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Kim SK, Liu X, Park J, Um D, Kilaru G, Chiang CM, Kang M, Huber KM, Kang K, Kim TK. Functional coordination of BET family proteins underlies altered transcription associated with memory impairment in fragile X syndrome. SCIENCE ADVANCES 2021; 7:7/21/eabf7346. [PMID: 34138732 PMCID: PMC8133748 DOI: 10.1126/sciadv.abf7346] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/30/2021] [Indexed: 05/07/2023]
Abstract
Bromodomain and extraterminal proteins (BET) are epigenetic readers that play critical roles in gene regulation. Pharmacologic inhibition of the bromodomain present in all BET family members is a promising therapeutic strategy for various diseases, but its impact on individual family members has not been well understood. Using a transcriptional induction paradigm in neurons, we have systematically demonstrated that three major BET family proteins (BRD2/3/4) participated in transcription with different recruitment kinetics, interdependency, and sensitivity to a bromodomain inhibitor, JQ1. In a mouse model of fragile X syndrome (FXS), BRD2/3 and BRD4 showed oppositely altered expression and chromatin binding, correlating with transcriptional dysregulation. Acute inhibition of CBP/p300 histone acetyltransferase (HAT) activity restored the altered binding patterns of BRD2 and BRD4 and rescued memory impairment in FXS. Our study emphasizes the importance of understanding the BET coordination controlled by a balanced action between HATs with different substrate specificity.
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Affiliation(s)
- Seung-Kyoon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Korea
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xihui Liu
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jongmin Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Korea
| | - Dahun Um
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Korea
| | - Gokhul Kilaru
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cheng-Ming Chiang
- Simmons Comprehensive Cancer Center, Department of Biochemistry, and Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mingon Kang
- Department of Computer Science, University of Nevada, Las Vegas, NV 89154, USA
| | - Kimberly M Huber
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Keunsoo Kang
- Department of Microbiology, Dankook University, Cheonan 31116, Korea.
| | - Tae-Kyung Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Korea.
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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202
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Hassanpour M, Biray Avci Ç, Rahbarghazi R, Rezabakhsh A, Nourazarian A, Nabat E, Fathi F, Khaksar M. Resveratrol reduced the detrimental effects of malondialdehyde on human endothelial cells. J Cardiovasc Thorac Res 2021; 13:131-140. [PMID: 34326967 PMCID: PMC8302894 DOI: 10.34172/jcvtr.2021.27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/11/2021] [Indexed: 11/18/2022] Open
Abstract
Introduction: According to the statistics, vascular injury occurs during the onset of diabetic changes after the production of several byproducts. Many authorities have focused to find an alternative therapy for diabetic patients. In this study, we investigated the therapeutic effects of natural polyphenol like resveratrol on human endothelial cells exposed to malondialdehyde for 48 hours. Methods: Human Umbilical Vein Endothelial Cells were randomly classified into four groups;control, malondialdehyde (2.5 mM), resveratrol (100 μM), and cells received the combined regime for 48 hours. Cell viability was determined by 3-(4, 5-dimethyl thiazol-2-yl) 2, 5-diphenyl-tetrazoliumbromide (MTT) assay. Griess reaction was performed to measure the content of Nitric oxide (NO).Apoptosis was studied by using real-time polymerase chain reaction (RT-PCR) and western blotting assays. Levels of receptor tyrosine kinases like VEGFR-1, -2, Tie-1, and -2 were analyzed by enzyme-linked immunosorbent assay(ELISA). The affinity of resveratrol and malondialdehyde to serum albumin was measured by Surface Plasmon Resonance Assay. Any changes in chromatin remodeling were detected by PCR array analysis. Results: Resveratrol reduced cytotoxicity and NO content inside cells induced by malondialdehyde(MDA) (P < 0.05). Endothelial cell apoptosis was decreased by the reduction of pro-apoptotic factor Bax and increase of Bcl-2 following the incubation with resveratrol (P < 0.05). MDA-induced receptor tyrosine kinases increase was inhibited by resveratrol and reached near-to-normal levels (P < 0.05).Surface Plasmon Resonance revealed a higher affinity of resveratrol to albumin compared to the malondialdehyde-albumin complex. Polymerase chain reaction (PCR) array revealed the potency of resveratrol in chromatin remodeling following the treatment with malondialdehyde (P < 0.05). Conclusion: Based on our findings, resveratrol has the potential to decrease diabetic vascular injury induced by lipid byproducts such as MDA.
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Affiliation(s)
- Mehdi Hassanpour
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Çıgır Biray Avci
- Department of Medical Biology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Reza Rahbarghazi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Aysa Rezabakhsh
- Cardiovascular Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Alireza Nourazarian
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elahe Nabat
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farzaneh Fathi
- Pharmaceutical Sciences Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Majid Khaksar
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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203
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Ghiboub M, Elfiky AMI, de Winther MPJ, Harker NR, Tough DF, de Jonge WJ. Selective Targeting of Epigenetic Readers and Histone Deacetylases in Autoimmune and Inflammatory Diseases: Recent Advances and Future Perspectives. J Pers Med 2021; 11:336. [PMID: 33922725 PMCID: PMC8145108 DOI: 10.3390/jpm11050336] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023] Open
Abstract
Histone deacetylases (HDACs) and bromodomain-containing proteins (BCPs) play a key role in chromatin remodeling. Based on their ability to regulate inducible gene expression in the context of inflammation and cancer, HDACs and BCPs have been the focus of drug discovery efforts, and numerous small-molecule inhibitors have been developed. However, dose-limiting toxicities of the first generation of inhibitors, which typically target multiple HDACs or BCPs, have limited translation to the clinic. Over the last decade, an increasing effort has been dedicated to designing class-, isoform-, or domain-specific HDAC or BCP inhibitors, as well as developing strategies for cell-specific targeted drug delivery. Selective inhibition of the epigenetic modulators is helping to elucidate the functions of individual epigenetic proteins and has the potential to yield better and safer therapeutic strategies. In accordance with this idea, several in vitro and in vivo studies have reported the ability of more selective HDAC/BCP inhibitors to recapitulate the beneficial effects of pan-inhibitors with less unwanted adverse events. In this review, we summarize the most recent advances with these strategies, discussing advantages and limitations of these approaches as well as some therapeutic perspectives, focusing on autoimmune and inflammatory diseases.
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Affiliation(s)
- Mohammed Ghiboub
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (M.G.); (A.M.I.E.)
- Adaptive Immunity Research Unit, Medicines Research Centre, GlaxoSmithKline, Stevenage SG1 2NY, UK; (N.R.H.); (D.F.T.)
| | - Ahmed M. I. Elfiky
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (M.G.); (A.M.I.E.)
- Adaptive Immunity Research Unit, Medicines Research Centre, GlaxoSmithKline, Stevenage SG1 2NY, UK; (N.R.H.); (D.F.T.)
| | - Menno P. J. de Winther
- Department of Medical Biochemistry, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
- Department of Medicine, Institute for Cardiovascular Prevention (IPEK), 80336 Munich, Germany
| | - Nicola R. Harker
- Adaptive Immunity Research Unit, Medicines Research Centre, GlaxoSmithKline, Stevenage SG1 2NY, UK; (N.R.H.); (D.F.T.)
| | - David F. Tough
- Adaptive Immunity Research Unit, Medicines Research Centre, GlaxoSmithKline, Stevenage SG1 2NY, UK; (N.R.H.); (D.F.T.)
| | - Wouter J. de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (M.G.); (A.M.I.E.)
- Department of Surgery, University of Bonn, 53127 Bonn, Germany
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204
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Das P, Badhe MR, Sahoo PK, Reddy RRK, Suryawanshi AR, Mohanty J. Immunoproteomic analysis of fish ectoparasite, Argulus siamensis antigens. Parasite Immunol 2021; 43:e12837. [PMID: 33811350 DOI: 10.1111/pim.12837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/25/2022]
Abstract
AIM An immunoproteomic approach was followed to identify immunoreactive antigens of fish ectoparasite, Argulus siamensis with rohu (Labeo rohita) immune sera for screening of potential vaccine candidates. MATERIALS AND RESULTS The whole adult Argulus antigen was run in 2D electrophoresis with IEF in 7 cm IPG strips of pH 4-7 and SDS-PAGE with 12% acrylamide concentration. Two parallel gels were run; one was stained with silver stain, and the other was Western blotted to nitrocellulose paper (NCP) and reacted with rohu anti-A siamensis sera. Fourteen protein spots corresponding to the spots developed in NCP were picked from the silver-stained gel and subjected to mass spectrometry in MALDI-TOF/TOF. The MS/MS spectra were analysed in MASCOT software with taxonomy 'other metazoa' and the proteins identified based on similarity with the proteins from heterologous species. The gene ontology analysis revealed a majority of proteins being involved in binding activity in 'molecular function' and belonging to metabolic processes in 'biologic process' categories. The possibility of these proteins as vaccine candidates against A siamensis is discussed in the paper. CONCLUSION Three of the identified proteins namely, bromodomain-containing protein, anaphase-promoting complex subunit 5 and elongation factor-2 could possibly serve as vaccine candidates against argulosis in carps.
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Affiliation(s)
- Priyanka Das
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
| | - Mohan R Badhe
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, India
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205
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Fang L, Hu Z, Yang Y, Chen P, Zhou J, Zhang H. Discovery of 3,5-dimethylisoxazole derivatives as novel, potent inhibitors for bromodomain and extraterminal domain (BET) family. Bioorg Med Chem 2021; 39:116133. [PMID: 33862375 DOI: 10.1016/j.bmc.2021.116133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 10/21/2022]
Abstract
Bromodomain and extra-terminal (BET) is a promising therapeutic target for various hematologic cancers. We used the BRD4 inhibitor compound 13 as a lead compound to develop a variety of compounds, and we introduced diverse groups into the position of the compound 13 orienting toward the ZA channel. A series of compounds (14-23, 38-41, 43, 47-49) bearing triazolopyridazine motif exhibited remarkable BRD4 protein inhibitory activities. Among them, compound 39 inhibited BRD4(BD1) protein with an IC50 of 0.003 μM was superior to lead compound 13. Meanwhile, compound 39 possess activity, IC50 = 2.1 μM, in antiproliferation activity against U266 cancer cells. On the other hand, compound 39 could arrest tumor cells into the G0/G1 phase and induce apoptosis, which was consistent with its results in inhibiting cell proliferation. Biological and biochemical data suggest that BRD4 protein might be a therapeutic target and that compound 39 is an excellent lead compound for further development.
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Affiliation(s)
- Lincheng Fang
- Center for Drug Discovery, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, China Pharmaceutical University, Nanjing 210009, PR China
| | - Zhaoxue Hu
- Center for Drug Discovery, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, China Pharmaceutical University, Nanjing 210009, PR China
| | - Yifei Yang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China
| | - Pan Chen
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, PR China
| | - Jinpei Zhou
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, PR China.
| | - Huibin Zhang
- Center for Drug Discovery, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, China Pharmaceutical University, Nanjing 210009, PR China.
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206
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Abstract
Nucleosomes wrap DNA and impede access for the machinery of transcription. The core histones that constitute nucleosomes are subject to a diversity of posttranslational modifications, or marks, that impact the transcription of genes. Their functions have sometimes been difficult to infer because the enzymes that write and read them are complex, multifunctional proteins. Here, we examine the evidence for the functions of marks and argue that the major marks perform a fairly small number of roles in either promoting transcription or preventing it. Acetylations and phosphorylations on the histone core disrupt histone-DNA contacts and/or destabilize nucleosomes to promote transcription. Ubiquitylations stimulate methylations that provide a scaffold for either the formation of silencing complexes or resistance to those complexes, and carry a memory of the transcriptional state. Tail phosphorylations deconstruct silencing complexes in particular contexts. We speculate that these fairly simple roles form the basis of transcriptional regulation by histone marks.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA;
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207
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Cao LJ, Zhang YJ, Dong SQ, Li XZ, Tong XT, Chen D, Wu ZY, Zheng XH, Xue WQ, Jia WH, Zhang JB. ATAD2 interacts with C/EBPβ to promote esophageal squamous cell carcinoma metastasis via TGF-β1/Smad3 signaling. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:109. [PMID: 33757572 PMCID: PMC7986551 DOI: 10.1186/s13046-021-01905-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 03/08/2021] [Indexed: 12/27/2022]
Abstract
Background Distant metastasis is the leading cause of death for esophageal squamous cell carcinoma (ESCC) with limited treatment options and unsatisfactory effectiveness. Bromodomain (BRD) containing proteins are emerging targets for cancer therapy with promising effects. As a unique member of BRD family, the function and molecular mechanism of ATAD2 in cancer development is seldomly investigated. Methods The clinical impact of ATAD2 was assessed both at RNA and protein level in 75 and 112 ESCC patients separately. The biological function of ATAD2 was investigated in vitro and in vivo. Signaling pathway and downstream effectors of ATAD2 were identified by RNA sequencing, luciferase reporter, co-immunoprecipitation, chromatin immunoprecipitation, immunofluorescence and western blot assay. Results We found that elevated ATAD2 expression was significantly associated with lymph node metastasis, advanced clinical stage as well as poor survival of ESCC patients. Silencing ATAD2 significantly suppressed ESCC cell migration and invasion in vitro, and inhibited tumor growth and lung metastasis in vivo. Mechanically, we identified a new cofactor, C/EBPβ. ATAD2 directly interacted with C/EBPβ and promoted its nuclear translocation, which directly bound to the promoter region of TGF-β1 and activated its expression. Further, we demonstrated that TGF-β1 activated its downstream effectors in a Smad3 dependent manner. In addition, we further found that ATAD2 promoted ESCC metastasis through TGF-β signaling induced Snail expression and the subsequent epithelial-mesenchymal transition. Conclusion Our findings demonstrated the pro-metastatic function of ATAD2 and uncovered the new molecular mechanism by regulating C/EBPβ/TGF-β1/Smad3/Snail signaling pathway, thus providing a potential target for the treatment of ESCC metastasis. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01905-x.
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Affiliation(s)
- Lian-Jing Cao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine,Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yi-Jun Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine,Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Si-Qi Dong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine,Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xi-Zhao Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine,Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xia-Ting Tong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine,Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dong Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine,Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zi-Yi Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine,Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiao-Hui Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine,Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wen-Qiong Xue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine,Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine,Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Jiang-Bo Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine,Sun Yat-sen University Cancer Center, Guangzhou, China.
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208
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Välimäki MJ, Leigh RS, Kinnunen SM, March AR, de Sande AH, Kinnunen M, Varjosalo M, Heinäniemi M, Kaynak BL, Ruskoaho H. GATA-targeted compounds modulate cardiac subtype cell differentiation in dual reporter stem cell line. Stem Cell Res Ther 2021; 12:190. [PMID: 33736688 PMCID: PMC7977156 DOI: 10.1186/s13287-021-02259-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/01/2021] [Indexed: 12/15/2022] Open
Abstract
Background Pharmacological modulation of cell fate decisions and developmental gene regulatory networks holds promise for the treatment of heart failure. Compounds that target tissue-specific transcription factors could overcome non-specific effects of small molecules and lead to the regeneration of heart muscle following myocardial infarction. Due to cellular heterogeneity in the heart, the activation of gene programs representing specific atrial and ventricular cardiomyocyte subtypes would be highly desirable. Chemical compounds that modulate atrial and ventricular cell fate could be used to improve subtype-specific differentiation of endogenous or exogenously delivered progenitor cells in order to promote cardiac regeneration. Methods Transcription factor GATA4-targeted compounds that have previously shown in vivo efficacy in cardiac injury models were tested for stage-specific activation of atrial and ventricular reporter genes in differentiating pluripotent stem cells using a dual reporter assay. Chemically induced gene expression changes were characterized by qRT-PCR, global run-on sequencing (GRO-seq) and immunoblotting, and the network of cooperative proteins of GATA4 and NKX2-5 were further explored by the examination of the GATA4 and NKX2-5 interactome by BioID. Reporter gene assays were conducted to examine combinatorial effects of GATA-targeted compounds and bromodomain and extraterminal domain (BET) inhibition on chamber-specific gene expression. Results GATA4-targeted compounds 3i-1000 and 3i-1103 were identified as differential modulators of atrial and ventricular gene expression. More detailed structure-function analysis revealed a distinct subclass of GATA4/NKX2-5 inhibitory compounds with an acetyl lysine-like domain that contributed to ventricular cells (%Myl2-eGFP+). Additionally, BioID analysis indicated broad interaction between GATA4 and BET family of proteins, such as BRD4. This indicated the involvement of epigenetic modulators in the regulation of GATA-dependent transcription. In this line, reporter gene assays with combinatorial treatment of 3i-1000 and the BET bromodomain inhibitor (+)-JQ1 demonstrated the cooperative role of GATA4 and BRD4 in the modulation of chamber-specific cardiac gene expression. Conclusions Collectively, these results indicate the potential for therapeutic alteration of cell fate decisions and pathological gene regulatory networks by GATA4-targeted compounds modulating chamber-specific transcriptional programs in multipotent cardiac progenitor cells and cardiomyocytes. The compound scaffolds described within this study could be used to develop regenerative strategies for myocardial regeneration. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-021-02259-z.
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Affiliation(s)
- Mika J Välimäki
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Helsinki, Finland
| | - Robert S Leigh
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Helsinki, Finland
| | - Sini M Kinnunen
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Helsinki, Finland
| | - Alexander R March
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Helsinki, Finland
| | - Ana Hernández de Sande
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Matias Kinnunen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Bogac L Kaynak
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Helsinki, Finland.
| | - Heikki Ruskoaho
- Drug Research Program, Division of Pharmacology and Pharmacotherapy, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, Helsinki, Finland.
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209
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Synthesis and Structure-Activity Relationships of Aristoyagonine Derivatives as Brd4 Bromodomain Inhibitors with X-ray Co-Crystal Research. Molecules 2021; 26:molecules26061686. [PMID: 33802888 PMCID: PMC8002823 DOI: 10.3390/molecules26061686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/08/2021] [Accepted: 03/10/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetic regulation is known to play a key role in progression of anti-cancer therapeutics. Lysine acetylation is an important mechanism in controlling gene expression. There has been increasing interest in bromodomain owing to its ability to modulate transcription of various genes as an epigenetic 'reader.' Herein, we report the design, synthesis, and X-ray studies of novel aristoyagonine (benzo[6,7]oxepino[4,3,2-cd]isoindol-2(1H)-one) derivatives and investigate their inhibitory effect against Brd4 bromodomain. Five compounds 8ab, 8bc, 8bd, 8be, and 8bf have been discovered with high binding affinity over the Brd4 protein. Co-crystal structures of these five inhibitors with human Brd4 bromodomain demonstrated that it has a key binding mode occupying the hydrophobic pocket, which is known to be the acetylated lysine binding site. These novel Brd4 bromodomain inhibitors demonstrated impressive inhibitory activity and mode of action for the treatment of cancer diseases.
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210
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Quezada E, Cappelli C, Diaz I, Jury N, Wightman N, Brown RH, Montecino M, van Zundert B. BET bromodomain inhibitors PFI-1 and JQ1 are identified in an epigenetic compound screen to enhance C9ORF72 gene expression and shown to ameliorate C9ORF72-associated pathological and behavioral abnormalities in a C9ALS/FTD model. Clin Epigenetics 2021; 13:56. [PMID: 33726839 PMCID: PMC7962347 DOI: 10.1186/s13148-021-01039-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/23/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND An intronic GGGGCC (G4C2) hexanucleotide repeat expansion (HRE) in the C9ORF72 gene is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), referred to as C9ALS/FTD. No cure or effective treatment exist for C9ALS/FTD. Three major molecular mechanisms have emerged to explain C9ALS/FTD disease mechanisms: (1) C9ORF72 loss-of-function through haploinsufficiency, (2) dipeptide repeat (DPR) proteins mediated toxicity by the translation of the repeat RNAs, and more controversial, (3) RNA-mediated toxicity by bidirectional transcription of the repeats that form intranuclear RNA foci. Recent studies indicate a double-hit pathogenic mechanism in C9ALS/FTD, where reduced C9ORF72 protein levels lead to impaired clearance of toxic DPRs. Here we explored whether pharmacological compounds can revert these pathological hallmarks in vitro and cognitive impairment in a C9ALS/FTD mouse model (C9BAC). We specifically focused our study on small molecule inhibitors targeting chromatin-regulating proteins (epidrugs) with the goal of increasing C9ORF72 gene expression and reduce toxic DPRs. RESULTS We generated luciferase reporter cell lines containing 10 (control) or ≥ 90 (mutant) G4C2 HRE located between exon 1a and 1b of the human C9ORF72 gene. In a screen of 14 different epidrugs targeting bromodomains, chromodomains and histone-modifying enzymes, we found that several bromodomain and extra-terminal domain (BET) inhibitors (BETi), including PFI-1 and JQ1, increased luciferase reporter activity. Using primary cortical cultures from C9BAC mice, we further found that PFI-1 treatment increased the expression of V1-V3 transcripts of the human mutant C9ORF72 gene, reduced poly(GP)-DPR inclusions but enhanced intranuclear RNA foci. We also tested whether JQ1, an BETi previously shown to reach the mouse brain by intraperitoneal (i.p.) injection, can revert behavioral abnormalities in C9BAC mice. Interestingly, it was found that JQ1 administration (daily i.p. administration for 7 days) rescued hippocampal-dependent cognitive deficits in C9BAC mice. CONCLUSIONS Our findings place BET bromodomain inhibitors as a potential therapy for C9ALS/FTD by ameliorating C9ORF72-associated pathological and behavioral abnormalities. Our finding that PFI-1 increases accumulation of intranuclear RNA foci is in agreement with recent data in flies suggesting that nuclear RNA foci can be neuroprotective by sequestering repeat transcripts that result in toxic DPRs.
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Affiliation(s)
- Esteban Quezada
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Claudio Cappelli
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Iván Diaz
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Nur Jury
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Nicholas Wightman
- Department of Neurology, University of Massachusetts Medical School (UMMS), Worcester, MA, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School (UMMS), Worcester, MA, USA
| | - Martín Montecino
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.
- FONDAP Center for Genome Regulation, Santiago, Chile.
| | - Brigitte van Zundert
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.
- Department of Neurology, University of Massachusetts Medical School (UMMS), Worcester, MA, USA.
- CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.
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211
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Browne JA, NandyMazumdar M, Paranjapye A, Leir SH, Harris A. The Bromodomain Containing 8 (BRD8) transcriptional network in human lung epithelial cells. Mol Cell Endocrinol 2021; 524:111169. [PMID: 33476703 PMCID: PMC8035426 DOI: 10.1016/j.mce.2021.111169] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/18/2020] [Accepted: 01/07/2021] [Indexed: 12/17/2022]
Abstract
Mechanisms regulating gene expression in the airway epithelium underlie its response to the environment. A network of transcription factors (TFs) and architectural proteins, modulate chromatin accessibility and recruit activating or repressive signals. Bromodomain-containing proteins function as TFs or by engaging methyltransferase or acetyltransferase activity to induce chromatin modifications. Here we investigate the role of Bromodomain Containing 8 (BRD8) in coordinating lung epithelial function. Sites of BRD8 occupancy genome-wide were mapped in human lung epithelial cell lines (Calu-3 and 16HBE14o-). CCCTC-Binding Factor (CTCF) was identified as a predicted co-factor of BRD8, based upon motif over-representation under BRD8 ChIP-seq peaks. Following siRNA-mediated depletion of BRD8, differentially expressed genes with nearby peaks of BRD8 occupancy were subject to gene ontology process enrichment analysis. BRD8 targets are enriched for genes involved in the innate immune response and the cell cycle. Depletion of BRD8 increased the secretion of the antimicrobial peptide beta-defensin 1 and multiple chemokines, and reduced cell proliferation.
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Affiliation(s)
- James A Browne
- Department of Genetics and Genome Sciences, Cleveland, OH, USA
| | | | | | - Shih-Hsing Leir
- Department of Genetics and Genome Sciences, Cleveland, OH, USA; Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, Cleveland, OH, USA; Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
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212
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Cribbs AP, Filippakopoulos P, Philpott M, Wells G, Penn H, Oerum H, Valge-Archer V, Feldmann M, Oppermann U. Dissecting the Role of BET Bromodomain Proteins BRD2 and BRD4 in Human NK Cell Function. Front Immunol 2021; 12:626255. [PMID: 33717143 PMCID: PMC7953504 DOI: 10.3389/fimmu.2021.626255] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/13/2021] [Indexed: 12/19/2022] Open
Abstract
Natural killer (NK) cells are innate lymphocytes that play a pivotal role in the immune surveillance and elimination of transformed or virally infected cells. Using a chemo-genetic approach, we identify BET bromodomain containing proteins BRD2 and BRD4 as central regulators of NK cell functions, including direct cytokine secretion, NK cell contact-dependent inflammatory cytokine secretion from monocytes as well as NK cell cytolytic functions. We show that both BRD2 and BRD4 control inflammatory cytokine production in NK cells isolated from healthy volunteers and from rheumatoid arthritis patients. In contrast, knockdown of BRD4 but not of BRD2 impairs NK cell cytolytic responses, suggesting BRD4 as critical regulator of NK cell mediated tumor cell elimination. This is supported by pharmacological targeting where the first-generation pan-BET bromodomain inhibitor JQ1(+) displays anti-inflammatory effects and inhibit tumor cell eradication, while the novel bivalent BET bromodomain inhibitor AZD5153, which shows differential activity towards BET family members, does not. Given the important role of both cytokine-mediated inflammatory microenvironment and cytolytic NK cell activities in immune-oncology therapies, our findings present a compelling argument for further clinical investigation.
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Affiliation(s)
- Adam P Cribbs
- Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, United Kingdom
| | | | - Martin Philpott
- Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, United Kingdom
| | - Graham Wells
- Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, United Kingdom
| | - Henry Penn
- Arthritis Centre, Northwick Park Hospital, Harrow, United Kingdom
| | - Henrik Oerum
- Roche Innovation Center Copenhagen A/S, Hørsholm, Denmark
| | - Viia Valge-Archer
- Bioscience, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Marc Feldmann
- Kennedy Institute of Rheumatology Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, Oxford, United Kingdom
| | - Udo Oppermann
- Botnar Research Center, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, National Institute of Health Research Oxford Biomedical Research Unit (BRU), University of Oxford, Oxford, United Kingdom.,Freiburg Institute of Advanced Studies, Freiburg, Germany.,Oxford Centre for Translational Myeloma Research, Oxford, United Kingdom
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213
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Paakinaho V, Lempiäinen JK, Sigismondo G, Niskanen EA, Malinen M, Jääskeläinen T, Varjosalo M, Krijgsveld J, Palvimo J. SUMOylation regulates the protein network and chromatin accessibility at glucocorticoid receptor-binding sites. Nucleic Acids Res 2021; 49:1951-1971. [PMID: 33524141 PMCID: PMC7913686 DOI: 10.1093/nar/gkab032] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 01/07/2021] [Accepted: 01/12/2021] [Indexed: 12/13/2022] Open
Abstract
Glucocorticoid receptor (GR) is an essential transcription factor (TF), controlling metabolism, development and immune responses. SUMOylation regulates chromatin occupancy and target gene expression of GR in a locus-selective manner, but the mechanism of regulation has remained elusive. Here, we identify the protein network around chromatin-bound GR by using selective isolation of chromatin-associated proteins and show that the network is affected by receptor SUMOylation, with several nuclear receptor coregulators and chromatin modifiers preferring interaction with SUMOylation-deficient GR and proteins implicated in transcriptional repression preferring interaction with SUMOylation-competent GR. This difference is reflected in our chromatin binding, chromatin accessibility and gene expression data, showing that the SUMOylation-deficient GR is more potent in binding and opening chromatin at glucocorticoid-regulated enhancers and inducing expression of target loci. Blockage of SUMOylation by a SUMO-activating enzyme inhibitor (ML-792) phenocopied to a large extent the consequences of GR SUMOylation deficiency on chromatin binding and target gene expression. Our results thus show that SUMOylation modulates the specificity of GR by regulating its chromatin protein network and accessibility at GR-bound enhancers. We speculate that many other SUMOylated TFs utilize a similar regulatory mechanism.
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Affiliation(s)
- Ville Paakinaho
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | | | | | - Einari A Niskanen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Marjo Malinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Tiina Jääskeläinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Jorma J Palvimo
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
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214
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Regadas I, Dahlberg O, Vaid R, Ho O, Belikov S, Dixit G, Deindl S, Wen J, Mannervik M. A unique histone 3 lysine 14 chromatin signature underlies tissue-specific gene regulation. Mol Cell 2021; 81:1766-1780.e10. [PMID: 33631105 DOI: 10.1016/j.molcel.2021.01.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/27/2021] [Accepted: 01/27/2021] [Indexed: 12/13/2022]
Abstract
Organismal development and cell differentiation critically depend on chromatin state transitions. However, certain developmentally regulated genes lack histone 3 lysine 9 and 27 acetylation (H3K9ac and H3K27ac, respectively) and histone 3 lysine 4 (H3K4) methylation, histone modifications common to most active genes. Here we describe a chromatin state featuring unique histone 3 lysine 14 acetylation (H3K14ac) peaks in key tissue-specific genes in Drosophila and human cells. Replacing H3K14 in Drosophila demonstrates that H3K14 is essential for expression of genes devoid of canonical histone modifications in the embryonic gut and larval wing imaginal disc, causing lethality and defective wing patterning. We find that the SWI/SNF protein Brahma (Brm) recognizes H3K14ac, that brm acts in the same genetic pathway as H3K14R, and that chromatin accessibility at H3K14ac-unique genes is decreased in H3K14R mutants. Our results show that acetylation of a single lysine is essential at genes devoid of canonical histone marks and uncover an important requirement for H3K14 in tissue-specific gene regulation.
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Affiliation(s)
- Isabel Regadas
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Olle Dahlberg
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Roshan Vaid
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Oanh Ho
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75237, Uppsala, Sweden
| | - Sergey Belikov
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Gunjan Dixit
- Department of Genome Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75237, Uppsala, Sweden
| | - Jiayu Wen
- Department of Genome Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600, Australia.
| | - Mattias Mannervik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden.
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215
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Patel K, Solomon PD, Walshe JL, Ford DJ, Wilkinson-White L, Payne RJ, Low JKK, Mackay JP. BET-Family Bromodomains Can Recognize Diacetylated Sequences from Transcription Factors Using a Conserved Mechanism. Biochemistry 2021; 60:648-662. [PMID: 33620209 DOI: 10.1021/acs.biochem.0c00816] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Almost all eukaryotic proteins receive diverse post-translational modifications (PTMs) that modulate protein activity. Many histone PTMs are well characterized, heavily influence gene regulation, and are often predictors of distinct transcriptional programs. Although our understanding of the histone PTM network has matured, much is yet to be understood about the roles of transcription factor (TF) PTMs, which might well represent a similarly complex and dynamic network of functional regulation. Members of the bromodomain and extra-terminal domain (BET) family of proteins recognize acetyllysine residues and relay the signals encoded by these modifications. Here, we have investigated the acetylation dependence of several functionally relevant BET-TF interactions in vitro using surface plasmon resonance, nuclear magnetic resonance, and X-ray crystallography. We show that motifs known to be acetylated in TFs E2F1 and MyoD1 can interact with all bromodomains of BRD2, BRD3, and BRD4. The interactions are dependent on diacetylation of the motifs and show a preference for the first BET bromodomain. Structural mapping of the interactions confirms a conserved mode of binding for the two TFs to the acetyllysine binding pocket of the BET bromodomains, mimicking that of other already established functionally important histone- and TF-BET interactions. We also examined a motif from the TF RelA that is known to be acetylated but were unable to observe any interaction, regardless of the acetylation state of the sequence. Our findings overall advance our understanding of BET-TF interactions and suggest a physical link between the important diacetylated motifs found in E2F1 and MyoD1 and the BET-family proteins.
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Affiliation(s)
- Karishma Patel
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Paul D Solomon
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - James L Walshe
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Daniel J Ford
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | | | - Richard J Payne
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
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216
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Combinations of histone post-translational modifications. Biochem J 2021; 478:511-532. [DOI: 10.1042/bcj20200170] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 01/13/2021] [Accepted: 01/18/2021] [Indexed: 12/20/2022]
Abstract
Histones are essential proteins that package the eukaryotic genome into its physiological state of nucleosomes, chromatin, and chromosomes. Post-translational modifications (PTMs) of histones are crucial to both the dynamic and persistent regulation of the genome. Histone PTMs store and convey complex signals about the state of the genome. This is often achieved by multiple variable PTM sites, occupied or unoccupied, on the same histone molecule or nucleosome functioning in concert. These mechanisms are supported by the structures of ‘readers’ that transduce the signal from the presence or absence of PTMs in specific cellular contexts. We provide background on PTMs and their complexes, review the known combinatorial function of PTMs, and assess the value and limitations of common approaches to measure combinatorial PTMs. This review serves as both a reference and a path forward to investigate combinatorial PTM functions, discover new synergies, and gather additional evidence supporting that combinations of histone PTMs are the central currency of chromatin-mediated regulation of the genome.
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217
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Xiong L, Mao X, Guo Y, Zhou Y, Chen M, Chen P, Yang S, Li L. Discovery of selective BPTF bromodomain inhibitors by screening and structure-based optimization. Biochem Biophys Res Commun 2021; 545:125-131. [PMID: 33548625 DOI: 10.1016/j.bbrc.2021.01.067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 01/20/2021] [Indexed: 02/08/2023]
Abstract
Bromodomain and PHD finger containing transcription factor (BPTF) is a multidomain protein that regulates the transcription of chromatin and is related to many cancers. Herein, we report the screening-based discovery of Cpd1, a compound with micromolar affinity to the BPTF bromodomain. Through structure-guided optimization, we synthesized a variety of new inhibitors. Among these compounds, Cpd8 and Cpd10 were highly potent and selective inhibitors, with KD values of 428 nM and 655 nM in ITC assays, respectively. The high activity was explained by the cocrystal structure of Cpd8 in complex with the BPTF bromodomain protein. Cpd8 and Cpd10 were able to stabilize the BPTF bromodomain protein in cells in a cellular thermal shift assay (CETSA). Cpd8 downregulated c-MYC expression in A549 cells. All experiments prove that these two compounds are potential BPTF inhibitors.
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Affiliation(s)
- Liang Xiong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Xin Mao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Yinping Guo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Yangli Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Mingxin Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Pei Chen
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Shengyong Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Linli Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China.
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218
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Abstract
BACKGROUND Bromodomain and extra-terminal (BET) proteins are epigenetic readers that bind to acetylated lysines of histones and regulate gene transcription. BET protein family members mediate the expression of various oncogenic drivers in ovarian cancer, such as the MYC and Neuregulin 1 (NRG1) genes. BRD4, the most thoroughly studied member of the BET family, is amplified in a significant subset of high-grade serous carcinomas (HGSC) of the ovary. It has been reported that BET inhibitors can attenuate the proliferation and dissemination of ovarian cancer cells by inhibiting oncogenic pathways, such as the FOXM1 and JAK/STAT pathways. BET inhibition can re-sensitize resistant ovarian cancer cells to already approved anticancer agents, including cisplatin and PARP inhibitors. This synergism was also confirmed in vivo in animal models. These and other preclinical results provide a promising basis for the application of BET inhibitors in ovarian cancer treatment. Currently, Phase I/II clinical trials explore the safety and efficacy profiles of BET inhibitors in various solid tumors, including ovarian tumors. Here, we review current knowledge on the molecular effects and preclinical activities of BET inhibitors in ovarian tumors. CONCLUSIONS BET proteins have emerged as new druggable targets for ovarian cancer. BET inhibitors may enhance antitumor activity when co-administered with conventional treatment regimens. Results from ongoing Phase I/II studies are anticipated to confirm this notion.
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219
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Wang N, Wu R, Tang D, Kang R. The BET family in immunity and disease. Signal Transduct Target Ther 2021; 6:23. [PMID: 33462181 PMCID: PMC7813845 DOI: 10.1038/s41392-020-00384-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/27/2020] [Accepted: 10/20/2020] [Indexed: 12/19/2022] Open
Abstract
Innate immunity serves as the rapid and first-line defense against invading pathogens, and this process can be regulated at various levels, including epigenetic mechanisms. The bromodomain and extraterminal domain (BET) family of proteins consists of four conserved mammalian members (BRD2, BRD3, BRD4, and BRDT) that regulate the expression of many immunity-associated genes and pathways. In particular, in response to infection and sterile inflammation, abnormally expressed or dysfunctional BETs are involved in the activation of pattern recognition receptor (e.g., TLR, NLR, and CGAS) pathways, thereby linking chromatin machinery to innate immunity under disease or pathological conditions. Mechanistically, the BET family controls the transcription of a wide range of proinflammatory and immunoregulatory genes by recognizing acetylated histones (mainly H3 and H4) and recruiting transcription factors (e.g., RELA) and transcription elongation complex (e.g., P-TEFb) to the chromatin, thereby promoting the phosphorylation of RNA polymerase II and subsequent transcription initiation and elongation. This review covers the accumulating data about the roles of the BET family in innate immunity, and discusses the attractive prospect of manipulating the BET family as a new treatment for disease.
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Affiliation(s)
- Nian Wang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Runliu Wu
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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220
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Noberini R, Robusti G, Bonaldi T. Mass spectrometry-based characterization of histones in clinical samples: applications, progresses, and challenges. FEBS J 2021; 289:1191-1213. [PMID: 33415821 PMCID: PMC9291046 DOI: 10.1111/febs.15707] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/24/2020] [Accepted: 01/06/2021] [Indexed: 12/12/2022]
Abstract
In the last 15 years, increasing evidence linking epigenetics to various aspects of cancer biology has prompted the investigation of histone post-translational modifications (PTMs) and histone variants in the context of clinical samples. The studies performed so far demonstrated the potential of this type of investigations for the discovery of both potential epigenetic biomarkers for patient stratification and novel epigenetic mechanisms potentially targetable for cancer therapy. Although traditionally the analysis of histones in clinical samples was performed through antibody-based methods, mass spectrometry (MS) has emerged as a more powerful tool for the unbiased, comprehensive, and quantitative investigation of histone PTMs and variants. MS has been extensively used for the analysis of epigenetic marks in cell lines and animal tissue and, thanks to recent technological advances, is now ready to be applied also to clinical samples. In this review, we will provide an overview on the quantitative MS-based analysis of histones, their PTMs and their variants in cancer clinical samples, highlighting current achievements and future perspectives for this novel field of research. Among the different MS-based approaches currently available for histone PTM profiling, we will focus on the 'bottom-up' strategy, namely the analysis of short proteolytic peptides, as it has been already successfully employed for the analysis of clinical samples.
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Affiliation(s)
- Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Giulia Robusti
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
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221
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Iyer H, Wahul AB, P K A, Sawant BS, Kumar A. A BRD's (BiRD's) eye view of BET and BRPF bromodomains in neurological diseases. Rev Neurosci 2021; 32:403-426. [PMID: 33661583 DOI: 10.1515/revneuro-2020-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/11/2020] [Indexed: 01/18/2023]
Abstract
Neurological disorders (NLDs) are among the top leading causes for disability worldwide. Dramatic changes in the epigenetic topography of the brain and nervous system have been found in many NLDs. Histone lysine acetylation has prevailed as one of the well characterised epigenetic modifications in these diseases. Two instrumental components of the acetylation machinery are the evolutionarily conserved Bromodomain and PHD finger containing (BRPF) and Bromo and Extra terminal domain (BET) family of proteins, also referred to as acetylation 'readers'. Several reasons, including their distinct mechanisms of modulation of gene expression and their property of being highly tractable small molecule targets, have increased their translational relevance. Thus, compounds which demonstrated promising results in targeting these proteins have advanced to clinical trials. They have been established as key role players in pathologies of cancer, cardiac diseases, renal diseases and rheumatic diseases. In addition, studies implicating the role of these bromodomains in NLDs are gaining pace. In this review, we highlight the findings of these studies, and reason for the plausible roles of all BET and BRPF members in NLDs. A comprehensive understanding of their multifaceted functions would be radical in the development of therapeutic interventions.
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Affiliation(s)
- Harish Iyer
- Epigenetics and Neuropsychiatric Disorders' Laboratory, CSIR - Centre for Cellular and Molecular Biology (CCMB), Hyderabad500007, India
| | - Abhipradnya B Wahul
- Epigenetics and Neuropsychiatric Disorders' Laboratory, CSIR - Centre for Cellular and Molecular Biology (CCMB), Hyderabad500007, India
| | - Annapoorna P K
- Epigenetics and Neuropsychiatric Disorders' Laboratory, CSIR - Centre for Cellular and Molecular Biology (CCMB), Hyderabad500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
| | - Bharvi S Sawant
- Epigenetics and Neuropsychiatric Disorders' Laboratory, CSIR - Centre for Cellular and Molecular Biology (CCMB), Hyderabad500007, India
| | - Arvind Kumar
- Epigenetics and Neuropsychiatric Disorders' Laboratory, CSIR - Centre for Cellular and Molecular Biology (CCMB), Hyderabad500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
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222
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Ma K, Han XX, Yang XM, Zhou SL. Proteolysis targeting chimera technology: a novel strategy for treating diseases of the central nervous system. Neural Regen Res 2021; 16:1944-1949. [PMID: 33642364 PMCID: PMC8343312 DOI: 10.4103/1673-5374.308075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Neurological diseases such as stroke, Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease are among the intractable diseases for which appropriate drugs and treatments are lacking. Proteolysis targeting chimera (PROTAC) technology is a novel strategy to solve this problem. PROTAC technology uses the ubiquitin-protease system to eliminate mutated, denatured, and harmful proteins in cells. It can be reused, and utilizes the protein destruction mechanism of the cells, thus making up for the deficiencies of traditional protein degradation methods. It can effectively target and degrade proteins, including proteins that are difficult to identify and bind. Therefore, it has extremely important implications for drug development and the treatment of neurological diseases. At present, the targeted degradation of mutant BTK, mHTT, Tau, EGFR, and other proteins using PROTAC technology is gaining attention. It is expected that corresponding treatment of nervous system diseases can be achieved. This review first focuses on the recent developments in PROTAC technology in terms of protein degradation, drug production, and treatment of central nervous system diseases, and then discusses its limitations. This review will provide a brief overview of the recent application of PROTAC technology in the treatment of central nervous system diseases.
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Affiliation(s)
- Ke Ma
- College of Life Science, Nantong University, Nantong, Jiangsu Province, China
| | - Xiao-Xiao Han
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Xiao-Ming Yang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
| | - Song-Lin Zhou
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu Province, China
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223
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Damiani E, Duran MN, Mohan N, Rajendran P, Dashwood RH. Targeting Epigenetic 'Readers' with Natural Compounds for Cancer Interception. J Cancer Prev 2020; 25:189-203. [PMID: 33409252 PMCID: PMC7783241 DOI: 10.15430/jcp.2020.25.4.189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/03/2020] [Accepted: 12/05/2020] [Indexed: 12/14/2022] Open
Abstract
Natural compounds from diverse sources, including botanicals and commonly consumed foods and beverages, exert beneficial health effects via mechanisms that impact the epigenome and gene expression during disease pathogenesis. By targeting the so-called epigenetic 'readers', 'writers', and 'erasers', dietary phytochemicals can reverse abnormal epigenome signatures in cancer cells and preneoplastic stages. Thus, such agents provide avenues for cancer interception via prevention or treatment/therapeutic strategies. To date, much of the focus on dietary agents has been directed towards writers (e.g., histone acetyltransferases) and erasers (e.g., histone deacetylases), with less attention given to epigenetic readers (e.g., BRD proteins). The drug JQ1 was developed as a prototype epigenetic reader inhibitor, selectively targeting members of the bromodomain and extraterminal domain (BET) family, such as BRD4. Clinical trials with JQ1 as a single agent, or in combination with standard of care therapy, revealed antitumor efficacy but not without toxicity or resistance. In pursuit of second-generation epigenetic reader inhibitors, attention has shifted to natural sources, including dietary agents that might be repurposed as 'JQ1-like' bioactives. This review summarizes the current status of nascent research activity focused on natural compounds as inhibitors of BET and other epigenetic 'reader' proteins, with a perspective on future directions and opportunities.
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Affiliation(s)
- Elisabetta Damiani
- Department of Life and Environmental Sciences, Polytechnic University of the Marche, Ancona, Italy
| | - Munevver N. Duran
- Center for Epigenetics & Disease Prevention, Texas A&M Health Science Center, TX, USA
| | - Nivedhitha Mohan
- Center for Epigenetics & Disease Prevention, Texas A&M Health Science Center, TX, USA
| | - Praveen Rajendran
- Center for Epigenetics & Disease Prevention, Texas A&M Health Science Center, TX, USA
| | - Roderick H. Dashwood
- Center for Epigenetics & Disease Prevention, Texas A&M Health Science Center, TX, USA
- Department of Translational Medical Sciences, Texas A&M College of Medicine, Houston, TX, USA
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224
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Gomathi K, Akshaya N, Srinaath N, Rohini M, Selvamurugan N. Histone acetyl transferases and their epigenetic impact on bone remodeling. Int J Biol Macromol 2020; 170:326-335. [PMID: 33373635 DOI: 10.1016/j.ijbiomac.2020.12.173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 12/13/2022]
Abstract
Bone remodeling is a complex event that maintains bone homeostasis. The epigenetic mechanism of the regulation of bone remodeling has been a major research focus over the past decades. Histone acetylation is an influential post-translational modification in chromatin architecture. Acetylation affects chromatin structure by offering binding signals for reader proteins that harbor acetyl-lysine recognition domains. This review summarizes recent data of histone acetylation in bone remodeling. The crux of this review is the functional role of histone acetyltransferases, the key promoters of histone acetylation. The functional regulation of acetylation via noncoding RNAs in bone remodeling is also discussed. Understanding the principles governing histone acetylation in bone remodeling would lead to the development of better epigenetic therapies for bone diseases.
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Affiliation(s)
- K Gomathi
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - N Akshaya
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - N Srinaath
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - M Rohini
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - N Selvamurugan
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India.
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225
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Zhu X, Liao Y, Tang L. Targeting BRD9 for Cancer Treatment: A New Strategy. Onco Targets Ther 2020; 13:13191-13200. [PMID: 33380808 PMCID: PMC7769155 DOI: 10.2147/ott.s286867] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/12/2020] [Indexed: 01/01/2023] Open
Abstract
Bromodomain-containing protein 9 (BRD9) is a newly identified subunit of the non-canonical barrier-to-autointegration factor (ncBAF) complex and a member of the bromodomain family IV. Studies have confirmed that BRD9 plays an oncogenic role in multiple cancer types, by regulating tumor cell growth. The tumor biological functions of BRD9 are mainly due to epigenetic modification mediated by its bromodomain. The bromodomain recruits the ncBAF complex to the promoter to regulate gene transcription. This review summarizes the potential mechanisms of action of BRD9 in carcinogenesis and the emerging strategies for targeting BRD9 for cancer therapeutics. Although the therapeutic potential of BRD9 has been exploited to some extent, research on the detailed biological mechanisms of BRD9 is still in its infancy. Therefore, targeting BRD9 to study its biological roles will be an attractive tool for cancer diagnosis and treatment, but it remains a great challenge.
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Affiliation(s)
- Xiuzuo Zhu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, People's Republic of China
| | - Yi Liao
- Department of Thoracic Surgery, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, People's Republic of China
| | - Liling Tang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, People's Republic of China
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226
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Yang Z, Zhou Y, Zhong L. Discovery of BAZ1A bromodomain inhibitors with the aid of virtual screening and activity evaluation. Bioorg Med Chem Lett 2020; 33:127745. [PMID: 33333161 DOI: 10.1016/j.bmcl.2020.127745] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 02/05/2023]
Abstract
BAZ1A is a bromodomain-containing protein, and has been recognized as a potential target for multiple diseases, particularly cancer. However, there is no BAZ1A inhibitor reported so far. In this study, we used a consensus docking/scoring strategy to screen for BAZ1A bromodomain inhibitors from commercial chemical libraries and an in-house chemical database. The retrieved hit compounds were evaluated experimentally and four compounds were found to be active against BAZ1A bromodomain. To the most active compounds, similarity and substructure searches were used to find more BAZ1A bromodomain inhibitors. Among all the obtained active compounds, Cpd-2 is the most potent one, which showed a KD value of 0.52 μM. The interaction model of Cpd-2 with BAZ1A bromodomain was revealed by molecular docking. In a cellular assay, Cpd-2 displayed good anti-viability activity against cancer cell lines expressing a high level of BAZ1A. Overall, we discovered a number of BAZ1A bromodomain inhibitors for the first time, which can be a good starting point for subsequent drug discovery targeting BAZ1A bromodomain.
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Affiliation(s)
- Zhenyu Yang
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China; School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0250, USA
| | - Yangli Zhou
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lei Zhong
- Personalized Drug Therapy Key Laboratory of Sichuan Province, Department of Pharmacy, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 610072, China.
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227
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Biomolecular condensates as arbiters of biochemical reactions inside the nucleus. Commun Biol 2020; 3:773. [PMID: 33319830 PMCID: PMC7738674 DOI: 10.1038/s42003-020-01517-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/24/2020] [Indexed: 12/20/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) has emerged as a central player in the assembly of membraneless compartments termed biomolecular condensates. These compartments are dynamic structures that can condense or dissolve under specific conditions to regulate molecular functions. Such properties allow biomolecular condensates to rapidly respond to changing endogenous or environmental conditions. Here, we review emerging roles for LLPS within the nuclear space, with a specific emphasis on genome organization, expression and repair. Our review highlights the emerging notion that biomolecular condensates regulate the sequential engagement of molecules in multistep biological processes. Laflamme and Mekhail discuss emerging nuclear roles for LLPS in genome organization, gene expression and DNA repair, highlighting the emerging notion that biomolecular condensates regulate the sequential engagement of molecules in multistep biological processes.
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228
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Combinatorial Epigenetic and Immunotherapy in Breast Cancer Management: A Literature Review. EPIGENOMES 2020; 4:epigenomes4040027. [PMID: 34968306 PMCID: PMC8594694 DOI: 10.3390/epigenomes4040027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 12/27/2022] Open
Abstract
Breast cancer is one of the leading causes of death among cancer patients worldwide. To date, there are several drugs that have been developed for breast cancer therapy. In the 21st century, immunotherapy is considered a pioneering method for improving the management of malignancies; however, breast cancer is an exception. According to the immunoediting model, many immunosuppressive cells contribute to immunological quiescence. Therefore, there is an urgent need to enhance the therapeutic efficacy of breast cancer treatments. In the last few years, numerous combinatorial therapies involving immune checkpoint blockade have been demonstrated that effectively improve clinical outcomes in breast cancer and combining these with methods of targeting epigenetic regulators is also an innovative strategy. Nevertheless, few studies have discussed the benefits of epi-drugs in non-cancerous cells. In this review, we give a brief overview of ongoing clinical trials involving combinatorial immunotherapy with epi-drugs in breast cancer and discuss the role of epi-drugs in the tumor microenvironment, including the results of recent research.
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229
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Tomaselli D, Mautone N, Mai A, Rotili D. Recent advances in epigenetic proteolysis targeting chimeras (Epi-PROTACs). Eur J Med Chem 2020; 207:112750. [DOI: 10.1016/j.ejmech.2020.112750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 01/03/2023]
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230
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USP24 stabilizes bromodomain containing proteins to promote lung cancer malignancy. Sci Rep 2020; 10:20870. [PMID: 33257797 PMCID: PMC7705756 DOI: 10.1038/s41598-020-78000-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/11/2020] [Indexed: 01/21/2023] Open
Abstract
Bromodomain (BRD)-containing proteins are important for chromatin remodeling to regulate gene expression. In this study, we found that the deubiquitinase USP24 interacted with BRD through its C-terminus increased the levels of most BRD-containing proteins through increasing their protein stability by the removal of ubiquitin from Lys391/Lys400 of the BRD. In addition, we found that USP24 and BRG1 could regulate each other through regulating the protein stability and the transcriptional activity, respectively, of the other, suggesting that the levels of USP24 and BRG1 are regulated to form a positive feedback loop in cancer progression. Loss of the interaction motif of USP24 eliminated the ability of USP24 to stabilize BRD-containing proteins and abolished the effect of USP24 on cancer progression, including its inhibition of cancer cell proliferation and promotion of cancer cell migration, suggesting that the interaction between USP24 and the BRD is important for USP24-mediated effects on cancer progression. The targeting of BRD-containing proteins has been developed as a strategy for cancer therapy. Based on our study, targeting USP24 to inhibit the levels of BRD-containing proteins may inhibit cancer progression.
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231
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Patel K, Solomon PD, Walshe JL, Low JKK, Mackay JP. The bromodomains of BET family proteins can recognize diacetylated histone H2A.Z. Protein Sci 2020; 30:464-476. [PMID: 33247496 DOI: 10.1002/pro.4006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/21/2020] [Accepted: 11/24/2020] [Indexed: 02/02/2023]
Abstract
Chemical modifications of histone tails influence genome accessibility and the transcriptional state of eukaryotic cells. Lysine acetylation is one of the most common modifications and acetyllysine-binding bromodomains (BDs) provide a means for acetyllysine marks to be translated into meaningful cellular responses. Here, we have investigated the mechanism underlying the reported association between the Bromodomain and Extra Terminal (BET) family of BD proteins and the essential histone variant H2A.Z. We use NMR spectroscopy to demonstrate a physical interaction between the N-terminal tail of H2A.Z and the BDs of BRD2, BRD3, and BRD4, and show that the interaction is dependent on lysine acetylation in H2A.Z. The BDs preferentially engage a diacetylated H2A.Z-K4acK7ac motif that is reminiscent of sequences found in other biologically important BET BD target proteins, including histones and transcription factors. A H2A.Z-K7acK11ac motif can also bind BET BDs-with a preference for the second BD of each protein. Chemical shift perturbation mapping of the interactions, together with an X-ray crystal structure of BRD2-BD1 bound to H2A.Z-K4acK7ac, shows that H2A.Z binds the canonical AcK binding pocket of the BDs. This mechanism mirrors the conserved binding mode that is unique to the BET BDs, in which two acetylation marks are read simultaneously by a single BD. Our findings provide structural corroboration of biochemical and cell biological data that link H2A.Z and BET-family proteins, suggesting that the function of H2A.Z is enacted through interactions with these chromatin readers.
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Affiliation(s)
- Karishma Patel
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Paul D Solomon
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - James L Walshe
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia.,Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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232
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Kalra P, McGraw L, Kimbrough JR, Pandey AK, Solberg J, Cui H, Divakaran A, John K, Hawkinson JE, Pomerantz WCK. Quantifying the Selectivity of Protein-Protein and Small Molecule Interactions with Fluorinated Tandem Bromodomain Reader Proteins. ACS Chem Biol 2020; 15:3038-3049. [PMID: 33138352 PMCID: PMC8185897 DOI: 10.1021/acschembio.0c00720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Multidomain bromodomain-containing proteins regulate gene expression via chromatin binding, interactions with the transcriptional machinery, and by recruiting enzymatic activity. Selective inhibition of members of the bromodomain and extra-terminal (BET) family is important to understand their role in disease and gene regulation, although due to the similar binding sites of BET bromodomains, selective inhibitor discovery has been challenging. To support the bromodomain inhibitor discovery process, here we report the first application of protein-observed fluorine (PrOF) NMR to the tandem bromodomains of BRD4 and BRDT to quantify the selectivity of their interactions with acetylated histones as well as small molecules. We further determine the selectivity profile of a new class of ligands, 1,4-acylthiazepanes, and find them to have ≥3-10-fold selectivity for the C-terminal bromodomain of both BRD4 and BRDT. Given the speed and lower protein concentration required over traditional protein-observed NMR methods, we envision that these fluorinated tandem proteins may find use in fragment screening and evaluating nucleosome and transcription factor interactions.
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Affiliation(s)
- Prakriti Kalra
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Logan McGraw
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Jennifer R Kimbrough
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Anil K Pandey
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Jonathan Solberg
- Institute for Therapeutics Discovery and Development, Department of Medicinal Chemistry, University of Minnesota, 717 Delaware Street SE, Minneapolis, Minnesota 55414, United States
| | - Huarui Cui
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - Anand Divakaran
- Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth St. SE, Minneapolis, Minnesota 55455, United States
| | - Kristen John
- Institute for Therapeutics Discovery and Development, Department of Medicinal Chemistry, University of Minnesota, 717 Delaware Street SE, Minneapolis, Minnesota 55414, United States
| | - Jon E Hawkinson
- Institute for Therapeutics Discovery and Development, Department of Medicinal Chemistry, University of Minnesota, 717 Delaware Street SE, Minneapolis, Minnesota 55414, United States
- Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth St. SE, Minneapolis, Minnesota 55455, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
- Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth St. SE, Minneapolis, Minnesota 55455, United States
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233
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Lee D, Lee DY, Hwang YS, Seo HR, Lee SA, Kwon J. The Bromodomain Inhibitor PFI-3 Sensitizes Cancer Cells to DNA Damage by Targeting SWI/SNF. Mol Cancer Res 2020; 19:900-912. [PMID: 33208498 DOI: 10.1158/1541-7786.mcr-20-0289] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 09/17/2020] [Accepted: 11/13/2020] [Indexed: 11/16/2022]
Abstract
Many chemotherapeutic drugs produce double-strand breaks (DSB) on cancer cell DNA, thereby inducing cell death. However, the DNA damage response (DDR) enables cancer cells to overcome DNA damage and escape cell death, often leading to therapeutic resistance and unsuccessful outcomes. It is therefore important to develop inhibitors that target DDR proteins to render cancer cells hypersensitive to DNA damage. Here, we investigated the applicability of PFI-3, a recently developed bromodomain inhibitor specifically targeting the SWI/SNF chromatin remodeler that functions to promote DSB repair, in cancer treatment. We verified that PFI-3 effectively blocks chromatin binding of its target bromodomains and dissociates the corresponding SWI/SNF proteins from chromatin. We then found that, while having little toxicity as a single agent, PFI-3 synergistically sensitizes several human cancer cell lines to DNA damage induced by chemotherapeutic drugs such as doxorubicin. This PFI-3 activity occurs only for the cancer cells that require SWI/SNF for DNA repair. Our mechanism studies show that PFI-3 exerts the DNA damage-sensitizing effect by directly blocking SWI/SNF's chromatin binding, which leads to defects in DSB repair and aberrations in damage checkpoints, eventually resulting in increase of cell death primarily via necrosis and senescence. This work therefore demonstrates the activity of PFI-3 to sensitize cancer cells to DNA damage and its mechanism of action via SWI/SNF targeting, providing an experimental rationale for developing PFI-3 as a sensitizing agent in cancer chemotherapy. IMPLICATIONS: This study, revealing the activity of PFI-3 to sensitize cancer cells to chemotherapeutic drugs, provides an experimental rationale for developing this bromodomain inhibitor as a sensitizing agent in cancer chemotherapy.
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Affiliation(s)
- Daye Lee
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, Republic of South Korea
| | - Da-Yeon Lee
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, Republic of South Korea
| | - You-Son Hwang
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, Republic of South Korea
| | - Hye-Ran Seo
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, Republic of South Korea
| | - Shin-Ai Lee
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, Republic of South Korea
| | - Jongbum Kwon
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, Republic of South Korea.
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234
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Espejo I, Di Croce L, Aranda S. The changing chromatome as a driver of disease: A panoramic view from different methodologies. Bioessays 2020; 42:e2000203. [PMID: 33169398 DOI: 10.1002/bies.202000203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/27/2020] [Indexed: 12/16/2022]
Abstract
Chromatin-bound proteins underlie several fundamental cellular functions, such as control of gene expression and the faithful transmission of genetic and epigenetic information. Components of the chromatin proteome (the "chromatome") are essential in human life, and mutations in chromatin-bound proteins are frequently drivers of human diseases, such as cancer. Proteomic characterization of chromatin and de novo identification of chromatin interactors could, thus, reveal important and perhaps unexpected players implicated in human physiology and disease. Recently, intensive research efforts have focused on developing strategies to characterize the chromatome composition. In this review, we provide an overview of the dynamic composition of the chromatome, highlight the importance of its alterations as a driving force in human disease (and particularly in cancer), and discuss the different approaches to systematically characterize the chromatin-bound proteome in a global manner.
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Affiliation(s)
- Isabel Espejo
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.,UniversitatPompeuFabra (UPF), Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Sergi Aranda
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
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235
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Dusek CO, Hadden MK. Targeting the GLI family of transcription factors for the development of anti-cancer drugs. Expert Opin Drug Discov 2020; 16:289-302. [PMID: 33006903 DOI: 10.1080/17460441.2021.1832078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION GLI1 is a transcription factor that has been identified as a downstream effector for multiple tumorigenic signaling pathways. These include the Hedgehog, RAS-RAF-MEK-ERK, and PI3K-AKT-mTOR pathways, which have all been separately validated as individual anti-cancer drug targets. The identification of GLI1 as a key transcriptional regulator for each of these pathways highlights its promise as a therapeutic target. Small molecule GLI1 inhibitors are potentially efficacious against human malignancies arising from multiple oncogenic mechanisms. AREAS COVERED This review provides an overview of the key oncogenic cellular pathways that regulate GLI1 transcriptional activity. It also provides a detailed account of small molecule GLI1 inhibitors that are currently under development as potential anti-cancer chemotherapeutics. EXPERT OPINION Interest in developing inhibitors of GLI1-mediated transcription has significantly increased as its role in multiple oncogenic signaling pathways has been elucidated. To date, it has proven difficult to directly target GLI1 with small molecules, and the majority of compounds that inhibit GLI1 activity function through indirect mechanisms. To date, no direct-acting GLI1 inhibitor has entered clinical trials. The identification and development of new scaffolds that can bind and directly inhibit GLI1 are essential to further advance this class of chemotherapeutics.
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Affiliation(s)
- Christopher O Dusek
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, United States
| | - M Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, United States
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236
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Lotke R, Schneeweiß U, Pietrek M, Günther T, Grundhoff A, Weidner-Glunde M, Schulz TF. Brd/BET Proteins Influence the Genome-Wide Localization of the Kaposi's Sarcoma-Associated Herpesvirus and Murine Gammaherpesvirus Major Latency Proteins. Front Microbiol 2020; 11:591778. [PMID: 33193257 PMCID: PMC7642799 DOI: 10.3389/fmicb.2020.591778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 09/28/2020] [Indexed: 01/22/2023] Open
Abstract
The rhadinoviruses Kaposi’s Sarcoma-associated herpesvirus (KSHV) and murine gammaherpesvirus (MHV-68) persist in infected hosts in a latent state that is characterized by the absence of virus production and by restricted viral gene expression. Their major latency protein, the latency-associated nuclear antigen (kLANA for KSHV and mLANA for MHV-68), is essential for viral genome maintenance and replication and involved in transcriptional regulation. Both kLANA and mLANA interact with cellular chromatin-associated proteins, among them the Bromodomain and Extra Terminal domain (Brd/BET) proteins, which recruit cellular and viral proteins to acetylated histones through their bromodomains and modulate cellular gene expression. Brd/BET proteins also play a role in the tethering, replication, segregation or integration of a diverse group of viral DNA genomes. In this study we explored if Brd/BET proteins influence the localization of the LANAs to preferential regions in the host chromatin and thereby contribute to kLANA- or mLANA-mediated transcriptional regulation. Using ChIP-Seq, we revealed a genome-wide co-enrichment of kLANA with Brd2/4 near cellular and viral transcriptional start sites (TSS). Treatment with I-BET151, an inhibitor of Brd/BET, displaced kLANA and Brd2/4 from TSS in the viral and host chromatin, but did not affect the direct binding of kLANA to kLANA-binding sites (LBS) in the KSHV latent origin of replication. Similarly, mLANA, but not a mLANA mutant deficient for binding to Brd2/4, also associated with cellular TSS. We compared the transcriptome of KSHV-infected with uninfected and kLANA-expressing human B cell lines, as well as a murine B cell line expressing mLANA or a Brd2/4-binding deficient mLANA mutant. We found that only a minority of cellular genes, whose TSS are occupied by kLANA or mLANA, is transcriptionally regulated by these latency proteins. Our findings extend previous reports on a preferential deposition of kLANA on cellular TSS and show that this characteristic chromatin association pattern is at least partially determined by the interaction of these viral latency proteins with members of the Brd/BET family of chromatin modulators.
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Affiliation(s)
- Rishikesh Lotke
- Institut für Virologie, Medizinische Hochschule Hannover, Hanover, Germany.,German Center for Infection Research, Hannover-Braunschweig and Hamburg Sites, Hanover, Germany
| | - Ulrike Schneeweiß
- Institut für Virologie, Medizinische Hochschule Hannover, Hanover, Germany
| | - Marcel Pietrek
- Institut für Virologie, Medizinische Hochschule Hannover, Hanover, Germany
| | - Thomas Günther
- Heinrich-Pette-Institut, Leibniz-Institut für Experimentelle Virologie, Hamburg, Germany
| | - Adam Grundhoff
- German Center for Infection Research, Hannover-Braunschweig and Hamburg Sites, Hanover, Germany.,Heinrich-Pette-Institut, Leibniz-Institut für Experimentelle Virologie, Hamburg, Germany
| | - Magdalena Weidner-Glunde
- Institut für Virologie, Medizinische Hochschule Hannover, Hanover, Germany.,German Center for Infection Research, Hannover-Braunschweig and Hamburg Sites, Hanover, Germany
| | - Thomas F Schulz
- Institut für Virologie, Medizinische Hochschule Hannover, Hanover, Germany.,German Center for Infection Research, Hannover-Braunschweig and Hamburg Sites, Hanover, Germany
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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.
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238
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A M, Latario CJ, Pickrell LE, Higgs HN. Lysine acetylation of cytoskeletal proteins: Emergence of an actin code. J Biophys Biochem Cytol 2020; 219:211455. [PMID: 33044556 PMCID: PMC7555357 DOI: 10.1083/jcb.202006151] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/26/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023] Open
Abstract
Reversible lysine acetylation of nuclear proteins such as histones is a long-established important regulatory mechanism for chromatin remodeling and transcription. In the cytoplasm, acetylation of a number of cytoskeletal proteins, including tubulin, cortactin, and the formin mDia2, regulates both cytoskeletal assembly and stability. More recently, acetylation of actin itself was revealed to regulate cytoplasmic actin polymerization through the formin INF2, with downstream effects on ER-to-mitochondrial calcium transfer, mitochondrial fission, and vesicle transport. This finding raises the possibility that actin acetylation, along with other post-translational modifications to actin, might constitute an "actin code," similar to the "histone code" or "tubulin code," controlling functional shifts to these central cellular proteins. Given the multiple roles of actin in nuclear functions, its modifications might also have important roles in gene expression.
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239
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Sarfaraz S, Muneer I, Liu H. Combining fragment docking with graph theory to improve ligand docking for homology model structures. J Comput Aided Mol Des 2020; 34:1237-1259. [PMID: 33034007 PMCID: PMC7544562 DOI: 10.1007/s10822-020-00345-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/24/2020] [Indexed: 11/30/2022]
Abstract
Computational protein–ligand docking is well-known to be prone to inaccuracies in input receptor structures, and it is challenging to obtain good docking results with computationally predicted receptor structures (e.g. through homology modeling). Here we introduce a fragment-based docking method and test if it reduces requirements on the accuracy of an input receptor structures relative to non-fragment docking approaches. In this method, small rigid fragments are docked first using AutoDock Vina to generate a large number of favorably docked poses spanning the receptor binding pocket. Then a graph theory maximum clique algorithm is applied to find combined sets of docked poses of different fragment types onto which the complete ligand can be properly aligned. On the basis of these alignments, possible binding poses of complete ligand are determined. This docking method is first tested for bound docking on a series of Cytochrome P450 (CYP450) enzyme–substrate complexes, in which experimentally determined receptor structures are used. For all complexes tested, ligand poses of less than 1 Å root mean square deviations (RMSD) from the actual binding positions can be recovered. Then the method is tested for unbound docking with modeled receptor structures for a number of protein–ligand complexes from different families including the very recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) protease. For all complexes, poses with RMSD less than 3 Å from actual binding positions can be recovered. Our results suggest that for docking with approximately modeled receptor structures, fragment-based methods can be more effective than common complete ligand docking approaches.
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Affiliation(s)
- Sara Sarfaraz
- School of life sciences, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Iqra Muneer
- School of life sciences, University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Haiyan Liu
- School of life sciences, University of Science and Technology of China, Hefei, 230026, Anhui, China.
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240
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Xiong Y, Zhang M, Li Y. Recent Advances in the Development of CBP/p300 Bromodomain Inhibitors. Curr Med Chem 2020; 27:5583-5598. [DOI: 10.2174/0929867326666190731141055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 12/22/2022]
Abstract
CBP and p300 are two closely related Histone Acetyltransferases (HATs) that interact
with numerous transcription factors and act to increase the expression of their target genes. Both
proteins contain a bromodomain flanking the HAT catalytic domain that is important in binding of
CBP/p300 to chromatin, which offers an opportunity to develop protein-protein interaction inhibitors.
Since their discovery in 2006, CBP/p300 bromodomains have attracted much interest as promising
new epigenetic targets for diverse human diseases, including inflammation, cancer, autoimmune
disorders, and cardiovascular disease. Herein, we present a comprehensive review of the
structure, function, and inhibitors of CBP/p300 bromodomains developed in the last several years,
which is expected to be beneficial to relevant studies.
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Affiliation(s)
- Ying Xiong
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Mingming Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yingxia Li
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
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241
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Bass AKA, El-Zoghbi MS, Nageeb ESM, Mohamed MFA, Badr M, Abuo-Rahma GEDA. Comprehensive review for anticancer hybridized multitargeting HDAC inhibitors. Eur J Med Chem 2020; 209:112904. [PMID: 33077264 DOI: 10.1016/j.ejmech.2020.112904] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/18/2020] [Accepted: 09/30/2020] [Indexed: 02/08/2023]
Abstract
Despite the encouraging clinical progress of chemotherapeutic agents in cancer treatment, innovation and development of new effective anticancer candidates still represents a challenging endeavor. With 15 million death every year in 2030 according to the estimates, cancer has increased rising of an alarm as a real crisis for public health and health systems worldwide. Therefore, scientist began to introduce innovative solutions to control the cancer global health problem. One of the promising strategies in this issue is the multitarget or smart hybrids having two or more pharmacophores targeting cancer. These rationalized hybrid molecules have gained great interests in cancer treatment as they are capable to simultaneously inhibit more than cancer pathway or target without drug-drug interactions and with less side effects. A prime important example of these hybrids, the HDAC hybrid inhibitors or referred as multitargeting HDAC inhibitors. The ability of HDAC inhibitors to synergistically improve the efficacy of other anti-cancer drugs and moreover, the ease of HDAC inhibitors cap group modification prompt many medicinal chemists to innovate and develop new generation of HDAC hybrid inhibitors. Notably, and during this short period, there are four HDAC inhibitor hybrids have entered different phases of clinical trials for treatment of different types of blood and solid tumors, namely; CUDC-101, CUDC-907, Tinostamustine, and Domatinostat. This review shed light on the most recent hybrids of HDACIs with one or more other cancer target pharmacophore. The designed multitarget hybrids include topoisomerase inhibitors, kinase inhibitors, nitric oxide releasers, antiandrogens, FLT3 and JAC-2 inhibitors, PDE5-inhibitors, NAMPT-inhibitors, Protease inhibitors, BRD4-inhibitors and other targets. This review may help researchers in development and discovery of new horizons in cancer treatment.
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Affiliation(s)
- Amr K A Bass
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Menoufia University, Menoufia, Egypt
| | - Mona S El-Zoghbi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Menoufia University, Menoufia, Egypt
| | - El-Shimaa M Nageeb
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
| | - Mamdouh F A Mohamed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Sohag University, 82524 Sohag, Egypt
| | - Mohamed Badr
- Department of Biochemistry, Faculty of Pharmacy, Menoufia University, Menoufia, Egypt
| | - Gamal El-Din A Abuo-Rahma
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Deraya University, New Minia, Minia, Egypt.
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242
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Bond AG, Testa A, Ciulli A. Stereoselective synthesis of allele-specific BET inhibitors. Org Biomol Chem 2020; 18:7533-7539. [PMID: 32756710 DOI: 10.1039/d0ob01165g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Developing stereoselective synthetic routes that are efficient and cost-effective allows easy access to biologically active molecules. Our previous syntheses of allele-selective bumped inhibitors of the Bromo and Extra-Terminal (BET) domain proteins, Brd2, Brd3, Brd4 and BrdT, required a wasteful, late-stage alkylation step and expensive chiral separation. To circumvent these limitations, we developed a route based on stereocontrolled alkylation of an N-Pf protected aspartic acid derivative that was used in a divergent, racemisation-free protocol to yield structurally diverse and enantiopure triazolodiazepines. With this approach, we synthesized bumped thienodiazepine-based BET inhibitor, ET-JQ1-OMe, in five steps and 99% ee without the need for chiral chromatography. Exquisite selectivity of ET-JQ1-OMe for Leu-Ala and Leu-Val mutants over wild-type bromodomain was established by isothermal titration calorimetry and X-ray crystallography. Our new approach provides unambiguous chemical evidence for the absolute stereochemistry of the active, allele-specific BET inhibitors and a viable route that will open wider access to this compound class.
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Affiliation(s)
- Adam G Bond
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK.
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243
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Tafessu A, Banaszynski LA. Establishment and function of chromatin modification at enhancers. Open Biol 2020; 10:200255. [PMID: 33050790 PMCID: PMC7653351 DOI: 10.1098/rsob.200255] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/22/2020] [Indexed: 12/17/2022] Open
Abstract
How a single genome can give rise to distinct cell types remains a fundamental question in biology. Mammals are able to specify and maintain hundreds of cell fates by selectively activating unique subsets of their genome. This is achieved, in part, by enhancers-genetic elements that can increase transcription of both nearby and distal genes. Enhancers can be identified by their unique chromatin signature, including transcription factor binding and the enrichment of specific histone post-translational modifications, histone variants, and chromatin-associated cofactors. How each of these chromatin features contributes to enhancer function remains an area of intense study. In this review, we provide an overview of enhancer-associated chromatin states, and the proteins and enzymes involved in their establishment. We discuss recent insights into the effects of the enhancer chromatin state on ongoing transcription versus their role in the establishment of new transcription programmes, such as those that occur developmentally. Finally, we highlight the role of enhancer chromatin in new conceptual advances in gene regulation such as condensate formation.
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Affiliation(s)
| | - Laura A. Banaszynski
- UT Southwestern Medical Center, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Research Institute, Hamon Center for Regenerative Science and Medicine, Dallas, TX 75390-8511, USA
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244
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Kim YH, Lazar MA. Transcriptional Control of Circadian Rhythms and Metabolism: A Matter of Time and Space. Endocr Rev 2020; 41:5835826. [PMID: 32392281 PMCID: PMC7334005 DOI: 10.1210/endrev/bnaa014] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/04/2020] [Indexed: 02/07/2023]
Abstract
All biological processes, living organisms, and ecosystems have evolved with the Sun that confers a 24-hour periodicity to life on Earth. Circadian rhythms arose from evolutionary needs to maximize daily organismal fitness by enabling organisms to mount anticipatory and adaptive responses to recurrent light-dark cycles and associated environmental changes. The clock is a conserved feature in nearly all forms of life, ranging from prokaryotes to virtually every cell of multicellular eukaryotes. The mammalian clock comprises transcription factors interlocked in negative feedback loops, which generate circadian expression of genes that coordinate rhythmic physiology. In this review, we highlight previous and recent studies that have advanced our understanding of the transcriptional architecture of the mammalian clock, with a specific focus on epigenetic mechanisms, transcriptomics, and 3-dimensional chromatin architecture. In addition, we discuss reciprocal ways in which the clock and metabolism regulate each other to generate metabolic rhythms. We also highlight implications of circadian biology in human health, ranging from genetic and environment disruptions of the clock to novel therapeutic opportunities for circadian medicine. Finally, we explore remaining fundamental questions and future challenges to advancing the field forward.
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Affiliation(s)
- Yong Hoon Kim
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, and Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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245
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Park SG, Lee D, Seo HR, Lee SA, Kwon J. Cytotoxic activity of bromodomain inhibitor NVS-CECR2-1 on human cancer cells. Sci Rep 2020; 10:16330. [PMID: 33004947 PMCID: PMC7529788 DOI: 10.1038/s41598-020-73500-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/15/2020] [Indexed: 02/07/2023] Open
Abstract
Bromodomain (BRD), a protein module that recognizes acetylated lysine residues on histones and other proteins, has recently emerged as a promising therapeutic target for human diseases such as cancer. While most of the studies have been focused on inhibitors against BRDs of the bromo- and extra-terminal domain (BET) family proteins, non-BET family BRD inhibitors remain largely unexplored. Here, we investigated a potential anticancer activity of the recently developed non-BET family BRD inhibitor NVS-CECR2-1 that targets the cat eye syndrome chromosome region, candidate 2 (CECR2). We show that NVS-CECR2-1 inhibits chromatin binding of CECR2 BRD and displaces CECR2 from chromatin within cells. NVS-CECR2-1 exhibits cytotoxic activity against various human cancer cells, killing SW48 colon cancer cells in particular with a submicromolar half maximum inhibition value mainly by inducing apoptosis. The sensitivity of the cancer cells to NVS-CECR2-1 is reduced by CECR2 depletion, suggesting that NVS-CECR2-1 exerts its activity by targeting CECR2. Interestingly, our data show that NVS-CECR2-1 also kills cancer cells by CECR2-independent mechanism. This study reports for the first time the cancer cell cytotoxic activity for NVS-CECR2-1 and provides a possibility of this BRD inhibitor to be developed as an anticancer therapeutic agent.
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Affiliation(s)
- Seul Gi Park
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea
| | - Daye Lee
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea
| | - Hye-Ran Seo
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea
| | - Shin-Ai Lee
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea.,Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892-4263, USA
| | - Jongbum Kwon
- Department of Life Science, The Research Center for Cellular Homeostasis, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Korea.
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246
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Recent progress on cheminformatics approaches to epigenetic drug discovery. Drug Discov Today 2020; 25:2268-2276. [PMID: 33010481 DOI: 10.1016/j.drudis.2020.09.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 08/31/2020] [Accepted: 09/17/2020] [Indexed: 12/16/2022]
Abstract
The ability of epigenetic markers to affect genome function has enabled transformative changes in drug discovery, especially in cancer and other emerging therapeutic areas. Concordant with the introduction of the term 'epi-informatics', the size of the epigenetically relevant chemical space has grown substantially and so did the number of applications of cheminformatic methods to epigenetics. Recent progress in epi-informatics has improved our understanding of the structure-epigenetic activity relationships and boosted the development of models predicting novel epigenetic agents. Herein, we review the advances in computational approaches to drug discovery of small molecules with epigenetic modulation profiles, summarize the current chemogenomics data available for epigenetic targets, and provide a perspective on the greater utility of biomedical knowledge mining as a means to advance the epigenetic drug discovery.
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247
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Li G, Tian Y, Zhu WG. The Roles of Histone Deacetylases and Their Inhibitors in Cancer Therapy. Front Cell Dev Biol 2020; 8:576946. [PMID: 33117804 PMCID: PMC7552186 DOI: 10.3389/fcell.2020.576946] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/04/2020] [Indexed: 12/14/2022] Open
Abstract
Genetic mutations and abnormal gene regulation are key mechanisms underlying tumorigenesis. Nucleosomes, which consist of DNA wrapped around histone cores, represent the basic units of chromatin. The fifth amino group (Nε) of histone lysine residues is a common site for post-translational modifications (PTMs), and of these, acetylation is the second most common. Histone acetylation is modulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), and is involved in the regulation of gene expression. Over the past two decades, numerous studies characterizing HDACs and HDAC inhibitors (HDACi) have provided novel and exciting insights concerning their underlying biological mechanisms and potential anti-cancer treatments. In this review, we detail the diverse structures of HDACs and their underlying biological functions, including transcriptional regulation, metabolism, angiogenesis, DNA damage response, cell cycle, apoptosis, protein degradation, immunity and other several physiological processes. We also highlight potential avenues to use HDACi as novel, precision cancer treatments.
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Affiliation(s)
- Guo Li
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Yuan Tian
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Wei-Guo Zhu
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
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248
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Park SW, Lee JM. Emerging Roles of BRD7 in Pathophysiology. Int J Mol Sci 2020; 21:ijms21197127. [PMID: 32992509 PMCID: PMC7583729 DOI: 10.3390/ijms21197127] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/20/2020] [Accepted: 09/23/2020] [Indexed: 12/16/2022] Open
Abstract
Bromodomain is a conserved structural module found in many chromatin-associated proteins. Bromodomain-containing protein 7 (BRD7) is a member of the bromodomain-containing protein family, and was discovered two decades ago as a protein that is downregulated in nasopharyngeal carcinoma. Since then, BRD7 has been implicated in a variety of cellular processes, including chromatin remodeling, transcriptional regulation, and cell cycle progression. Decreased BRD7 activity underlies the pathophysiological properties of various diseases in different organs. BRD7 plays an important role in the pathogenesis of many cancers and, more recently, its roles in the regulation of metabolism and obesity have also been highlighted. Here, we review the involvement of BRD7 in a variety of pathophysiological conditions, with a focus on glucose homeostasis, obesity, and cancer.
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Affiliation(s)
- Sang Won Park
- Division of Endocrinology, Boston Children’s Hospital, Boston, MA 02115, USA;
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Correspondence:
| | - Junsik M. Lee
- Division of Endocrinology, Boston Children’s Hospital, Boston, MA 02115, USA;
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249
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Epigenetic mechanisms underlying stress-induced depression. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2020; 156:87-126. [PMID: 33461666 DOI: 10.1016/bs.irn.2020.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Stressful life events are a major contributor to the development of major depressive disorder. Environmental perturbations like stress change gene expression in the brain, leading to altered behavior. Gene expression is ultimately regulated by chromatin structure and the epigenetic modifications of DNA and the histone proteins that make up chromatin. Studies over the past two decades have demonstrated that stress alters the epigenetic landscape in several brain regions relevant for depressive-like behavior in rodents. This chapter will discuss epigenetic mechanisms of brain histone acetylation, histone methylation, and DNA methylation that contribute to adult stress-induced depressive-like behavior in rodents. Several biological themes have emerged from the examination of the brain transcriptome after stress such as alterations in the neuroimmune response, neurotrophic factors, and synaptic structure. The epigenetic mechanisms regulating these processes will be highlighted. Finally, pharmacological and genetic manipulations of epigenetic enzymes in rodent models of depression will be discussed as these approaches have demonstrated the ability to reverse stress-induced depressive-like behaviors and provide proof-of-concept as novel avenues for the treatment of clinical depression.
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250
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PCAF-Mediated Histone Acetylation Promotes Replication Fork Degradation by MRE11 and EXO1 in BRCA-Deficient Cells. Mol Cell 2020; 80:327-344.e8. [PMID: 32966758 DOI: 10.1016/j.molcel.2020.08.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/22/2020] [Accepted: 08/26/2020] [Indexed: 12/12/2022]
Abstract
Stabilization of stalled replication forks is a prominent mechanism of PARP (Poly(ADP-ribose) Polymerase) inhibitor (PARPi) resistance in BRCA-deficient tumors. Epigenetic mechanisms of replication fork stability are emerging but remain poorly understood. Here, we report the histone acetyltransferase PCAF (p300/CBP-associated) as a fork-associated protein that promotes fork degradation in BRCA-deficient cells by acetylating H4K8 at stalled replication forks, which recruits MRE11 and EXO1. A H4K8ac binding domain within MRE11/EXO1 is required for their recruitment to stalled forks. Low PCAF levels, which we identify in a subset of BRCA2-deficient tumors, stabilize stalled forks, resulting in PARPi resistance in BRCA-deficient cells. Furthermore, PCAF activity is tightly regulated by ATR (ataxia telangiectasia and Rad3-related), which phosphorylates PCAF on serine 264 (S264) to limit its association and activity at stalled forks. Our results reveal PCAF and histone acetylation as critical regulators of fork stability and PARPi responses in BRCA-deficient cells, which provides key insights into targeting BRCA-deficient tumors and identifying epigenetic modulators of chemotherapeutic responses.
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