gene expression during spermatogenesis. Mol Reprod Dev 2021; 88:141-157. [PMID: 33469999 DOI: 10.1002/mrd.23449] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/13/2020] [Accepted: 12/27/2020] [Indexed: 11/09/2022]
Abstract
BRDT, a member of the BET family of double bromodomain-containing proteins, is essential for spermatogenesis in the mouse and has been postulated to be a key regulator of transcription in meiotic and post-meiotic cells. To understand the function of BRDT in these processes, we first characterized the genome-wide distribution of the BRDT binding sites, in particular within gene units, by ChIP-Seq analysis of enriched fractions of pachytene spermatocytes and round spermatids. In both cell types, BRDT binding sites were mainly located in promoters, first exons, and introns of genes. BRDT binding sites in promoters overlapped with several histone modifications and histone variants associated with active transcription, and were enriched for consensus sequences for specific transcription factors, including MYB, RFX, ETS, and ELF1 in pachytene spermatocytes, and JunD, c-Jun, CRE, and RFX in round spermatids. Subsequent integration of the ChIP-seq data with available transcriptome data revealed that stage-specific gene expression programs are associated with BRDT binding to their gene promoters, with most of the BDRT-bound genes being upregulated. Gene Ontology analysis further identified unique sets of genes enriched in diverse biological processes essential for meiosis and spermiogenesis between the two cell types, suggesting distinct developmentally stage-specific functions for BRDT. Taken together, our data suggest that BRDT cooperates with different transcription factors at distinctive chromatin regions within gene units to regulate diverse downstream target genes that function in male meiosis and spermiogenesis.
Collapse
Affiliation(s)
- Yoon Ra Her
- Department of Genetics & Development, Columbia University Medical Center, New York, New York, USA
| | - Li Wang
- Department of Genetics & Development, Columbia University Medical Center, New York, New York, USA
| | - Iouri Chepelev
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA.,Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Marcia Manterola
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Binyamin Berkovits
- Department of Genetics & Development, Columbia University Medical Center, New York, New York, USA
| | - Kairong Cui
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Debra J Wolgemuth
- Department of Genetics & Development, Columbia University Medical Center, New York, New York, USA.,Department Obstetrics & Gynecology, Columbia University Medical Center, New York, New York, USA.,Institute of Human Nutrition, Columbia University Medical Center, New York, New York, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
| |
Collapse
|
52
|
Regulating the Regulators: The Role of Histone Deacetylase 1 (HDAC1) in Erythropoiesis. Int J Mol Sci 2020; 21:ijms21228460. [PMID: 33187090 PMCID: PMC7696854 DOI: 10.3390/ijms21228460] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
Histone deacetylases (HDACs) play important roles in transcriptional regulation in eukaryotic cells. Class I deacetylase HDAC1/2 often associates with repressor complexes, such as Sin3 (Switch Independent 3), NuRD (Nucleosome remodeling and deacetylase) and CoREST (Corepressor of RE1 silencing transcription factor) complexes. It has been shown that HDAC1 interacts with and modulates all essential transcription factors for erythropoiesis. During erythropoiesis, histone deacetylase activity is dramatically reduced. Consistently, inhibition of HDAC activity promotes erythroid differentiation. The reduction of HDAC activity not only results in the activation of transcription activators such as GATA-1 (GATA-binding factor 1), TAL1 (TAL BHLH Transcription Factor 1) and KLF1 (Krüpple-like factor 1), but also represses transcription repressors such as PU.1 (Putative oncogene Spi-1). The reduction of histone deacetylase activity is mainly through HDAC1 acetylation that attenuates HDAC1 activity and trans-repress HDAC2 activity through dimerization with HDAC1. Therefore, the acetylation of HDAC1 can convert the corepressor complex to an activator complex for gene activation. HDAC1 also can deacetylate non-histone proteins that play a role on erythropoiesis, therefore adds another layer of gene regulation through HDAC1. Clinically, it has been shown HDACi can reactivate fetal globin in adult erythroid cells. This review will cover the up to date research on the role of HDAC1 in modulating key transcription factors for erythropoiesis and its clinical relevance.
Collapse
|
53
|
Padmanabhan A, Alexanian M, Linares-Saldana R, González-Terán B, Andreoletti G, Huang Y, Connolly AJ, Kim W, Hsu A, Duan Q, Winchester SAB, Felix F, Perez-Bermejo JA, Wang Q, Li L, Shah PP, Haldar SM, Jain R, Srivastava D. BRD4 (Bromodomain-Containing Protein 4) Interacts with GATA4 (GATA Binding Protein 4) to Govern Mitochondrial Homeostasis in Adult Cardiomyocytes. Circulation 2020; 142:2338-2355. [PMID: 33094644 DOI: 10.1161/circulationaha.120.047753] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Gene regulatory networks control tissue homeostasis and disease progression in a cell type-specific manner. Ubiquitously expressed chromatin regulators modulate these networks, yet the mechanisms governing how tissue specificity of their function is achieved are poorly understood. BRD4 (bromodomain-containing protein 4), a member of the BET (bromo- and extraterminal domain) family of ubiquitously expressed acetyl-lysine reader proteins, plays a pivotal role as a coactivator of enhancer signaling across diverse tissue types in both health and disease and has been implicated as a pharmacological target in heart failure. However, the cell-specific role of BRD4 in adult cardiomyocytes remains unknown. METHODS We combined conditional mouse genetics, unbiased transcriptomic and epigenomic analyses, and classic molecular biology and biochemical approaches to understand the mechanism by which BRD4 in adult cardiomyocyte homeostasis. RESULTS Here, we show that cardiomyocyte-specific deletion of Brd4 in adult mice leads to acute deterioration of cardiac contractile function with mutant animals demonstrating a transcriptomic signature characterized by decreased expression of genes critical for mitochondrial energy production. Genome-wide occupancy data show that BRD4 enriches at many downregulated genes (including the master coactivators Ppargc1a, Ppargc1b, and their downstream targets) and preferentially colocalizes with GATA4 (GATA binding protein 4), a lineage-determining cardiac transcription factor not previously implicated in regulation of adult cardiac metabolism. BRD4 and GATA4 form an endogenous complex in cardiomyocytes and interact in a bromodomain-independent manner, revealing a new functional interaction partner for BRD4 that can direct its locus and tissue specificity. CONCLUSIONS These results highlight a novel role for a BRD4-GATA4 module in cooperative regulation of a cardiomyocyte-specific gene program governing bioenergetic homeostasis in the adult heart.
Collapse
Affiliation(s)
- Arun Padmanabhan
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.).,Division of Cardiology, Department of Medicine (A.P., S.M.H.), University of California, San Francisco
| | - Michael Alexanian
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.)
| | - Ricardo Linares-Saldana
- Institute of Regenerative Medicine, Penn Cardiovascular Institute, Departments of Medicine and Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA (R.L.-S., W.K., Q.W., L.L., P.P.S., R.J.)
| | - Bárbara González-Terán
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.)
| | - Gaia Andreoletti
- Bakar Computational Health Sciences Institute (G.A.), University of California, San Francisco
| | - Yu Huang
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.)
| | - Andrew J Connolly
- Department of Pathology (A.J.C.), University of California, San Francisco
| | - Wonho Kim
- Institute of Regenerative Medicine, Penn Cardiovascular Institute, Departments of Medicine and Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA (R.L.-S., W.K., Q.W., L.L., P.P.S., R.J.)
| | - Austin Hsu
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.)
| | - Qiming Duan
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.)
| | - Sarah A B Winchester
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.)
| | - Franco Felix
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.)
| | - Juan A Perez-Bermejo
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.)
| | - Qiaohong Wang
- Institute of Regenerative Medicine, Penn Cardiovascular Institute, Departments of Medicine and Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA (R.L.-S., W.K., Q.W., L.L., P.P.S., R.J.)
| | - Li Li
- Institute of Regenerative Medicine, Penn Cardiovascular Institute, Departments of Medicine and Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA (R.L.-S., W.K., Q.W., L.L., P.P.S., R.J.)
| | - Parisha P Shah
- Institute of Regenerative Medicine, Penn Cardiovascular Institute, Departments of Medicine and Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA (R.L.-S., W.K., Q.W., L.L., P.P.S., R.J.)
| | - Saptarsi M Haldar
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.).,Division of Cardiology, Department of Medicine (A.P., S.M.H.), University of California, San Francisco
| | - Rajan Jain
- Institute of Regenerative Medicine, Penn Cardiovascular Institute, Departments of Medicine and Cell and Developmental Biology, Perelman School of Medicine, Philadelphia, PA (R.L.-S., W.K., Q.W., L.L., P.P.S., R.J.)
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA (A.P., M.A., B.G.-T., Y.H., A.H., Q.D., S.A.B.W., F.F., J.A.P.-B., S.M.H., D.S.).,Department of Pediatrics (D.S.), University of California, San Francisco.,Department of Biochemistry and Biophysics (D.S.), University of California, San Francisco.,Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA (D.S.)
| |
Collapse
|
54
|
Abstract
Large DNA-encoded libraries of cyclic peptides are emerging as powerful sources of molecules to tackle challenging drug targets. The structural and functional diversity contained within these libraries is, however, little explored. Here we demonstrate that one such library contains members that use unexpectedly diverse mechanisms to recognize the same surface on the same target proteins with high affinity and specificity. This range of binding modes is much larger than observed in natural ligands of the same proteins, demonstrating the power and versatility of the technology. Our data also reveal opportunities for the development of more sophisticated approaches to achieving specificity when trying to selectively target one member of a family of closely related proteins. Cyclic peptide library screening technologies show immense promise for identifying drug leads and chemical probes for challenging targets. However, the structural and functional diversity encoded within such libraries is largely undefined. We have systematically profiled the affinity, selectivity, and structural features of library-derived cyclic peptides selected to recognize three closely related targets: the acetyllysine-binding bromodomain proteins BRD2, -3, and -4. We report affinities as low as 100 pM and specificities of up to 106-fold. Crystal structures of 13 peptide–bromodomain complexes reveal remarkable diversity in both structure and binding mode, including both α-helical and β-sheet structures as well as bivalent binding modes. The peptides can also exhibit a high degree of structural preorganization. Our data demonstrate the enormous potential within these libraries to provide diverse binding modes against a single target, which underpins their capacity to yield highly potent and selective ligands.
Collapse
|
55
|
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.
Collapse
|
56
|
Andrikopoulou A, Liontos M, Koutsoukos K, Dimopoulos MA, Zagouri F. The emerging role of BET inhibitors in breast cancer. Breast 2020; 53:152-163. [PMID: 32827765 PMCID: PMC7451423 DOI: 10.1016/j.breast.2020.08.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/13/2020] [Accepted: 08/10/2020] [Indexed: 01/10/2023] Open
Abstract
Bromodomain and extraterminal domain (BET) proteins are epigenetic molecules that regulate the expression of multiple genes involved in carcinogenesis. Breast cancer is an heterogenous disease emerging from aberrant gene expression and epigenetic alteration patterns. Amplification or overexpression of BET proteins has been identified in breast tumors highlighting their clinical significance. Development of BET inhibitors that disrupt BET protein binding to acetylated lysine residues of chromatin and suppress transcription of various oncogenes has shown promising results in breast cancer cells and xenograft models. Currently, Phase I/II clinical trials explore safety and efficacy of BET inhibitors in solid tumors and breast cancer. Treatment-emergent toxicities have been reported, including thrombocytopenia and gastrointestinal disorders. Preliminary results demonstrated greater response rates to BET inhibitors in combination with already approved anticancer agents. Consistently, BET inhibition sensitized breast tumors to chemotherapy drugs, hormone therapy and PI3K inhibitors in vitro. This article aims to review all existing preclinical and clinical evidence regarding BET inhibitors in breast cancer.
Collapse
Affiliation(s)
- Angeliki Andrikopoulou
- Oncology Unit, Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece.
| | - Michalis Liontos
- Oncology Unit, Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece.
| | - Konstantinos Koutsoukos
- Oncology Unit, Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece.
| | - Meletios-Athanasios Dimopoulos
- Oncology Unit, Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece.
| | - Flora Zagouri
- Oncology Unit, Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece.
| |
Collapse
|
57
|
Design, synthesis and biological evaluation of novel 6-phenyl-1,3a,4,10b-tetrahydro-2H-benzo[c]thiazolo[4,5-e]azepin-2-one derivatives as potential BRD4 inhibitors. Bioorg Med Chem 2020; 28:115601. [DOI: 10.1016/j.bmc.2020.115601] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 12/20/2022]
|
58
|
Liang D, Yu Y, Ma Z. Novel strategies targeting bromodomain-containing protein 4 (BRD4) for cancer drug discovery. Eur J Med Chem 2020; 200:112426. [DOI: 10.1016/j.ejmech.2020.112426] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/28/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022]
|
59
|
Petretich M, Demont EH, Grandi P. Domain-selective targeting of BET proteins in cancer and immunological diseases. Curr Opin Chem Biol 2020; 57:184-193. [PMID: 32741705 DOI: 10.1016/j.cbpa.2020.02.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 12/13/2022]
Abstract
Cancer and inflammation are strongly interconnected processes. Chronic inflammatory pathologies can be at the heart of tumor development; similarly, tumor-elicited inflammation is a consequence of many cancers. The mechanistic interdependence between cancer and inflammatory pathologies points toward common protein effectors which represent potential shared targets for pharmacological intervention. Epigenetic mechanisms often drive resistance to cancer therapy and immunomodulatory strategies. The bromodomain and extraterminal domain (BET) proteins are epigenetic adapters which play a major role in controlling cell proliferation and the production of inflammatory mediators. A plethora of small molecules aimed at inhibiting BET protein function to treat cancer and inflammatory diseases have populated academic and industry efforts in the last 10 years. In this review, we will discuss recent pharmacological approaches aimed at targeting a single or a subset of the eight bromodomains within the BET family which have the potential to tease apart clinical efficacy and safety signals of BET inhibitors.
Collapse
Affiliation(s)
- Massimo Petretich
- Cellzome GmbH, Functional Genomics R&D, GlaxoSmithKline, 69117 Heidelberg, Germany
| | - Emmanuel H Demont
- Medicinal Chemistry, GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | - Paola Grandi
- Cellzome GmbH, Functional Genomics R&D, GlaxoSmithKline, 69117 Heidelberg, Germany.
| |
Collapse
|
60
|
Slavish PJ, Chi L, Yun MK, Tsurkan L, Martinez NE, Jonchere B, Chai SC, Connelly M, Waddell MB, Das S, Neale G, Li Z, Shadrick WR, Olsen RR, Freeman KW, Low JA, Price JE, Young BM, Bharatham N, Boyd VA, Yang J, Lee RE, Morfouace M, Roussel MF, Chen T, Savic D, Guy RK, White SW, Shelat AA, Potter PM. Bromodomain-Selective BET Inhibitors Are Potent Antitumor Agents against MYC-Driven Pediatric Cancer. Cancer Res 2020; 80:3507-3518. [PMID: 32651255 DOI: 10.1158/0008-5472.can-19-3934] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/27/2020] [Accepted: 06/29/2020] [Indexed: 11/16/2022]
Abstract
Inhibition of members of the bromodomain and extraterminal (BET) family of proteins has proven a valid strategy for cancer chemotherapy. All BET identified to date contain two bromodomains (BD; BD1 and BD2) that are necessary for recognition of acetylated lysine residues in the N-terminal regions of histones. Chemical matter that targets BET (BETi) also interact via these domains. Molecular and cellular data indicate that BD1 and BD2 have different biological roles depending upon their cellular context, with BD2 particularly associated with cancer. We have therefore pursued the development of BD2-selective molecules both as chemical probes and as potential leads for drug development. Here we report the structure-based generation of a novel series of tetrahydroquinoline analogs that exhibit >50-fold selectivity for BD2 versus BD1. This selective targeting resulted in engagement with BD-containing proteins in cells, resulting in modulation of MYC proteins and downstream targets. These compounds were potent cytotoxins toward numerous pediatric cancer cell lines and were minimally toxic to nontumorigenic cells. In addition, unlike the pan BETi (+)-JQ1, these BD2-selective inhibitors demonstrated no rebound expression effects. Finally, we report a pharmacokinetic-optimized, metabolically stable derivative that induced growth delay in a neuroblastoma xenograft model with minimal toxicity. We conclude that BD2-selective agents are valid candidates for antitumor drug design for pediatric malignancies driven by the MYC oncogene. SIGNIFICANCE: This study presents bromodomain-selective BET inhibitors that act as antitumor agents and demonstrates that these molecules have in vivo activity towards neuroblastoma, with essentially no toxicity.
Collapse
Affiliation(s)
- P Jake Slavish
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Liying Chi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Mi-Kyung Yun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Lyudmila Tsurkan
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Nancy E Martinez
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Barbara Jonchere
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sergio C Chai
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michele Connelly
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - M Brett Waddell
- Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sourav Das
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Geoffrey Neale
- Hartwell Center, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Zhenmei Li
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - William R Shadrick
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Rachelle R Olsen
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kevin W Freeman
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jonathan A Low
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jeanine E Price
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Brandon M Young
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Nagakumar Bharatham
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Vincent A Boyd
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jun Yang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Marie Morfouace
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Martine F Roussel
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Daniel Savic
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - R Kiplin Guy
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Stephen W White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Anang A Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Philip M Potter
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee.
| |
Collapse
|
61
|
Zhang J, Chen P, Zhu P, Zheng P, Wang T, Wang L, Xu C, Zhou J, Zhang H. Development of small-molecule BRD4 degraders based on pyrrolopyridone derivative. Bioorg Chem 2020; 99:103817. [DOI: 10.1016/j.bioorg.2020.103817] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 12/30/2022]
|
62
|
Zhu Z, Song J, Guo Y, Huang Z, Chen X, Dang X, Huang Y, Wang Y, Ou W, Yang Y, Yu W, Liu CY, Cui L. LAMB3 promotes tumour progression through the AKT-FOXO3/4 axis and is transcriptionally regulated by the BRD2/acetylated ELK4 complex in colorectal cancer. Oncogene 2020; 39:4666-4680. [PMID: 32398865 DOI: 10.1038/s41388-020-1321-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/23/2020] [Accepted: 04/28/2020] [Indexed: 12/19/2022]
Abstract
Aberrant expression of laminin-332 promotes tumour growth and metastasis in multiple cancers. However, the dysregulated expression and mechanism of action of LAMB3, which encodes the β3 subunit of laminin-332, and the mechanism underlying dysregulated LAMB3 expression in CRC remain obscure. Here, we show that LAMB3 is overexpressed in CRC and that this overexpression is correlated with tumour metastasis and poor prognosis. Overexpression of LAMB3 promoted cell proliferation and cell migration in vitro and tumour growth and metastasis in vivo, while knockdown of LAMB3 elicited opposing effects. LAMB3 inhibited the tumour suppressive function of FOXO3/4 by activating AKT in CRC. Both the BET inhibitor JQ1 and the MEK inhibitor U0126 decreased the mRNA level of LAMB3 in multiple CRC cells. Mechanistically, ELK4 cooperated with BRD2 to regulate the transcription of LAMB3 in CRC by directly binding to the ETS binding motifs in the LAMB3 promoter. ELK4 was as acetylated at K125, which enhanced the interaction between ELK4 and BRD2. JQ1 disrupted the interaction between ELK4 and BRD2, resulting in decreased binding of BRD2 to the LAMB3 promoter and downregulation of LAMB3 transcription. Both ELK4 and BRD2 expression was associated with LAMB3 expression in CRC. LAMB3 expression was also negatively correlated with FOXO3/4 in CRC. Our study reveals the pro-tumorigenic role of LAMB3 through the AKT-FOXO3/4 axis and the transcriptional mechanism of LAMB3 in CRC, demonstrating that LAMB3 is a potential therapeutic target that can be targeted by BET inhibitors and MEK inhibitors.
Collapse
Affiliation(s)
- Zhehui Zhu
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, 200092, Shanghai, China
- Shanghai Colorectal Cancer Research Center, 200092, Shanghai, China
| | - Jinglue Song
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, 200092, Shanghai, China
| | - Yuegui Guo
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, 200092, Shanghai, China
| | - Zhenyu Huang
- Shanghai Colorectal Cancer Research Center, 200092, Shanghai, China
| | - Xiaojian Chen
- Shanghai Colorectal Cancer Research Center, 200092, Shanghai, China
| | - Xuening Dang
- Shanghai Colorectal Cancer Research Center, 200092, Shanghai, China
| | - Yuji Huang
- Shanghai Colorectal Cancer Research Center, 200092, Shanghai, China
| | - Yuhan Wang
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, 200092, Shanghai, China
| | - Weijun Ou
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, 200092, Shanghai, China
| | - Yili Yang
- Suzhou Institute of Systems Medicine, Center for Systems Medicine Research, Chinese Academy of Medical Sciences, 215123, Suzhou, Jiangsu, China
| | - Wei Yu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Zhongshan Hospital, Fudan University, 200438, Shanghai, China.
| | - Chen-Ying Liu
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, 200092, Shanghai, China.
- Shanghai Colorectal Cancer Research Center, 200092, Shanghai, China.
| | - Long Cui
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, 200092, Shanghai, China.
- Shanghai Colorectal Cancer Research Center, 200092, Shanghai, China.
| |
Collapse
|
63
|
Sheppard GS, Wang L, Fidanze SD, Hasvold LA, Liu D, Pratt JK, Park CH, Longenecker K, Qiu W, Torrent M, Kovar PJ, Bui M, Faivre E, Huang X, Lin X, Wilcox D, Zhang L, Shen Y, Albert DH, Magoc TJ, Rajaraman G, Kati WM, McDaniel KF. Discovery of N-Ethyl-4-[2-(4-fluoro-2,6-dimethyl-phenoxy)-5-(1-hydroxy-1-methyl-ethyl)phenyl]-6-methyl-7-oxo-1 H-pyrrolo[2,3- c]pyridine-2-carboxamide (ABBV-744), a BET Bromodomain Inhibitor with Selectivity for the Second Bromodomain. J Med Chem 2020; 63:5585-5623. [PMID: 32324999 DOI: 10.1021/acs.jmedchem.0c00628] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The BET family of proteins consists of BRD2, BRD3, BRD4, and BRDt. Each protein contains two distinct bromodomains (BD1 and BD2). BET family bromodomain inhibitors under clinical development for oncology bind to each of the eight bromodomains with similar affinities. We hypothesized that it may be possible to achieve an improved therapeutic index by selectively targeting subsets of the BET bromodomains. Both BD1 and BD2 are highly conserved across family members (>70% identity), whereas BD1 and BD2 from the same protein exhibit a larger degree of divergence (∼40% identity), suggesting selectivity between BD1 and BD2 of all family members would be more straightforward to achieve. Exploiting the Asp144/His437 and Ile146/Val439 sequence differences (BRD4 BD1/BD2 numbering) allowed the identification of compound 27 demonstrating greater than 100-fold selectivity for BRD4 BD2 over BRD4 BD1. Further optimization to improve BD2 selectivity and oral bioavailability resulted in the clinical development compound 46 (ABBV-744).
Collapse
Affiliation(s)
- George S Sheppard
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Le Wang
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Steven D Fidanze
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Lisa A Hasvold
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Dachun Liu
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - John K Pratt
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Chang H Park
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Kenton Longenecker
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Wei Qiu
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Maricel Torrent
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Peter J Kovar
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Mai Bui
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Emily Faivre
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Xiaoli Huang
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Xiaoyu Lin
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Denise Wilcox
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Lu Zhang
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Yu Shen
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Daniel H Albert
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Terrance J Magoc
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Ganesh Rajaraman
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Warren M Kati
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Keith F McDaniel
- Oncology Discovery, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| |
Collapse
|
64
|
Role of BET Inhibitors in Triple Negative Breast Cancers. Cancers (Basel) 2020; 12:cancers12040784. [PMID: 32218352 PMCID: PMC7226117 DOI: 10.3390/cancers12040784] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/20/2020] [Accepted: 03/24/2020] [Indexed: 12/20/2022] Open
Abstract
Bromodomain and extraterminal domain (BET) proteins have evolved as key multifunctional super-regulators that control gene expression. These proteins have been shown to upregulate transcriptional machinery leading to over expression of genes involved in cell proliferation and carcinogenesis. Based on favorable preclinical evidence of BET inhibitors in various cancer models; currently, 26 clinical trials are underway in various stages of study on various hematological and solid organ cancers. Unfortunately, preliminary evidence for these clinical studies does not support the application of BET inhibitors as monotherapy in cancer treatment. Furthermore, the combinatorial efficiency of BET inhibitors with other chemo-and immunotherapeutic agents remain elusive. In this review, we will provide a concise summary of the molecular basis and preliminary clinical outcomes of BET inhibitors in cancer therapy, with special focus on triple negative breast cancer.
Collapse
|
65
|
Trivedi A, Mehrotra A, Baum CE, Lewis B, Basuroy T, Blomquist T, Trumbly R, Filipp FV, Setaluri V, de la Serna IL. Bromodomain and extra-terminal domain (BET) proteins regulate melanocyte differentiation. Epigenetics Chromatin 2020; 13:14. [PMID: 32151278 PMCID: PMC7063807 DOI: 10.1186/s13072-020-00333-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 02/19/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Pharmacologic inhibition of bromodomain and extra-terminal (BET) proteins is currently being explored as a new therapeutic approach in cancer. Some studies have also implicated BET proteins as regulators of cell identity and differentiation through their interactions with lineage-specific factors. However, the role of BET proteins has not yet been investigated in melanocyte differentiation. Melanocyte inducing transcription factor (MITF) is the master regulator of melanocyte differentiation, essential for pigmentation and melanocyte survival. In this study, we tested the hypothesis that BET proteins regulate melanocyte differentiation through interactions with MITF. RESULTS Here we show that chemical inhibition of BET proteins prevents differentiation of unpigmented melanoblasts into pigmented melanocytes and results in de-pigmentation of differentiated melanocytes. BET inhibition also slowed cell growth, without causing cell death, increasing the number of cells in G1. Transcriptional profiling revealed that BET inhibition resulted in decreased expression of pigment-specific genes, including many MITF targets. The expression of pigment-specific genes was also down-regulated in melanoma cells, but to a lesser extent. We found that RNAi depletion of the BET family members, bromodomain-containing protein 4 (BRD4) and bromodomain-containing protein 2 (BRD2) inhibited expression of two melanin synthesis enzymes, TYR and TYRP1. Both BRD4 and BRD2 were detected on melanocyte promoters surrounding MITF-binding sites, were associated with open chromatin structure, and promoted MITF binding to these sites. Furthermore, BRD4 and BRD2 physically interacted with MITF. CONCLUSION These findings indicate a requirement for BET proteins in the regulation of pigmentation and melanocyte differentiation. We identified changes in pigmentation specific gene expression that occur upon BET inhibition in melanoblasts, melanocytes, and melanoma cells.
Collapse
Affiliation(s)
- Archit Trivedi
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614 USA
| | - Aanchal Mehrotra
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614 USA
- Present Address: Department of Genome Sciences, University of Washington School of Medicine, 1959 NE Pacific St, Seattle, WA 98195 USA
| | - Caitlin E. Baum
- Department of Pathology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614 USA
| | - Brandon Lewis
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614 USA
| | - Tupa Basuroy
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614 USA
- Present Address: Cancer Center Division, Massachusetts General Hospital Harvard Medical School, 149 Thirteenth Street, 7th Floor, Charlestown, MA 02129 USA
| | - Thomas Blomquist
- Department of Pathology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614 USA
| | - Robert Trumbly
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614 USA
| | - Fabian V. Filipp
- Cancer Systems Biology, Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, München, 85764 Germany
- School of Life Sciences Weihenstephan, Technical University München, Maximus-von-Imhof-Forum 3, Freising, 85354 Germany
| | - Vijayasaradhi Setaluri
- Department of Dermatology, University of Wisconsin-Madison, The School of Medicine and Public Health, 1 S. Park Street, Madison, WI 53715 USA
| | - Ivana L. de la Serna
- Department of Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3035 Arlington Ave, Toledo, OH 43614 USA
| |
Collapse
|
66
|
Werner MT, Wang H, Hamagami N, Hsu SC, Yano JA, Stonestrom AJ, Behera V, Zong Y, Mackay JP, Blobel GA. Comparative structure-function analysis of bromodomain and extraterminal motif (BET) proteins in a gene-complementation system. J Biol Chem 2020; 295:1898-1914. [PMID: 31792058 PMCID: PMC7029111 DOI: 10.1074/jbc.ra119.010679] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 11/17/2019] [Indexed: 11/06/2022] Open
Abstract
The widely expressed bromodomain and extraterminal motif (BET) proteins bromodomain-containing protein 2 (BRD2), BRD3, and BRD4 are multifunctional transcriptional regulators that bind acetylated chromatin via their conserved tandem bromodomains. Small molecules that target BET bromodomains are being tested for various diseases but typically do not discern between BET family members. Genomic distributions and protein partners of BET proteins have been described, but the basis for differences in BET protein function within a given lineage remains unclear. By establishing a gene knockout-rescue system in a Brd2-null erythroblast cell line, here we compared a series of mutant and chimeric BET proteins for their ability to modulate cell growth, differentiation, and gene expression. We found that the BET N-terminal halves bearing the bromodomains convey marked differences in protein stability but do not account for specificity in BET protein function. Instead, when BET proteins were expressed at comparable levels, their specificity was largely determined by the C-terminal half. Remarkably, a chimeric BET protein comprising the N-terminal half of the structurally similar short BRD4 isoform (BRD4S) and the C-terminal half of BRD2 functioned similarly to intact BRD2. We traced part of the BRD2-specific activity to a previously uncharacterized short segment predicted to harbor a coiled-coil (CC) domain. Deleting the CC segment impaired BRD2's ability to restore growth and differentiation, and the CC region functioned in conjunction with the adjacent ET domain to impart BRD2-like activity onto BRD4S. In summary, our results identify distinct BET protein domains that regulate protein turnover and biological activities.
Collapse
Affiliation(s)
- Michael T Werner
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104.
| | - Hongxin Wang
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| | - Nicole Hamagami
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| | - Sarah C Hsu
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Jennifer A Yano
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| | - Aaron J Stonestrom
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Vivek Behera
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Yichen Zong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Gerd A Blobel
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104.
| |
Collapse
|
67
|
Selective inhibition of the BD2 bromodomain of BET proteins in prostate cancer. Nature 2020; 578:306-310. [PMID: 31969702 DOI: 10.1038/s41586-020-1930-8] [Citation(s) in RCA: 231] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/25/2019] [Indexed: 12/24/2022]
Abstract
Proteins of the bromodomain and extra-terminal (BET) domain family are epigenetic readers that bind acetylated histones through their bromodomains to regulate gene transcription. Dual-bromodomain BET inhibitors (DbBi) that bind with similar affinities to the first (BD1) and second (BD2) bromodomains of BRD2, BRD3, BRD4 and BRDt have displayed modest clinical activity in monotherapy cancer trials. A reduced number of thrombocytes in the blood (thrombocytopenia) as well as symptoms of gastrointestinal toxicity are dose-limiting adverse events for some types of DbBi1-5. Given that similar haematological and gastrointestinal defects were observed after genetic silencing of Brd4 in mice6, the platelet and gastrointestinal toxicities may represent on-target activities associated with BET inhibition. The two individual bromodomains in BET family proteins may have distinct functions7-9 and different cellular phenotypes after pharmacological inhibition of one or both bromodomains have been reported10,11, suggesting that selectively targeting one of the bromodomains may result in a different efficacy and tolerability profile compared with DbBi. Available compounds that are selective to individual domains lack sufficient potency and the pharmacokinetics properties that are required for in vivo efficacy and tolerability assessment10-13. Here we carried out a medicinal chemistry campaign that led to the discovery of ABBV-744, a highly potent and selective inhibitor of the BD2 domain of BET family proteins with drug-like properties. In contrast to the broad range of cell growth inhibition induced by DbBi, the antiproliferative activity of ABBV-744 was largely, but not exclusively, restricted to cell lines of acute myeloid leukaemia and prostate cancer that expressed the full-length androgen receptor (AR). ABBV-744 retained robust activity in prostate cancer xenografts, and showed fewer platelet and gastrointestinal toxicities than the DbBi ABBV-07514. Analyses of RNA expression and chromatin immunoprecipitation followed by sequencing revealed that ABBV-744 displaced BRD4 from AR-containing super-enhancers and inhibited AR-dependent transcription, with less impact on global transcription compared with ABBV-075. These results underscore the potential value of selectively targeting the BD2 domain of BET family proteins for cancer therapy.
Collapse
|
68
|
Bechter O, Schöffski P. Make your best BET: The emerging role of BET inhibitor treatment in malignant tumors. Pharmacol Ther 2020; 208:107479. [PMID: 31931101 DOI: 10.1016/j.pharmthera.2020.107479] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/15/2019] [Indexed: 12/17/2022]
Abstract
Bromodomains are protein-protein interaction modules with a great diversity in terms of number of proteins and their function. The bromodomain and extraterminal protein (BET) represents a distinct subclass of bromodomain proteins mainly involved in transcriptional regulation via their interaction with acetylated chromatin. In cancer cells BET proteins are found to be altered in many ways such as overexpression, mutations and fusions of BET proteins or their interference with cancer relevant signaling pathways and transcriptional programs in order to sustain cancer growth and viability. Blocking BET protein function with small molecules is associated with therapeutic activity. Consequently, a variety of small molecules have been developed and a number of phase I clinical trials have explored their tolerability and efficacy in patients with solid tumors and hematological malignancies. We will review the rational for applying BET inhibitors in the clinic and we will discuss the toxicity profile as well as efficacy of this new class of protein inhibitors. We will also highlight the emerging problem of treatment resistance and the potential these drugs might have when combined with other anti-cancer therapies.
Collapse
Affiliation(s)
- Oliver Bechter
- Leuven Cancer Institute, Department of General Medical Oncology, University Hospitals Leuven, Belgium; Department of Oncology, KU, Leuven, Belgium.
| | - Patrick Schöffski
- Leuven Cancer Institute, Department of General Medical Oncology, University Hospitals Leuven, Belgium; Department of Oncology, KU, Leuven, Belgium.
| |
Collapse
|
69
|
Jacques C, Lavaud M, Georges S, Tesfaye R, Baud’huin M, Lamoureux F, Ory B. BET bromodomains’ functions in bone-related pathologies. Epigenomics 2020; 12:127-144. [DOI: 10.2217/epi-2019-0172] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Throughout life, bones are subjected to the so-called ‘bone-remodeling’ process, which is a balanced mechanism between the apposition and the resorption of bone. This remodeling process depends on the activities of bone-specialized cells, namely the osteoblasts and the osteoclasts. Any deregulation in this process results in bone-related pathologies, classified as either metabolic nonmalignant diseases (such as osteoporosis) or malignant primary bone sarcomas. As these pathologies are not characterized by common targetable genetic alterations, epigenetic strategies could be relevant and promising options. Recently, targeting epigenetic regulators such as the bromodomains and extraterminal domains (BET) readers have achieved success in numerous other pathologies, including cancers. In this review, we highlight the current state of the art in terms of the diverse implications of BET bromodomain proteins in the bone’s biology and its defects. Consequently, their role in bone-related pathologies will also be developed, especially in the context of the primary bone sarcomas.
Collapse
Affiliation(s)
- Camille Jacques
- Nantes Université, INSERM, Bone sarcomas & remodeling of calcified tissues, UMR 1238, F-44000 Nantes, France
| | - Melanie Lavaud
- Nantes Université, INSERM, Bone sarcomas & remodeling of calcified tissues, UMR 1238, F-44000 Nantes, France
| | - Steven Georges
- Nantes Université, INSERM, Bone sarcomas & remodeling of calcified tissues, UMR 1238, F-44000 Nantes, France
| | - Robel Tesfaye
- Nantes Université, INSERM, Bone sarcomas & remodeling of calcified tissues, UMR 1238, F-44000 Nantes, France
- ‘Niches & Epigenetics of Tumors’ Network from Cancéropôle Grand Ouest
| | - Marc Baud’huin
- Nantes Université, INSERM, Bone sarcomas & remodeling of calcified tissues, UMR 1238, F-44000 Nantes, France
| | - François Lamoureux
- Nantes Université, INSERM, Bone sarcomas & remodeling of calcified tissues, UMR 1238, F-44000 Nantes, France
| | - Benjamin Ory
- Nantes Université, INSERM, Bone sarcomas & remodeling of calcified tissues, UMR 1238, F-44000 Nantes, France
- ‘Niches & Epigenetics of Tumors’ Network from Cancéropôle Grand Ouest
| |
Collapse
|
70
|
Walsh L, Haley KE, Moran B, Mooney B, Tarrant F, Madden SF, Di Grande A, Fan Y, Das S, Rueda OM, Dowling CM, Varešlija D, Chin SF, Linn S, Young LS, Jirström K, Crown JP, Bernards R, Caldas C, Gallagher WM, O'Connor DP, Ní Chonghaile T. BET Inhibition as a Rational Therapeutic Strategy for Invasive Lobular Breast Cancer. Clin Cancer Res 2019; 25:7139-7150. [PMID: 31409615 DOI: 10.1158/1078-0432.ccr-19-0713] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 06/13/2019] [Accepted: 08/07/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Invasive lobular carcinoma (ILC) is a subtype of breast cancer accounting for 10% of breast tumors. The majority of patients are treated with endocrine therapy; however, endocrine resistance is common in estrogen receptor-positive breast cancer and new therapeutic strategies are needed. Bromodomain and extraterminal inhibitors (BETi) are effective in diverse types of breast cancer but they have not yet been assessed in ILC. EXPERIMENTAL DESIGN We assessed whether targeting the BET proteins with JQ1 could serve as an effective therapeutic strategy in ILC in both 2D and 3D models. We used dynamic BH3 profiling and RNA-sequencing (RNA-seq) to identify transcriptional reprograming enabling resistance to JQ1-induced apoptosis. As part of the RATHER study, we obtained copy-number alterations and RNA-seq on 61 ILC patient samples. RESULTS Certain ILC cell lines were sensitive to JQ1, while others were intrinsically resistant to JQ1-induced apoptosis. JQ1 treatment led to an enhanced dependence on antiapoptotic proteins and a transcriptional rewiring inducing fibroblast growth factor receptor 1 (FGFR1). This increase in FGFR1 was also evident in invasive ductal carcinoma (IDC) cell lines. The combination of JQ1 and FGFR1 inhibitors was highly effective at inhibiting growth in both 2D and 3D models of ILC and IDC. Interestingly, we found in the RATHER cohort of 61 ILC patients that 20% had FGFR1 amplification and we showed that high BRD3 mRNA expression was associated with poor survival specifically in ILC. CONCLUSIONS We provide evidence that BETi either alone or in combination with FGFR1 inhibitors or BH3 mimetics may be a useful therapeutic strategy for recurrent ILC patients.
Collapse
Affiliation(s)
- Louise Walsh
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Kathryn E Haley
- Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Bruce Moran
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Brian Mooney
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Finbarr Tarrant
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Stephen F Madden
- Data Science Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Alessandra Di Grande
- Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Yue Fan
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Sudipto Das
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Oscar M Rueda
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Catríona M Dowling
- Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Damir Varešlija
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Suet-Feung Chin
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Sabine Linn
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Leonie S Young
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Karin Jirström
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | | | - Rene Bernards
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Carlos Caldas
- Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, England
| | - William M Gallagher
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Darran P O'Connor
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland.
| | - Tríona Ní Chonghaile
- Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| |
Collapse
|
71
|
Gutiérrez L, Caballero N, Fernández-Calleja L, Karkoulia E, Strouboulis J. Regulation of GATA1 levels in erythropoiesis. IUBMB Life 2019; 72:89-105. [PMID: 31769197 DOI: 10.1002/iub.2192] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/14/2019] [Indexed: 12/15/2022]
Abstract
GATA1 is considered as the "master" transcription factor in erythropoiesis. It regulates at the transcriptional level all aspects of erythroid maturation and function, as revealed by gene knockout studies in mice and by genome-wide occupancies in erythroid cells. The GATA1 protein contains two zinc finger domains and an N-terminal transactivation domain. GATA1 translation results in the production of the full-length protein and of a shorter variant (GATA1s) lacking the N-terminal transactivation domain, which is functionally deficient in supporting erythropoiesis. GATA1 protein abundance is highly regulated in erythroid cells at different levels, including transcription, mRNA translation, posttranslational modifications, and protein degradation, in a differentiation-stage-specific manner. Maintaining high GATA1 protein levels is essential in the early stages of erythroid maturation, whereas downregulating GATA1 protein levels is a necessary step in terminal erythroid differentiation. The importance of maintaining proper GATA1 protein homeostasis in erythropoiesis is demonstrated by the fact that both GATA1 loss and its overexpression result in lethal anemia. Importantly, alterations in any of those GATA1 regulatory checkpoints have been recognized as an important cause of hematological disorders such as dyserythropoiesis (with or without thrombocytopenia), β-thalassemia, Diamond-Blackfan anemia, myelodysplasia, or leukemia. In this review, we provide an overview of the multilevel regulation of GATA1 protein homeostasis in erythropoiesis and of its deregulation in hematological disease.
Collapse
Affiliation(s)
- Laura Gutiérrez
- Platelet Research Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Department of Medicine, Universidad de Oviedo, Oviedo, Spain
| | - Noemí Caballero
- Platelet Research Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Luis Fernández-Calleja
- Platelet Research Lab, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Elena Karkoulia
- Institute of Molecular Biology and Biotechnology, Foundation of Research & Technology Hellas, Heraklion, Crete, Greece
| | - John Strouboulis
- Cancer Comprehensive Center, School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| |
Collapse
|
72
|
Abstract
Mutated or dysregulated transcription factors represent a unique class of drug targets that mediate aberrant gene expression, including blockade of differentiation and cell death gene expression programmes, hallmark properties of cancers. Transcription factor activity is altered in numerous cancer types via various direct mechanisms including chromosomal translocations, gene amplification or deletion, point mutations and alteration of expression, as well as indirectly through non-coding DNA mutations that affect transcription factor binding. Multiple approaches to target transcription factor activity have been demonstrated, preclinically and, in some cases, clinically, including inhibition of transcription factor-cofactor protein-protein interactions, inhibition of transcription factor-DNA binding and modulation of levels of transcription factor activity by altering levels of ubiquitylation and subsequent proteasome degradation or by inhibition of regulators of transcription factor expression. In addition, several new approaches to targeting transcription factors have recently emerged including modulation of auto-inhibition, proteolysis targeting chimaeras (PROTACs), use of cysteine reactive inhibitors, targeting intrinsically disordered regions of transcription factors and combinations of transcription factor inhibitors with kinase inhibitors to block the development of resistance. These innovations in drug development hold great promise to yield agents with unique properties that are likely to impact future cancer treatment.
Collapse
Affiliation(s)
- John H Bushweller
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
| |
Collapse
|
73
|
Romano O, Miccio A. GATA factor transcriptional activity: Insights from genome-wide binding profiles. IUBMB Life 2019; 72:10-26. [PMID: 31574210 DOI: 10.1002/iub.2169] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/05/2019] [Indexed: 01/07/2023]
Abstract
The members of the GATA family of transcription factors have homologous zinc fingers and bind to similar sequence motifs. Recent advances in genome-wide technologies and the integration of bioinformatics data have led to a better understanding of how GATA factors regulate gene expression; GATA-factor-induced transcriptional and epigenetic changes have now been analyzed at unprecedented levels of detail. Here, we review the results of genome-wide studies of GATA factor occupancy in human and murine cell lines and primary cells (as determined by chromatin immunoprecipitation sequencing), and then discuss the molecular mechanisms underlying the mediation of transcriptional and epigenetic regulation by GATA factors.
Collapse
Affiliation(s)
- Oriana Romano
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Annarita Miccio
- Laboratory of chromatin and gene regulation during development, Imagine Institute, INSERM UMR, Paris, France.,Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France
| |
Collapse
|
74
|
The Cornelia de Lange Syndrome-associated factor NIPBL interacts with BRD4 ET domain for transcription control of a common set of genes. Cell Death Dis 2019; 10:548. [PMID: 31320616 PMCID: PMC6639259 DOI: 10.1038/s41419-019-1792-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/17/2019] [Accepted: 07/02/2019] [Indexed: 01/19/2023]
Abstract
Mutations in NIPBL are the major cause of Cornelia de Lange Syndrome (CdLS). NIPBL is the cohesin-loading factor and has recently been associated with the BET (bromodomains and extra-terminal (ET) domain) proteins BRD2 and BRD4. Related to this, a CdLS-like phenotype has been described associated to BRD4 mutations. Here, we show direct interaction of NIPBL with different BET members in yeast, and selective interaction with BRD4 in cells, being the ET domain involved in the interaction. To understand the relationship between NIPBL and BET proteins, we have performed RNA-Seq expression analysis following depletion of the different proteins. Results indicate that genes regulated by NIPBL largely overlap with those regulated by BRD4 but not with those regulated by BRD2. ChIP-Seq analysis indicates preferential NIPBL occupancy at promoters, and knockdown experiments show mutual stabilization of NIPBL and BRD4 on co-regulated promoters. Moreover, human fibroblasts from CdLS probands with mutations in NIPBL show reduced BRD4 at co-occupied promoters. Functional analysis in vivo, using mutants of Drosophila melanogaster, confirmed the genetic interaction between Nipped-B and fs(1)h, the orthologs of human NIPBL and BRD4, respectively. Thus, we provide evidence for NIPBL and BRD4 cooperation in transcriptional regulation, which should contribute to explain the recently observed CdLS-like phenotype associated with BRD4 mutations.
Collapse
|
75
|
Abstract
Less than a decade ago, it was shown that bromodomains, acetyl lysine 'reader' modules found in proteins with varied functions, were highly tractable small-molecule targets. This is an unusual property for protein-protein or protein-peptide interaction domains, and it prompted a wave of chemical probe discovery to understand the biological potential of new agents that targeted bromodomains. The original examples, inhibitors of the bromodomain and extra-terminal (BET) class of bromodomains, showed enticing anti-inflammatory and anticancer activities, and several compounds have since advanced to human clinical trials. Here, we review the current state of BET inhibitor biology in relation to clinical development, and we discuss the next wave of bromodomain inhibitors with clinical potential in oncology and non-oncology indications. The lessons learned from BET inhibitor programmes should affect efforts to develop drugs that target non-BET bromodomains and other epigenetic readers.
Collapse
|
76
|
Acetylation & Co: an expanding repertoire of histone acylations regulates chromatin and transcription. Essays Biochem 2019; 63:97-107. [PMID: 30940741 PMCID: PMC6484784 DOI: 10.1042/ebc20180061] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 12/12/2022]
Abstract
Packaging the long and fragile genomes of eukaryotic species into nucleosomes is all well and good, but how do cells gain access to the DNA again after it has been bundled away? The solution, in every species from yeast to man, is to post-translationally modify histones, altering their chemical properties to either relax the chromatin, label it for remodelling or make it more compact still. Histones are subject to a myriad of modifications: acetylation, methylation, phosphorylation, ubiquitination etc. This review focuses on histone acylations, a diverse group of modifications which occur on the ε-amino group of Lysine residues and includes the well-characterised Lysine acetylation. Over the last 50 years, histone acetylation has been extensively characterised, with the discovery of histone acetyltransferases (HATs) and histone deacetylases (HDACs), and global mapping experiments, revealing an association of hyperacetylated histones with accessible, transcriptionally active chromatin. More recently, there has been an explosion in the number of unique short chain ‘acylations’ identified by MS, including: propionylation, butyrylation, crotonylation, succinylation, malonylation and 2-hydroxyisobutyrylation. These novel modifications add a range of chemical environments to histones, and similar to acetylation, appear to accumulate at transcriptional start sites and correlate with gene activity.
Collapse
|
77
|
Behera V, Stonestrom AJ, Hamagami N, Hsiung CC, Keller CA, Giardine B, Sidoli S, Yuan ZF, Bhanu NV, Werner MT, Wang H, Garcia BA, Hardison RC, Blobel GA. Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription. Cell Rep 2019; 27:400-415.e5. [PMID: 30970245 PMCID: PMC6664437 DOI: 10.1016/j.celrep.2019.03.057] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/30/2018] [Accepted: 03/14/2019] [Indexed: 12/12/2022] Open
Abstract
Global changes in chromatin organization and the cessation of transcription during mitosis are thought to challenge the resumption of appropriate transcription patterns after mitosis. The acetyl-lysine binding protein BRD4 has been previously suggested to function as a transcriptional "bookmark" on mitotic chromatin. Here, genome-wide location analysis of BRD4 in erythroid cells, combined with data normalization and peak characterization approaches, reveals that BRD4 widely occupies mitotic chromatin. However, removal of BRD4 from mitotic chromatin does not impair post-mitotic activation of transcription. Additionally, histone mass spectrometry reveals global preservation of most posttranslational modifications (PTMs) during mitosis. In particular, H3K14ac, H3K27ac, H3K122ac, and H4K16ac widely mark mitotic chromatin, especially at lineage-specific genes, and predict BRD4 mitotic binding genome wide. Therefore, BRD4 is likely not a mitotic bookmark but only a "passenger." Instead, mitotic histone acetylation patterns may constitute the actual bookmarks that restore lineage-specific transcription patterns after mitosis.
Collapse
Affiliation(s)
- Vivek Behera
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aaron J Stonestrom
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicole Hamagami
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Chris C Hsiung
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA
| | - Belinda Giardine
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA
| | - Simone Sidoli
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zuo-Fei Yuan
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Natarajan V Bhanu
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael T Werner
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hongxin Wang
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA
| | - Gerd A Blobel
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
78
|
Chaytor L, Simcock M, Nakjang S, Heath R, Walker L, Robson C, Jones D, Gaughan L. The Pioneering Role of GATA2 in Androgen Receptor Variant Regulation Is Controlled by Bromodomain and Extraterminal Proteins in Castrate-Resistant Prostate Cancer. Mol Cancer Res 2019; 17:1264-1278. [DOI: 10.1158/1541-7786.mcr-18-1231] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/25/2019] [Accepted: 02/28/2019] [Indexed: 11/16/2022]
|
79
|
Zhang Z, Parker MP, Graw S, Novikova LV, Fedosyuk H, Fontes JD, Koestler DC, Peterson KR, Slawson C. O-GlcNAc homeostasis contributes to cell fate decisions during hematopoiesis. J Biol Chem 2019; 294:1363-1379. [PMID: 30523150 PMCID: PMC6349094 DOI: 10.1074/jbc.ra118.005993] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/29/2018] [Indexed: 11/06/2022] Open
Abstract
The addition of a single β-d-GlcNAc sugar (O-GlcNAc) by O-GlcNAc-transferase (OGT) and O-GlcNAc removal by O-GlcNAcase (OGA) maintain homeostatic O-GlcNAc levels on cellular proteins. Changes in protein O-GlcNAcylation regulate cellular differentiation and cell fate decisions, but how these changes affect erythropoiesis, an essential process in blood cell formation, remains unclear. Here, we investigated the role of O-GlcNAcylation in erythropoiesis by using G1E-ER4 cells, which carry the erythroid-specific transcription factor GATA-binding protein 1 (GATA-1) fused to the estrogen receptor (GATA-1-ER) and therefore undergo erythropoiesis after β-estradiol (E2) addition. We observed that during G1E-ER4 differentiation, overall O-GlcNAc levels decrease, and physical interactions of GATA-1 with both OGT and OGA increase. RNA-Seq-based transcriptome analysis of G1E-ER4 cells differentiated in the presence of the OGA inhibitor Thiamet-G (TMG) revealed changes in expression of 433 GATA-1 target genes. ChIP results indicated that the TMG treatment decreases the occupancy of GATA-1, OGT, and OGA at the GATA-binding site of the lysosomal protein transmembrane 5 (Laptm5) gene promoter. TMG also reduced the expression of genes involved in differentiation of NB4 and HL60 human myeloid leukemia cells, suggesting that O-GlcNAcylation is involved in the regulation of hematopoietic differentiation. Sustained treatment of G1E-ER4 cells with TMG before differentiation reduced hemoglobin-positive cells and increased stem/progenitor cell surface markers. Our results show that alterations in O-GlcNAcylation disrupt transcriptional programs controlling erythropoietic lineage commitment, suggesting a role for O-GlcNAcylation in regulating hematopoietic cell fate.
Collapse
Affiliation(s)
- Zhen Zhang
- Departments of Biochemistry and Molecular Biology, Kansas City, Kansas 66160
| | - Matthew P Parker
- Departments of Biochemistry and Molecular Biology, Kansas City, Kansas 66160
| | | | - Lesya V Novikova
- Departments of Biochemistry and Molecular Biology, Kansas City, Kansas 66160
| | - Halyna Fedosyuk
- Departments of Biochemistry and Molecular Biology, Kansas City, Kansas 66160
| | - Joseph D Fontes
- Departments of Biochemistry and Molecular Biology, Kansas City, Kansas 66160; Cancer Center, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Devin C Koestler
- Biostatistics, Kansas City, Kansas 66160; Cancer Center, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Kenneth R Peterson
- Departments of Biochemistry and Molecular Biology, Kansas City, Kansas 66160; Cancer Center, University of Kansas Medical Center, Kansas City, Kansas 66160; Anatomy and Cell Biology, Kansas City, Kansas 66160.
| | - Chad Slawson
- Departments of Biochemistry and Molecular Biology, Kansas City, Kansas 66160; Cancer Center, University of Kansas Medical Center, Kansas City, Kansas 66160.
| |
Collapse
|
80
|
Tremblay M, Sanchez-Ferras O, Bouchard M. GATA transcription factors in development and disease. Development 2018; 145:145/20/dev164384. [DOI: 10.1242/dev.164384] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
ABSTRACT
The GATA family of transcription factors is of crucial importance during embryonic development, playing complex and widespread roles in cell fate decisions and tissue morphogenesis. GATA proteins are essential for the development of tissues derived from all three germ layers, including the skin, brain, gonads, liver, hematopoietic, cardiovascular and urogenital systems. The crucial activity of GATA factors is underscored by the fact that inactivating mutations in most GATA members lead to embryonic lethality in mouse models and are often associated with developmental diseases in humans. In this Primer, we discuss the unique and redundant functions of GATA proteins in tissue morphogenesis, with an emphasis on their regulation of lineage specification and early organogenesis.
Collapse
Affiliation(s)
- Mathieu Tremblay
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal H3A 1A3, Canada
| | - Oraly Sanchez-Ferras
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal H3A 1A3, Canada
| | - Maxime Bouchard
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal H3A 1A3, Canada
| |
Collapse
|
81
|
Andrieu GP, Shafran JS, Deeney JT, Bharadwaj KR, Rangarajan A, Denis GV. BET proteins in abnormal metabolism, inflammation, and the breast cancer microenvironment. J Leukoc Biol 2018; 104:265-274. [PMID: 29493812 PMCID: PMC6134394 DOI: 10.1002/jlb.5ri0917-380rr] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 02/10/2018] [Accepted: 02/10/2018] [Indexed: 12/21/2022] Open
Abstract
Obesity and its associated pathology Type 2 diabetes are two chronic metabolic and inflammatory diseases that promote breast cancer progression, metastasis, and poor outcomes. Emerging critical opinion considers unresolved inflammation and abnormal metabolism separately from obesity; settings where they do not co-occur can inform disease mechanism. In breast cancer, the tumor microenvironment is often infiltrated with T effector and T regulatory cells programmed by metabolic signaling. The pathways by which tumor cells evade immune surveillance, immune therapies, and take advantage of antitumor immunity are poorly understood, but likely depend on metabolic inflammation in the microenvironment. Immune functions are abnormal in metabolic disease, and lessons learned from preclinical studies in lean and metabolically normal environments may not translate to patients with obesity and metabolic disease. This problem is made more urgent by the rising incidence of breast cancer among women who are not obese but who have metabolic disease and associated inflammation, a phenotype common in Asia. The somatic BET proteins, comprising BRD2, BRD3, and BRD4, are new critical regulators of metabolism, coactivate transcription of genes that encode proinflammatory cytokines in immune cell subsets infiltrating the microenvironment, and could be important targets in breast cancer immunotherapy. These transcriptional coregulators are well known to regulate tumor cell progression, but only recently identified as critical for metabolism, metastasis, and expression of immune checkpoint molecules. We consider interrelationships among metabolism, inflammation, and breast cancer aggressiveness relevant to the emerging threat of breast cancer among women with metabolic disease, but without obesity.
Collapse
Affiliation(s)
| | - Jordan S. Shafran
- Cancer Center, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Jude T. Deeney
- Department of Medicine, Section of Endocrinology, Obesity Research Center, Evans Biomedical Research Center; Boston University School of Medicine, Boston, Massachusetts, USA
| | - Kishan R. Bharadwaj
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, India
| | - Annapoorni Rangarajan
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bengaluru, India
| | - Gerald V. Denis
- Cancer Center, Boston University School of Medicine, Boston, Massachusetts, USA
| |
Collapse
|
82
|
Itoh Y. Chemical Protein Degradation Approach and its Application to Epigenetic Targets. CHEM REC 2018; 18:1681-1700. [PMID: 29893461 DOI: 10.1002/tcr.201800032] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/24/2018] [Indexed: 12/17/2022]
Abstract
In addition to traditional drugs, such as enzyme inhibitors, receptor agonists/antagonists, and protein-protein interaction inhibitors as well as genetic technology, such as RNA interference and the CRISPR/Cas9 system, protein knockdown approaches using proteolysis-targeting chimeras (PROTACs) have attracted much attention. PROTACs, which induce selective degradation of their target protein via the ubiquitin-proteasome system, are useful for the down-regulation of various proteins, including disease-related proteins and epigenetic proteins. Recent reports have shown that chemical protein knockdown is possible not only in cells, but also in vivo and this approach is expected to be used as the therapeutic strategy for several diseases. Thus, this approach may be a significant technique to complement traditional drugs and genetic ablation and will be more widely used for drug discovery and chemical biology studies in the future. In this personal account, a history of chemical protein knockdown is introduced, and its features, recent progress in the epigenetics field, and future outlooks are discussed.
Collapse
Affiliation(s)
- Yukihiro Itoh
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| |
Collapse
|
83
|
|
84
|
|
85
|
Wai DCC, Szyszka TN, Campbell AE, Kwong C, Wilkinson-White LE, Silva APG, Low JKK, Kwan AH, Gamsjaeger R, Chalmers JD, Patrick WM, Lu B, Vakoc CR, Blobel GA, Mackay JP. The BRD3 ET domain recognizes a short peptide motif through a mechanism that is conserved across chromatin remodelers and transcriptional regulators. J Biol Chem 2018; 293:7160-7175. [PMID: 29567837 PMCID: PMC5949996 DOI: 10.1074/jbc.ra117.000678] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/08/2018] [Indexed: 12/31/2022] Open
Abstract
Members of the bromodomain and extra-terminal domain (BET) family of proteins (bromodomain-containing (BRD) 2, 3, 4, and T) are widely expressed and highly conserved regulators of gene expression in eukaryotes. These proteins have been intimately linked to human disease, and more than a dozen clinical trials are currently underway to test BET-protein inhibitors as modulators of cancer. However, although it is clear that these proteins use their bromodomains to bind both histones and transcription factors bearing acetylated lysine residues, the molecular mechanisms by which BET family proteins regulate gene expression are not well defined. In particular, the functions of the other domains such as the ET domain have been less extensively studied. Here, we examine the properties of the ET domain of BRD3 as a protein/protein interaction module. Using a combination of pulldown and biophysical assays, we demonstrate that BRD3 binds to a range of chromatin-remodeling complexes, including the NuRD, BAF, and INO80 complexes, via a short linear "KIKL" motif in one of the complex subunits. NMR-based structural analysis revealed that, surprisingly, this mode of interaction is shared by the AF9 and ENL transcriptional coregulators that contain an acetyl-lysine-binding YEATS domain and regulate transcriptional elongation. This observation establishes a functional commonality between these two families of cancer-related transcriptional regulators. In summary, our data provide insight into the mechanisms by which BET family proteins might link chromatin acetylation to transcriptional outcomes and uncover an unexpected functional similarity between BET and YEATS family proteins.
Collapse
Affiliation(s)
- Dorothy C C Wai
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Taylor N Szyszka
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Amy E Campbell
- Division of Hematology, Children's Hospital of Philadelphia, and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Cherry Kwong
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Lorna E Wilkinson-White
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Ana P G Silva
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Ann H Kwan
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - Roland Gamsjaeger
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia
| | - James D Chalmers
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Wayne M Patrick
- Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand
| | - Bin Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | | | - Gerd A Blobel
- Division of Hematology, Children's Hospital of Philadelphia, and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia.
| |
Collapse
|
86
|
Abdullah M, Berthiaume JM, Willis MS. Tumor necrosis factor receptor-associated factor 6 as a nuclear factor kappa B-modulating therapeutic target in cardiovascular diseases: at the heart of it all. Transl Res 2018; 195:48-61. [PMID: 29175266 PMCID: PMC5898986 DOI: 10.1016/j.trsl.2017.10.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/17/2017] [Accepted: 10/30/2017] [Indexed: 02/06/2023]
Abstract
Inflammatory and immune signaling has been documented as a root cause of many cardiovascular pathologies. In this review, we explore the emerging role of tumor necrosis factor receptor-associated factor 6 (TRAF6)-nuclear factor kappa B (NF-κB) signaling axis in atherosclerosis, ischemic heart disease, pathologic cardiac hypertrophy or heart failure, myocarditis, and sepsis-induced cardiomyopathy. We discuss the current understanding of cardiac inflammation in heart disease, present the TRAF6 signaling axis in the heart, then summarize what is known about TRAF6 in pathophysiology of heart disease including proof-of-concept studies that identify the utility of blocking TRAF6 to attenuate cardiac dysfunction, which suggests that TRAF6 is a novel, druggable target in treating cardiovascular disease incurred by inflammatory processes.
Collapse
Affiliation(s)
- Muhammad Abdullah
- Department of Biochemistry, QuaidiAzam University, Islamabad, Pakistan; Department of Pathology & Laboratory Medicine, University of North Carolina, Chapel Hill, NC
| | - Jessica M Berthiaume
- Department of Physiology & Biophysics, Case Western Reserve University, Cleveland, Ohio
| | - Monte S Willis
- Department of Pathology & Laboratory Medicine, University of North Carolina, Chapel Hill, NC; Department of Pharmacology, University of North Carolina, Chapel Hill, NC.
| |
Collapse
|
87
|
Luna-Peláez N, García-Domínguez M. Lyar-Mediated Recruitment of Brd2 to the Chromatin Attenuates Nanog Downregulation Following Induction of Differentiation. J Mol Biol 2018; 430:1084-1097. [PMID: 29505757 DOI: 10.1016/j.jmb.2018.02.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/08/2018] [Accepted: 02/26/2018] [Indexed: 01/24/2023]
Abstract
During development, cellular differentiation programs need tight regulation for proper display of the activity of multiple factors in time and space. Chromatin adaptors of the BET family (Brd2, Brd3, Brd4 and Brdt in vertebrates) are transcription co-regulators tightly associated with the progression of the cell cycle. A key question regarding their function is whether they work as part of the general transcription machinery or, on the contrary, they are precisely recruited to the chromatin through specific transcription factors. Here, we report the selective recruitment of Brd2 to the chromatin by the transcription factor Lyar. We show that Lyar downregulation results in Brd2 dissociation from a number of promoters studied. On the contrary, dissociation of BET proteins from the chromatin has no effect on Lyar occupancy. Under differentiation conditions, the absence of Lyar leads to impaired downregulation of the pluripotency gene Nanog, with concomitant reduction in the upregulation of differentiation markers. Interestingly, following the induction of differentiation, Brd2 depletion exhibits the same effects as expressing a truncated Lyar molecule lacking the Brd2 interacting domain. Both approaches result in stronger Nanog repression, indicating that Lyar-mediated recruitment of Brd2 moderates Nanog downregulation when differentiation is triggered. Moreover, expression of truncated Lyar leads to impaired differentiation and increased apoptosis. Thus, Lyar-mediated recruitment of Brd2 would participate in preserving a proper timing for Nanog silencing ensuring the appropriate establishment of the differentiation program.
Collapse
Affiliation(s)
- Noelia Luna-Peláez
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain
| | - Mario García-Domínguez
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain.
| |
Collapse
|
88
|
Fratta E, Montico B, Rizzo A, Colizzi F, Sigalotti L, Dolcetti R. Epimutational profile of hematologic malignancies as attractive target for new epigenetic therapies. Oncotarget 2018; 7:57327-57350. [PMID: 27329599 PMCID: PMC5302993 DOI: 10.18632/oncotarget.10033] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/28/2016] [Indexed: 12/31/2022] Open
Abstract
In recent years, recurrent somatic mutations in epigenetic regulators have been identified in patients with hematological malignancies. Furthermore, chromosomal translocations in which the fusion protein partners are themselves epigenetic regulators or where epigenetic regulators are recruited/targeted by oncogenic fusion proteins have also been described. Evidence has accumulated showing that "epigenetic drugs" are likely to provide clinical benefits in several hematological malignancies, granting their approval for the treatment of myelodysplastic syndromes and cutaneous T-cell lymphomas. A large number of pre-clinical and clinical trials evaluating epigenetic drugs alone or in combination therapies are ongoing. The aim of this review is to provide a comprehensive summary of known epigenetic alterations and of the current use of epigenetic drugs for the treatment of hematological malignancies.
Collapse
Affiliation(s)
- Elisabetta Fratta
- Cancer Bio-Immunotherapy Unit, Centro di Riferimento Oncologico, IRCCS, National Cancer Institute, Aviano, PN, Italy
| | - Barbara Montico
- Cancer Bio-Immunotherapy Unit, Centro di Riferimento Oncologico, IRCCS, National Cancer Institute, Aviano, PN, Italy
| | - Aurora Rizzo
- Cancer Bio-Immunotherapy Unit, Centro di Riferimento Oncologico, IRCCS, National Cancer Institute, Aviano, PN, Italy
| | - Francesca Colizzi
- Cancer Bio-Immunotherapy Unit, Centro di Riferimento Oncologico, IRCCS, National Cancer Institute, Aviano, PN, Italy
| | - Luca Sigalotti
- Cancer Bio-Immunotherapy Unit, Centro di Riferimento Oncologico, IRCCS, National Cancer Institute, Aviano, PN, Italy
| | - Riccardo Dolcetti
- Cancer Bio-Immunotherapy Unit, Centro di Riferimento Oncologico, IRCCS, National Cancer Institute, Aviano, PN, Italy.,University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
| |
Collapse
|
89
|
Ali I, Conrad RJ, Verdin E, Ott M. Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics. Chem Rev 2018; 118:1216-1252. [PMID: 29405707 PMCID: PMC6609103 DOI: 10.1021/acs.chemrev.7b00181] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational acetylation of lysine residues has emerged as a key regulatory mechanism in all eukaryotic organisms. Originally discovered in 1963 as a unique modification of histones, acetylation marks are now found on thousands of nonhistone proteins located in virtually every cellular compartment. Here we summarize key findings in the field of protein acetylation over the past 20 years with a focus on recent discoveries in nuclear, cytoplasmic, and mitochondrial compartments. Collectively, these findings have elevated protein acetylation as a major post-translational modification, underscoring its physiological relevance in gene regulation, cell signaling, metabolism, and disease.
Collapse
Affiliation(s)
- Ibraheem Ali
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Ryan J. Conrad
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| |
Collapse
|
90
|
Runcie AC, Zengerle M, Chan KH, Testa A, van Beurden L, Baud MGJ, Epemolu O, Ellis LCJ, Read KD, Coulthard V, Brien A, Ciulli A. Optimization of a "bump-and-hole" approach to allele-selective BET bromodomain inhibition. Chem Sci 2018; 9:2452-2468. [PMID: 29732121 PMCID: PMC5909127 DOI: 10.1039/c7sc02536j] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 01/23/2018] [Indexed: 12/27/2022] Open
Abstract
Allele-specific chemical genetics enables selective inhibition within families of highly-conserved proteins.
Allele-specific chemical genetics enables selective inhibition within families of highly-conserved proteins. The four BET (bromodomain & extra-terminal domain) proteins – BRD2, BRD3, BRD4 and BRDT bind acetylated chromatin via their bromodomains and regulate processes such as cell proliferation and inflammation. BET bromodomains are of particular interest, as they are attractive therapeutic targets but existing inhibitors are pan-selective. We previously established a bump-&-hole system for the BET bromodomains, pairing a leucine/alanine mutation with an ethyl-derived analogue of an established benzodiazepine scaffold. Here we optimize upon this system with the introduction of a more conservative and less disruptive leucine/valine mutation. Extensive structure–activity-relationships of diverse benzodiazepine analogues guided the development of potent, mutant-selective inhibitors with desirable physiochemical properties. The active enantiomer of our best compound – 9-ME-1 – shows ∼200 nM potency, >100-fold selectivity for the L/V mutant over wild-type and excellent DMPK properties. Through a variety of in vitro and cellular assays we validate the capabilities of our optimized system, and then utilize it to compare the relative importance of the first and second bromodomains to chromatin binding. These experiments confirm the primacy of the first bromodomain in all BET proteins, but also significant variation in the importance of the second bromodomain. We also show that, despite having a minor role in chromatin recognition, BRD4 BD2 is still essential for gene expression, likely through the recruitment of non-histone proteins. The disclosed inhibitor:mutant pair provides a powerful tool for future cellular and in vivo target validation studies.
Collapse
Affiliation(s)
- A C Runcie
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - M Zengerle
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - K-H Chan
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - A Testa
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - L van Beurden
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - M G J Baud
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - O Epemolu
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - L C J Ellis
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - K D Read
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| | - V Coulthard
- Reach Separations Ltd , BioCity Nottingham , Nottingham , UK
| | - A Brien
- Reach Separations Ltd , BioCity Nottingham , Nottingham , UK
| | - A Ciulli
- Division of Biological Chemistry and Drug Discovery , School of Life Sciences , University of Dundee , Dundee , Scotland , UK .
| |
Collapse
|
91
|
Shadrick WR, Slavish PJ, Chai SC, Waddell B, Connelly M, Low JA, Tallant C, Young BM, Bharatham N, Knapp S, Boyd VA, Morfouace M, Roussel MF, Chen T, Lee RE, Kiplin Guy R, Shelat AA, Potter PM. Exploiting a water network to achieve enthalpy-driven, bromodomain-selective BET inhibitors. Bioorg Med Chem 2018; 26:25-36. [PMID: 29170024 PMCID: PMC5733700 DOI: 10.1016/j.bmc.2017.10.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 10/20/2017] [Accepted: 10/30/2017] [Indexed: 12/24/2022]
Abstract
Within the last decade, the Bromodomain and Extra-Terminal domain family (BET) of proteins have emerged as promising drug targets in diverse clinical indications including oncology, auto-immune disease, heart failure, and male contraception. The BET family consists of four isoforms (BRD2, BRD3, BRD4, and BRDT/BRDT6) which are distinguished by the presence of two tandem bromodomains (BD1 and BD2) that independently recognize acetylated-lysine (KAc) residues and appear to have distinct biological roles. BET BD1 and BD2 bromodomains differ at five positions near the substrate binding pocket: the variation in the ZA channel induces different water networks nearby. We designed a set of congeneric 2- and 3-heteroaryl substituted tetrahydroquinolines (THQ) to differentially engage bound waters in the ZA channel with the goal of achieving bromodomain selectivity. SJ830599 (9) showed modest, but consistent, selectivity for BRD2-BD2. Using isothermal titration calorimetry, we showed that the binding of all THQ analogs in our study to either of the two bromodomains was enthalpy driven. Remarkably, the binding of 9 to BRD2-BD2 was marked by negative entropy and was entirely driven by enthalpy, consistent with significant restriction of conformational flexibility and/or engagement with bound waters. Co-crystallography studies confirmed that 9 did indeed stabilize a water-mediated hydrogen bond network. Finally, we report that 9 retained cytotoxicity against several pediatric cancer cell lines with EC50 values comparable to BET inhibitor (BETi) clinical candidates.
Collapse
Affiliation(s)
- William R Shadrick
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Peter J Slavish
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Sergio C Chai
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Brett Waddell
- Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Michele Connelly
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jonathan A Low
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Cynthia Tallant
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK; Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Brandon M Young
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Nagakumar Bharatham
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Stefan Knapp
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK; Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Vincent A Boyd
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Marie Morfouace
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Martine F Roussel
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Richard E Lee
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - R Kiplin Guy
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Anang A Shelat
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
| | - Philip M Potter
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| |
Collapse
|
92
|
Hsu SC, Blobel GA. The Role of Bromodomain and Extraterminal Motif (BET) Proteins in Chromatin Structure. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 82:37-43. [PMID: 29196562 DOI: 10.1101/sqb.2017.82.033829] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bromodomain and extraterminal motif (BET) proteins have been widely investigated for their roles in gene regulation and their potential as therapeutic targets in cancer. Pharmacologic BET inhibitors target the conserved bromodomain-acetyllysine interaction and do not distinguish between BRD2, BRD3, and BRD4. Thus, comparatively little is known regarding the distinct roles played by individual family members, as well as the underlying mechanisms that drive the transcriptional effects of BET inhibitors. Here we review studies regarding the contributions of BET proteins to genome structure and function, including recent work identifying a role for BRD2 as a component of functional and physical chromatin domain boundaries. We also discuss directions of future studies aimed at providing insights into broader architectural functions of BET proteins and their roles in chromatin domain boundary formation.
Collapse
Affiliation(s)
- Sarah C Hsu
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Gerd A Blobel
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104
| |
Collapse
|
93
|
CRISPR/Cas9 knockouts reveal genetic interaction between strain-transcendent erythrocyte determinants of Plasmodium falciparum invasion. Proc Natl Acad Sci U S A 2017; 114:E9356-E9365. [PMID: 29078358 DOI: 10.1073/pnas.1711310114] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
During malaria blood-stage infections, Plasmodium parasites interact with the RBC surface to enable invasion followed by intracellular proliferation. Critical factors involved in invasion have been identified using biochemical and genetic approaches including specific knockdowns of genes of interest from primary CD34+ hematopoietic stem cells (cRBCs). Here we report the development of a robust in vitro culture system to produce RBCs that allow the generation of gene knockouts via CRISPR/Cas9 using the immortal JK-1 erythroleukemia line. JK-1 cells spontaneously differentiate, generating cells at different stages of erythropoiesis, including terminally differentiated nucleated RBCs that we term "jkRBCs." A screen of small-molecule epigenetic regulators identified several bromodomain-specific inhibitors that promote differentiation and enable production of synchronous populations of jkRBCs. Global surface proteomic profiling revealed that jkRBCs express all known Pfalciparum host receptors in a similar fashion to cRBCs and that multiple Pfalciparum strains invade jkRBCs at comparable levels to cRBCs and RBCs. Using CRISPR/Cas9, we deleted two host factors, basigin (BSG) and CD44, for which no natural nulls exist. BSG interacts with the parasite ligand Rh5, a prominent vaccine candidate. A BSG knockout was completely refractory to parasite invasion in a strain-transcendent manner, confirming the essential role for BSG during invasion. CD44 was recently identified in an RNAi screen of blood group genes as a host factor for invasion, and we show that CD44 knockout results in strain-transcendent reduction in invasion. Furthermore, we demonstrate a functional interaction between these two determinants in mediating Pfalciparum erythrocyte invasion.
Collapse
|
94
|
The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries. Mol Cell 2017; 66:102-116.e7. [PMID: 28388437 DOI: 10.1016/j.molcel.2017.02.027] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 02/05/2017] [Accepted: 02/27/2017] [Indexed: 01/02/2023]
Abstract
Bromodomain and extraterminal motif (BET) proteins are pharmacologic targets for the treatment of diverse diseases, yet the roles of individual BET family members remain unclear. We find that BRD2, but not BRD4, co-localizes with the architectural/insulator protein CCCTC-binding factor (CTCF) genome-wide. CTCF recruits BRD2 to co-bound sites whereas BRD2 is dispensable for CTCF occupancy. Disruption of a CTCF/BRD2-occupied element positioned between two unrelated genes enables regulatory influence to spread from one gene to another, suggesting that CTCF and BRD2 form a transcriptional boundary. Accordingly, single-molecule mRNA fluorescence in situ hybridization (FISH) reveals that, upon site-specific CTCF disruption or BRD2 depletion, expression of the two genes becomes increasingly correlated. HiC shows that BRD2 depletion weakens boundaries co-occupied by CTCF and BRD2, but not those that lack BRD2. These findings indicate that BRD2 supports boundary activity, and they raise the possibility that pharmacologic BET inhibitors can influence gene expression in part by perturbing domain boundary function.
Collapse
|
95
|
Roberts TC, Etxaniz U, Dall'Agnese A, Wu SY, Chiang CM, Brennan PE, Wood MJA, Puri PL. BRD3 and BRD4 BET Bromodomain Proteins Differentially Regulate Skeletal Myogenesis. Sci Rep 2017; 7:6153. [PMID: 28733670 PMCID: PMC5522382 DOI: 10.1038/s41598-017-06483-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 06/14/2017] [Indexed: 12/22/2022] Open
Abstract
Myogenic differentiation proceeds through a highly coordinated cascade of gene activation that necessitates epigenomic changes in chromatin structure. Using a screen of small molecule epigenetic probes we identified three compounds which inhibited myogenic differentiation in C2C12 myoblasts; (+)-JQ1, PFI-1, and Bromosporine. These molecules target Bromodomain and Extra Terminal domain (BET) proteins, which are epigenetic readers of acetylated histone lysine tail residues. BETi-mediated anti-myogenic effects were also observed in a model of MYOD1-mediated myogenic conversion of human fibroblasts, and in primary mouse and human myoblasts. All three BET proteins BRD2, BRD3 and BRD4 exhibited distinct and dynamic patterns of protein expression over the course of differentiation without concomitant changes in mRNA levels, suggesting that BET proteins are regulated at the post-transcriptional level. Specific BET protein knockdown by RNA interference revealed that BRD4 was required for myogenic differentiation, whereas BRD3 down-regulation resulted in enhanced myogenic differentiation. ChIP experiments revealed a preferential binding of BRD4 to the Myog promoter during C2C12 myoblast differentiation, co-incident with increased levels of H3K27 acetylation. These results have identified an essential role for BET proteins in the regulation of skeletal myogenesis, and assign distinct functions to BRD3 and BRD4.
Collapse
Affiliation(s)
- Thomas C Roberts
- Sanford Burnham Prebys Medical Discovery Institute, Development, Aging and Regeneration Program, La Jolla, CA, 92037, USA. .,Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX, UK.
| | - Usue Etxaniz
- Sanford Burnham Prebys Medical Discovery Institute, Development, Aging and Regeneration Program, La Jolla, CA, 92037, USA
| | - Alessandra Dall'Agnese
- Sanford Burnham Prebys Medical Discovery Institute, Development, Aging and Regeneration Program, La Jolla, CA, 92037, USA
| | - Shwu-Yuan Wu
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas, 75390, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas, 75390, USA
| | - Cheng-Ming Chiang
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas, 75390, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas, 75390, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas, 75390, USA
| | - Paul E Brennan
- Structural Genomics Consortium and Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Matthew J A Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX, UK
| | - Pier Lorenzo Puri
- Sanford Burnham Prebys Medical Discovery Institute, Development, Aging and Regeneration Program, La Jolla, CA, 92037, USA. .,IRCCS Fondazione Santa Lucia, Rome, Italy.
| |
Collapse
|
96
|
Xu Y, Vakoc CR. Targeting Cancer Cells with BET Bromodomain Inhibitors. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026674. [PMID: 28213432 DOI: 10.1101/cshperspect.a026674] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cancer cells are often hypersensitive to the targeting of transcriptional regulators, which may reflect the deregulated gene expression programs that underlie malignant transformation. One of the most prominent transcriptional vulnerabilities in human cancer to emerge in recent years is the bromodomain and extraterminal (BET) family of proteins, which are coactivators that link acetylated transcription factors and histones to the activation of RNA polymerase II. Despite unclear mechanisms underlying the gene specificity of BET protein function, small molecules targeting these regulators preferentially suppress the transcription of cancer-promoting genes. As a consequence, BET inhibitors elicit anticancer activity in numerous malignant contexts at doses that can be tolerated by normal tissues, a finding supported by animal studies and by phase I clinical trials in human cancer patients. In this review, we will discuss the remarkable, and often perplexing, therapeutic effects of BET bromodomain inhibition in cancer.
Collapse
Affiliation(s)
- Yali Xu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | | |
Collapse
|
97
|
Wang LL, Zhou LB, Shu J, Li NN, Zhang HW, Jin R, Zhuang LL, Zhou GP. Up-regulation of IRF-3 expression through GATA-1 acetylation by histone deacetylase inhibitor in lung adenocarcinoma A549 cells. Oncotarget 2017; 8:75943-75951. [PMID: 29100282 PMCID: PMC5652676 DOI: 10.18632/oncotarget.18371] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/21/2017] [Indexed: 11/30/2022] Open
Abstract
Interferon regulatory factor 3 (IRF-3) is an important transcription factor for interferon genes. Although its functional activation by viral infection has been widely explicated, the regulatory mechanism of IRF-3 gene expression in cancer cells is poorly understood. In this study, we demonstrated treatment of lung adenocarcinoma A549 cells with trichostatin A (TSA) and valproic acid (VPA), two different classes of histone deacetylase inhibitors, strongly stimulated IRF-3 gene expression. Truncated and mutated IRF-3 promoter indicated that a specific GATA-1 element was responsible for TSA-induced activation of IRF-3 promoter. Chromatin immunoprecipitation and electrophoretic mobility shift assay showed that TSA treatment increased the binding affinity of GATA-1 to IRF-3 promoter. Using immunoprecipitation assay and immunoblotting, we demonstrated that TSA increased the level of acetylated GATA-1 in A549 cells. In summary, our study implied that TSA enhanced IRF-3 gene expression through increased GATA-1 recruitment to IRF-3 promoter and the acetylation level of GATA-1 in lung adenocarcinoma A549 cells.
Collapse
Affiliation(s)
- Lu-Lu Wang
- Department of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Lan-Bo Zhou
- Grade 2013 Clinical Class 7, The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Jin Shu
- Department of Pediatric Respiration, Affiliated Wuxi People's Hospital, Nanjing Medical University, Wuxi, Jiangsu, China
| | - Nan-Nan Li
- Department of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Hui-Wen Zhang
- Department of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Rui Jin
- Department of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Li-Li Zhuang
- Department of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Guo-Ping Zhou
- Department of Pediatrics, The First Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu Province, China
| |
Collapse
|
98
|
Selective BET bromodomain inhibition as an antifungal therapeutic strategy. Nat Commun 2017; 8:15482. [PMID: 28516956 PMCID: PMC5454392 DOI: 10.1038/ncomms15482] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 03/31/2017] [Indexed: 12/14/2022] Open
Abstract
Invasive fungal infections cause significant morbidity and mortality among immunocompromised individuals, posing an urgent need for new antifungal therapeutic strategies. Here we investigate a chromatin-interacting module, the bromodomain (BD) from the BET family of proteins, as a potential antifungal target in Candida albicans, a major human fungal pathogen. We show that the BET protein Bdf1 is essential in C. albicans and that mutations inactivating its two BDs result in a loss of viability in vitro and decreased virulence in mice. We report small-molecule compounds that inhibit C. albicans Bdf1 with high selectivity over human BDs. Crystal structures of the Bdf1 BDs reveal binding modes for these inhibitors that are sterically incompatible with the human BET-binding pockets. Furthermore, we report a dibenzothiazepinone compound that phenocopies the effects of a Bdf1 BD-inactivating mutation on C. albicans viability. These findings establish BET inhibition as a promising antifungal therapeutic strategy and identify Bdf1 as an antifungal drug target that can be selectively inhibited without antagonizing human BET function. BET proteins bind chromatin through their bromodomains (BDs) to regulate transcription and chromatin remodelling. Here, the authors show that the BET protein Bdf1 is essential for the fungal pathogen Candida albicans, and report compounds that inhibit the Bdf1 BDs with high selectivity over human BDs.
Collapse
|
99
|
Liu Z, Wang P, Chen H, Wold EA, Tian B, Brasier AR, Zhou J. Drug Discovery Targeting Bromodomain-Containing Protein 4. J Med Chem 2017; 60:4533-4558. [PMID: 28195723 PMCID: PMC5464988 DOI: 10.1021/acs.jmedchem.6b01761] [Citation(s) in RCA: 215] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
BRD4,
the most extensively studied member of the BET family, is
an epigenetic regulator that localizes to DNA via binding to acetylated
histones and controls the expression of therapeutically important
gene regulatory networks through the recruitment of transcription
factors to form mediator complexes, phosphorylating RNA polymerase
II, and by its intrinsic histone acetyltransferase activity. Disrupting
the protein–protein interactions between BRD4 and acetyl-lysine
has been shown to effectively block cell proliferation in cancer,
cytokine production in acute inflammation, and so forth. To date,
significant efforts have been devoted to the development of BRD4 inhibitors,
and consequently, a dozen have progressed to human clinical trials.
Herein, we summarize the advances in drug discovery and development
of BRD4 inhibitors by focusing on their chemotypes, in vitro and in
vivo activity, selectivity, relevant mechanisms of action, and therapeutic
potential. Opportunities and challenges to achieve selective and efficacious
BRD4 inhibitors as a viable therapeutic strategy for human diseases
are also highlighted.
Collapse
Affiliation(s)
- Zhiqing Liu
- Chemical Biology Program, Department of Pharmacology and Toxicology, ‡Department of Internal Medicine, §Sealy Center for Molecular Medicine, ξInstitute for Translational Sciences, University of Texas Medical Branch , Galveston, Texas 77555, United States
| | - Pingyuan Wang
- Chemical Biology Program, Department of Pharmacology and Toxicology, ‡Department of Internal Medicine, §Sealy Center for Molecular Medicine, ξInstitute for Translational Sciences, University of Texas Medical Branch , Galveston, Texas 77555, United States
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, ‡Department of Internal Medicine, §Sealy Center for Molecular Medicine, ξInstitute for Translational Sciences, University of Texas Medical Branch , Galveston, Texas 77555, United States
| | - Eric A Wold
- Chemical Biology Program, Department of Pharmacology and Toxicology, ‡Department of Internal Medicine, §Sealy Center for Molecular Medicine, ξInstitute for Translational Sciences, University of Texas Medical Branch , Galveston, Texas 77555, United States
| | - Bing Tian
- Chemical Biology Program, Department of Pharmacology and Toxicology, ‡Department of Internal Medicine, §Sealy Center for Molecular Medicine, ξInstitute for Translational Sciences, University of Texas Medical Branch , Galveston, Texas 77555, United States
| | - Allan R Brasier
- Chemical Biology Program, Department of Pharmacology and Toxicology, ‡Department of Internal Medicine, §Sealy Center for Molecular Medicine, ξInstitute for Translational Sciences, University of Texas Medical Branch , Galveston, Texas 77555, United States
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, ‡Department of Internal Medicine, §Sealy Center for Molecular Medicine, ξInstitute for Translational Sciences, University of Texas Medical Branch , Galveston, Texas 77555, United States
| |
Collapse
|
100
|
Abstract
The discovery of the GATA binding protein (GATA factor) transcription factor family revolutionized hematology. Studies of GATA proteins have yielded vital contributions to our understanding of how hematopoietic stem and progenitor cells develop from precursors, how progenitors generate red blood cells, how hemoglobin synthesis is regulated, and the molecular underpinnings of nonmalignant and malignant hematologic disorders. This thrilling journey began with mechanistic studies on a β-globin enhancer- and promoter-binding factor, GATA-1, the founding member of the GATA family. This work ushered in the cloning of related proteins, GATA-2-6, with distinct and/or overlapping expression patterns. Herein, we discuss how the hematopoietic GATA factors (GATA-1-3) function via a battery of mechanistic permutations, which can be GATA factor subtype, cell type, and locus specific. Understanding this intriguing protein family requires consideration of how the mechanistic permutations are amalgamated into circuits to orchestrate processes of interest to the hematologist and more broadly.
Collapse
|