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Ma Z, Zhang C, Bolinger AA, Zhou J. An updated patent review of BRD4 degraders. Expert Opin Ther Pat 2024. [PMID: 39219068 DOI: 10.1080/13543776.2024.2400166] [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: 03/05/2024] [Revised: 05/17/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024]
Abstract
INTRODUCTION Bromodomain-containing protein 4 (BRD4), an important epigenetic reader, is closely associated with the pathogenesis and development of many diseases, including various cancers, inflammation, and infectious diseases. Targeting BRD4 inhibition or protein elimination with small molecules represents a promising therapeutic strategy, particularly for cancer therapy. AREAS COVERED The recent advances of patented BRD4 degraders were summarized. The challenges, opportunities, and future directions for developing novel potent and selective BRD4 degraders are also discussed. The patents of BRD4 degraders were searched with SciFinder and Cortellis Drug Discovery Intelligence database. EXPERT OPINION BRD4 degraders exhibit superior efficacy and selectivity to BRD4 inhibitors, given their unique mechanism of protein degradation instead of protein inhibition. Excitingly, RNK05047 is now in phase I/II clinical trials, indicating that selective BRD4 protein degradation may offer a viable therapeutic strategy, particularly for cancer. Targeting BRD4 with small molecule BRD4 degraders provides a promising approach with the potential to overcome therapeutic resistance for treating various BRD4-associated diseases.
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Affiliation(s)
- Zonghui Ma
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Cun Zhang
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Andrew A Bolinger
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX, USA
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Zhang Y, Fong KW, Mao F, Wang R, Allison DB, Napier D, He D, Liu J, Zhang Y, Chen J, Kong Y, Li C, Li G, Liu J, Li Z, Zhu H, Wang C, Liu X. Elevating PLK1 overcomes BETi resistance in prostate cancer via triggering BRD4 phosphorylation-dependent degradation in mitosis. Cell Rep 2024; 43:114431. [PMID: 38968071 PMCID: PMC11334074 DOI: 10.1016/j.celrep.2024.114431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 04/20/2024] [Accepted: 06/18/2024] [Indexed: 07/07/2024] Open
Abstract
Bromodomain-containing protein 4 (BRD4) has emerged as a promising therapeutic target in prostate cancer (PCa). Understanding the mechanisms of BRD4 stability could enhance the clinical response to BRD4-targeted therapy. In this study, we report that BRD4 protein levels are significantly decreased during mitosis in a PLK1-dependent manner. Mechanistically, we show that BRD4 is primarily phosphorylated at T1186 by the CDK1/cyclin B complex, recruiting PLK1 to phosphorylate BRD4 at S24/S1100, which are recognized by the APC/CCdh1 complex for proteasome pathway degradation. We find that PLK1 overexpression lowers SPOP mutation-stabilized BRD4, consequently rendering PCa cells re-sensitized to BRD4 inhibitors. Intriguingly, we report that sequential treatment of docetaxel and JQ1 resulted in significant inhibition of PCa. Collectively, the results support that PLK1-phosphorylated BRD4 triggers its degradation at M phase. Sequential treatment of docetaxel and JQ1 overcomes BRD4 accumulation-associated bromodomain and extra-terminal inhibitor (BETi) resistance, which may shed light on the development of strategies to treat PCa.
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Affiliation(s)
- Yanquan Zhang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA.
| | - Ka-Wing Fong
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Fengyi Mao
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Ruixin Wang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Derek B Allison
- Pathology & Laboratory Medicine, University of Kentucky, Lexington, KY 40508, USA
| | - Dana Napier
- Biospecimen Procurement & Translational Pathology Shared Resource Facility, University of Kentucky, Lexington, KY 40536, USA
| | - Daheng He
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Jinpeng Liu
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Yeqing Zhang
- Department of Biology, College of Arts & Sciences, University of Kentucky, Lexington, KY 40506, USA
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Yifan Kong
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Chaohao Li
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Guangbing Li
- Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Jinghui Liu
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Zhiguo Li
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Chi Wang
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Xiaoqi Liu
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA.
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Pu KL, Kang H, Li L. Therapeutic targets for age-related macular degeneration: proteome-wide Mendelian randomization and colocalization analyses. Front Neurol 2024; 15:1400557. [PMID: 38903171 PMCID: PMC11187347 DOI: 10.3389/fneur.2024.1400557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/24/2024] [Indexed: 06/22/2024] Open
Abstract
Background Currently, effective therapeutic drugs for age-related macular degeneration (AMD) are urgently needed, and it is crucial to explore new treatment targets. The proteome is indispensable for exploring disease targets, so we conducted a Mendelian randomization (MR) of the proteome to identify new targets for AMD and its related subtypes. Methods The plasma protein level data used in this study were obtained from two large-scale studies of protein quantitative trait loci (pQTL), comprising 35,559 and 54,219 samples, respectively. The expression quantitative trait loci (eQTL) data were sourced from eQTLGen and GTEx Version 8. The discovery set for AMD data and subtypes was derived from the FinnGen study, consisting of 9,721 AMD cases and 381,339 controls, 5,239 wet AMD cases and 273,920 controls, and 6,651 dry AMD cases and 272,504 controls. The replication set for AMD data was obtained from the study by Winkler TW et al., comprising 14,034 cases and 91,234 controls. Summary Mendelian randomization (SMR) analysis was employed to assess the association between QTL data and AMD and its subtypes, while colocalization analysis was performed to determine whether they share causal variants. Additionally, chemical exploration and molecular docking were utilized to validate potential drugs targeting the identified proteins. Results SMR and colocalization analysis jointly identified risk-associated proteins for AMD and its subtypes, including 5 proteins (WARS1, BRD2, IL20RB, TGFB1, TNFRSF10A) associated with AMD, 2 proteins (WARS1, IL20RB) associated with Dry-AMD, and 9 proteins (COL10A1, WARS1, VTN, SDF2, LBP, CD226, TGFB1, TNFRSF10A, CSF2) associated with Wet-AMD. The results revealed potential therapeutic chemicals, and molecular docking indicated a good binding between the chemicals and protein structures. Conclusion Proteome-wide MR have identified risk-associated proteins for AMD and its subtypes, suggesting that these proteins may serve as potential therapeutic targets worthy of further clinical investigation.
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Affiliation(s)
- Kun-Lin Pu
- Pengzhou Hospital of Traditional Chinese Medicine, Chengdu, China
| | - Hong Kang
- Department of Thoracic Surgery, Sichuan Cancer Hospital, Chengdu, China
| | - Li Li
- Pengzhou Hospital of Traditional Chinese Medicine, Chengdu, China
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Hazawa M, Ikliptikawati DK, Iwashima Y, Lin DC, Jiang Y, Qiu Y, Makiyama K, Matsumoto K, Kobayashi A, Nishide G, Keesiang L, Yoshino H, Minamoto T, Suzuki T, Kobayashi I, Meguro-Horike M, Jiang YY, Nishiuchi T, Konno H, Koeffler HP, Hosomichi K, Tajima A, Horike SI, Wong RW. Super-enhancer trapping by the nuclear pore via intrinsically disordered regions of proteins in squamous cell carcinoma cells. Cell Chem Biol 2024; 31:792-804.e7. [PMID: 37924814 DOI: 10.1016/j.chembiol.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/07/2023] [Accepted: 10/10/2023] [Indexed: 11/06/2023]
Abstract
Master transcription factors such as TP63 establish super-enhancers (SEs) to drive core transcriptional networks in cancer cells, yet the spatiotemporal regulation of SEs within the nucleus remains unknown. The nuclear pore complex (NPC) may tether SEs to the nuclear pore where RNA export rates are maximal. Here, we report that NUP153, a component of the NPC, anchors SEs to the NPC and enhances TP63 expression by maximizing mRNA export. This anchoring is mediated through protein-protein interaction between the intrinsically disordered regions (IDRs) of NUP153 and the coactivator BRD4. Silencing of NUP153 excludes SEs from the nuclear periphery, decreases TP63 expression, impairs cellular growth, and induces epidermal differentiation of squamous cell carcinoma. Overall, this work reveals the critical roles of NUP153 IDRs in the regulation of SE localization, thus providing insights into a new layer of gene regulation at the epigenomic and spatial level.
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Affiliation(s)
- Masaharu Hazawa
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; Faculty of Biological Science and Technology, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; Laboratory of molecular cell biology, School of Natural System, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan.
| | - Dini Kurnia Ikliptikawati
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Yuki Iwashima
- Laboratory of molecular cell biology, School of Natural System, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - De-Chen Lin
- Herman Ostrow School of Dentistry, Center for Craniofacial Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, Los Angeles, CA, USA
| | - Yuan Jiang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, P.R.China; University of Science and Technology of China, Hefei 230026, P.R.China
| | - Yujia Qiu
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Kei Makiyama
- Division of Transdisciplinary Sciences, Graduate School of Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Koki Matsumoto
- Division of Transdisciplinary Sciences, Graduate School of Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Akiko Kobayashi
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Goro Nishide
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Lim Keesiang
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Hironori Yoshino
- Department of Radiation Science, Hirosaki University Graduate School of Health Sciences, Hirosaki, Aomori 036-8564, Japan
| | - Toshinari Minamoto
- Division of Translational and Clinical Oncology, Cancer Research Institute, Kanazawa University, Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Takeshi Suzuki
- Division of Functional Genomics, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Isao Kobayashi
- Faculty of Biological Science and Technology, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Makiko Meguro-Horike
- Advanced Science Research Center, Institute for Gene Research, Kanazawa University, Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Yan-Yi Jiang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, P.R.China; University of Science and Technology of China, Hefei 230026, P.R.China
| | - Takumi Nishiuchi
- Division of Integrated Omics research, Bioscience Core Facility Research Center for Experimental Modeling of Human Disease, Kanazawa University 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Hiroki Konno
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - H Phillip Koeffler
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kazuyoshi Hosomichi
- Laboratory of Computational Genomics, School of Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Shin-Ichi Horike
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; Advanced Science Research Center, Institute for Gene Research, Kanazawa University, Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Richard W Wong
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; Faculty of Biological Science and Technology, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; Laboratory of molecular cell biology, School of Natural System, Institute of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan.
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Xu F, Lu S, Pan N, Zhao F, Jia X, Wang S, Zhang Y, Zhou Y. Bromodomain protein 4 is a key molecular driver of TGFβ1-induced hepatic stellate cell activation. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119569. [PMID: 37597774 DOI: 10.1016/j.bbamcr.2023.119569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 08/03/2023] [Accepted: 08/13/2023] [Indexed: 08/21/2023]
Abstract
Liver fibrosis is characterized by the excessive deposition of extracellular matrix in liver. Chronic liver injury induces the activation of hepatic stellate cell (HSCs), a key step in liver fibrogenesis. The activated HSC is the primary source of ECM and contributes significantly to liver fibrosis. TGFβ1 is the most potent pro-fibrotic cytokine. Bromodomain protein 4 (BrD4), an epigenetic reader of histone acetylation marks, was crucial for profibrotic gene expression in HSCs. The present study aimed to investigate the roles of BRD4 in TGFβ1-dependent HSC activation and liver fibrosis, focusing on TGFβ1-induced alterations of the levels of the fibrotic-related important proteins in HSCs by employing the heterozygous TGFβ1 knockout mice and BrD4 knockdown in vivo and in vitro. Results revealed that BrD4 protein level was significantly upregulated by TGFβ1 and BrD4 knockdown reduced TGFβ1-induced HSC activation and liver fibrosis. BrD4 was required for the influences of TGFβ1 on PDGFβ receptor and on the pathways of Smad3, Stat3, and Akt. BrD4 also mediated TGFβ1-induced increases in histone acetyltransferase p300, the pivotal pro-inflammatory NFkB p65, and tissue inhibitor of metalloproteinase 1 whereas BrD4 reduced Caspase-3 protein levels in HSCs during liver injury, independent of TGFβ1. Further experiments indicated the interaction between TGFβ1-induced BrD4 and NFkB p65 in HSCs and in liver of TAA-induced liver injury. Human cirrhotic livers were demonstrated a parallel increase in the protein levels of BrD4 and NFkB p65 in HSCs. This study revealed that BrD4 was a key molecular driver of TGFβ1-induced HSC activation and liver fibrosis.
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Affiliation(s)
- Feifan Xu
- Department of Biochemistry & Molecular Biology, Medical School, Nantong University, Qi xiou Road 19, Nantong 226001, Jiangsu, China
| | - Sidan Lu
- Department of Biochemistry & Molecular Biology, Medical School, Nantong University, Qi xiou Road 19, Nantong 226001, Jiangsu, China
| | - Nachuan Pan
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
| | - Feifei Zhao
- Department of Biochemistry & Molecular Biology, Medical School, Nantong University, Qi xiou Road 19, Nantong 226001, Jiangsu, China
| | - Xin Jia
- Department of Biochemistry & Molecular Biology, Medical School, Nantong University, Qi xiou Road 19, Nantong 226001, Jiangsu, China
| | - Shouwei Wang
- Department of Clinical Laboratory, Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong), 500 Yonghe Road, Nantong 226011, Jiangsu, China
| | - Yali Zhang
- Department of Biochemistry & Molecular Biology, Medical School, Nantong University, Qi xiou Road 19, Nantong 226001, Jiangsu, China.
| | - Yajun Zhou
- Department of Biochemistry & Molecular Biology, Medical School, Nantong University, Qi xiou Road 19, Nantong 226001, Jiangsu, China.
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Yang H, Sui P, Guo Y, Chen S, Maloof ME, Ge G, Nihozeko F, Delma CR, Zhu G, Zhang P, Ye Z, Medina EA, Ayad NG, Mesa R, Nimer SD, Chiang C, Xu M, Chen Y, Yang F. Loss of BRD4 induces cell senescence in HSC/HPCs by deregulating histone H3 clipping. EMBO Rep 2023; 24:e57032. [PMID: 37650863 PMCID: PMC10561362 DOI: 10.15252/embr.202357032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/28/2023] [Accepted: 08/10/2023] [Indexed: 09/01/2023] Open
Abstract
Bromodomain-containing protein 4 (BRD4) is overexpressed and functionally implicated in various myeloid malignancies. However, the role of BRD4 in normal hematopoiesis remains largely unknown. Here, utilizing an inducible Brd4 knockout mouse model, we find that deletion of Brd4 (Brd4Δ/Δ ) in the hematopoietic system impairs hematopoietic stem cell (HSC) self-renewal and differentiation, which associates with cell cycle arrest and senescence. ATAC-seq analysis shows increased chromatin accessibility in Brd4Δ/Δ hematopoietic stem/progenitor cells (HSC/HPCs). Genome-wide mapping with cleavage under target and release using nuclease (CUT&RUN) assays demonstrate that increased global enrichment of H3K122ac and H3K4me3 in Brd4Δ/Δ HSC/HPCs is associated with the upregulation of senescence-specific genes. Interestingly, Brd4 deletion increases clipped H3 (cH3) which correlates with the upregulation of senescence-specific genes and results in a higher frequency of senescent HSC/HPCs. Re-expression of BRD4 reduces cH3 levels and rescues the senescence rate in Brd4Δ/Δ HSC/HPCs. This study unveils an important role of BRD4 in HSC/HPC function by preventing H3 clipping and suppressing senescence gene expression.
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Affiliation(s)
- Hui Yang
- Department of Cell Systems and AnatomyUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Pinpin Sui
- Department of Cell Systems and AnatomyUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Ying Guo
- Department of Cell Systems and AnatomyUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Shi Chen
- Department of Molecular MedicineUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Marie E Maloof
- Sylvester Comprehensive Cancer CenterUniversity of Miami Miller School of MedicineMiamiFLUSA
| | - Guo Ge
- Department of Cell Systems and AnatomyUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Francine Nihozeko
- Department of Cell Systems and AnatomyUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Caroline R Delma
- Department of Pathology and Laboratory Medicine, Division of HematopathologyUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Ganqian Zhu
- Department of Molecular MedicineUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Peng Zhang
- Department of Cell Systems and AnatomyUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Zhenqing Ye
- Department of Population Health SciencesUniversity of Texas Health San AntonioSan AntonioTXUSA
- Greehey Children's Cancer Research InstituteUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Edward A Medina
- Department of Pathology and Laboratory Medicine, Division of HematopathologyUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Nagi G Ayad
- Department of Oncology, Lombardi Comprehensive Cancer CenterGeorgetown UniversityWashingtonDCUSA
| | - Ruben Mesa
- Mays Cancer CenterUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Stephen D Nimer
- Sylvester Comprehensive Cancer CenterUniversity of Miami Miller School of MedicineMiamiFLUSA
| | - Cheng‐Ming Chiang
- Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Mingjiang Xu
- Department of Molecular MedicineUniversity of Texas Health San AntonioSan AntonioTXUSA
- Mays Cancer CenterUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Yidong Chen
- Department of Population Health SciencesUniversity of Texas Health San AntonioSan AntonioTXUSA
- Greehey Children's Cancer Research InstituteUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Feng‐Chun Yang
- Department of Cell Systems and AnatomyUniversity of Texas Health San AntonioSan AntonioTXUSA
- Mays Cancer CenterUniversity of Texas Health San AntonioSan AntonioTXUSA
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Bardani E, Kallemi P, Tselika M, Katsarou K, Kalantidis K. Spotlight on Plant Bromodomain Proteins. BIOLOGY 2023; 12:1076. [PMID: 37626962 PMCID: PMC10451976 DOI: 10.3390/biology12081076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/28/2023] [Accepted: 07/30/2023] [Indexed: 08/27/2023]
Abstract
Bromodomain-containing proteins (BRD-proteins) are the "readers" of histone lysine acetylation, translating chromatin state into gene expression. They act alone or as components of larger complexes and exhibit diverse functions to regulate gene expression; they participate in chromatin remodeling complexes, mediate histone modifications, serve as scaffolds to recruit transcriptional regulators or act themselves as transcriptional co-activators or repressors. Human BRD-proteins have been extensively studied and have gained interest as potential drug targets for various diseases, whereas in plants, this group of proteins is still not well investigated. In this review, we aimed to concentrate scientific knowledge on these chromatin "readers" with a focus on Arabidopsis. We organized plant BRD-proteins into groups based on their functions and domain architecture and summarized the published work regarding their interactions, activity and diverse functions. Overall, it seems that plant BRD-proteins are indispensable components and fine-tuners of the complex network plants have built to regulate development, flowering, hormone signaling and response to various biotic or abiotic stresses. This work will facilitate the understanding of their roles in plants and highlight BRD-proteins with yet undiscovered functions.
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Affiliation(s)
- Eirini Bardani
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
| | - Paraskevi Kallemi
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
| | - Martha Tselika
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
| | - Konstantina Katsarou
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
| | - Kriton Kalantidis
- Department of Biology, University of Crete, Voutes University Campus, 71500 Heraklion, Greece; (E.B.); (P.K.); (M.T.)
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
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Çınaroğlu SS, Biggin PC. The role of loop dynamics in the prediction of ligand-protein binding enthalpy. Chem Sci 2023; 14:6792-6805. [PMID: 37350814 PMCID: PMC10284145 DOI: 10.1039/d2sc06471e] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/31/2023] [Indexed: 06/24/2023] Open
Abstract
The enthalpic and entropic components of ligand-protein binding free energy reflect the interactions and dynamics between ligand and protein. Despite decades of study, our understanding and hence our ability to predict these individual components remains poor. In recent years, there has been substantial effort and success in the prediction of relative and absolute binding free energies, but the prediction of the enthalpic (and entropic) contributions in biomolecular systems remains challenging. Indeed, it is not even clear what kind of performance in terms of accuracy could currently be obtained for such systems. It is, however, relatively straight-forward to compute the enthalpy of binding. We thus evaluated the performance of absolute enthalpy of binding calculations using molecular dynamics simulation for ten inhibitors against a member of the bromodomain family, BRD4-1, against isothermal titration calorimetry data. Initial calculations, with the AMBER force-field showed good agreement with experiment (R2 = 0.60) and surprisingly good accuracy with an average of root-mean-square error (RMSE) = 2.49 kcal mol-1. Of the ten predictions, three were obvious outliers that were all over-predicted compared to experiment. Analysis of various simulation factors, including parameterization, buffer concentration and conformational dynamics, revealed that the behaviour of a loop (the ZA loop on the periphery of the binding site) strongly dictates the enthalpic prediction. Consistent with previous observations, the loop exists in two distinct conformational states and by considering one or the other or both states, the prediction for the three outliers can be improved dramatically to the point where the R2 = 0.95 and the accuracy in terms of RMSE improves to 0.90 kcal mol-1. However, performance across force-fields is not consistent: if OPLS and CHARMM are used, different outliers are observed and the correlation with the ZA loop behaviour is not recapitulated, likely reflecting parameterization as a confounding problem. The results provide a benchmark standard for future study and comparison.
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Affiliation(s)
- Süleyman Selim Çınaroğlu
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford South Parks Road Oxford OX1 3QU UK +44 (0)1865 613238 +44 (0)1865 613305
| | - Philip C Biggin
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford South Parks Road Oxford OX1 3QU UK +44 (0)1865 613238 +44 (0)1865 613305
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9
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Eischer N, Arnold M, Mayer A. Emerging roles of BET proteins in transcription and co-transcriptional RNA processing. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1734. [PMID: 35491403 DOI: 10.1002/wrna.1734] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/06/2022] [Accepted: 04/09/2022] [Indexed: 01/31/2023]
Abstract
Transcription by RNA polymerase II (Pol II) gives rise to all nuclear protein-coding and a large set of non-coding RNAs, and is strictly regulated and coordinated with RNA processing. Bromodomain and extraterminal (BET) family proteins including BRD2, BRD3, and BRD4 have been implicated in the regulation of Pol II transcription in mammalian cells. However, only recent technological advances have allowed the analysis of direct functions of individual BET proteins with high precision in cells. These studies shed new light on the molecular mechanisms of transcription control by BET proteins challenging previous longstanding views. The most studied BET protein, BRD4, emerges as a master regulator of transcription elongation with roles also in coupling nascent transcription with RNA processing. In contrast, BRD2 is globally required for the formation of transcriptional boundaries to restrict enhancer activity to nearby genes. Although these recent findings suggest non-redundant functions of BRD4 and BRD2 in Pol II transcription, more research is needed for further clarification. Little is known about the roles of BRD3. Here, we illuminate experimental work that has initially linked BET proteins to Pol II transcription in mammalian cells, outline main methodological breakthroughs that have strongly advanced the understanding of BET protein functions, and discuss emerging roles of individual BET proteins in transcription and transcription-coupled RNA processing. Finally, we propose an updated model for the function of BRD4 in transcription and co-transcriptional RNA maturation. This article is categorized under: RNA Processing > 3' End Processing RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Nicole Eischer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Mirjam Arnold
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
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10
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Zhou Y, Overhulse JM, Dupper NJ, Guo Y, Kashemirov BA, Wei K, Govin J, Petosa C, McKenna CE. Toward more potent imidazopyridine inhibitors of Candida albicans Bdf1: Modeling the role of structural waters in selective ligand binding. J Comput Chem 2022; 43:2121-2130. [PMID: 36190786 PMCID: PMC9669269 DOI: 10.1002/jcc.26997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/14/2022] [Accepted: 08/03/2022] [Indexed: 01/12/2023]
Abstract
Novel agents to treat invasive fungal infections are urgently needed because the small number of established targets in pathogenic fungi makes the existing drug repertoire particularly vulnerable to the emergence of resistant strains. Recently, we reported that Candida albicans Bdf1, a bromodomain and extra-terminal domain (BET) bromodomain with paired acetyl-lysine (AcK) binding sites (BD1 and BD2) is essential for fungal cell growth and that an imidazopyridine (1) binds to BD2 with selectivity versus both BD1 and human BET bromodomains. Bromodomain binding pockets contain a conserved array of structural waters. Molecular dynamics simulations now reveal that one water molecule is less tightly bound to BD2 than to BD1, explaining the site selectivity of 1. This insight is useful in the performance of ligand docking studies to guide design of more effective Bdf1 inhibitors, as illustrated by the design of 10 new imidazopyridine BD2 ligands 1a-j, for which experimental binding and site selectivity data are presented.
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Affiliation(s)
- Yingsheng Zhou
- Department of ChemistryUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Justin M. Overhulse
- Department of ChemistryUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Nathan J. Dupper
- Department of ChemistryUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Yanchun Guo
- Department of ChemistryUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Boris A. Kashemirov
- Department of ChemistryUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Kaiyao Wei
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS)Grenoble38000France,Univ. Grenoble Alpes, Inserm, CNRS, Institute for Advanced Biosciences (IAB)Grenoble38000France
| | - Jérôme Govin
- Univ. Grenoble Alpes, Inserm, CNRS, Institute for Advanced Biosciences (IAB)Grenoble38000France
| | - Carlo Petosa
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS)Grenoble38000France
| | - Charles E. McKenna
- Department of ChemistryUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
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11
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Lyu Q, Yang Q, Hao J, Yue Y, Wang X, Tian J, An L. A small proportion of X-linked genes contribute to X chromosome upregulation in early embryos via BRD4-mediated transcriptional activation. Curr Biol 2022; 32:4397-4410.e5. [PMID: 36108637 DOI: 10.1016/j.cub.2022.08.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/30/2022] [Accepted: 08/19/2022] [Indexed: 02/08/2023]
Abstract
Females have two X chromosomes and males have only one in most mammals. X chromosome inactivation (XCI) occurs in females to equalize X-dosage between sexes. Besides, mammals also balance the dosage between X chromosomes and autosomes via X chromosome upregulation (XCU) to fine-tune X-linked expression and thus maintain genomic homeostasis. Despite some studies highlighting the importance of XCU in somatic cells, little is known about how XCU is achieved and its developmental role during early embryogenesis. Herein, using mouse preimplantation embryos as the model, we reported that XCU initially occurs upon major zygotic genome activation and co-regulates X-linked expression in cooperation with imprinted XCI during preimplantation development. An in-depth analysis further indicated, unexpectedly, only a small proportion of, but not X chromosome-wide, X-linked genes contribute greatly to XCU. Furthermore, we identified that bromodomain containing 4 (BRD4) plays a key role in the transcription activation of XCU during preimplantation development. BRD4 deficiency or inhibition caused an impaired XCU, thus leading to reduced developmental potential and mitochondrial dysfunctions of blastocysts. Our finding was also supported by the tight association of BRD4 dysregulation and XCU disruption in the pathology of cholangiocarcinoma. Thus, our results not only advanced the current knowledge of X-dosage compensation and provided a mechanism for understanding XCU initiation but also presented an important clue for understanding the developmental and pathological role of XCU.
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Affiliation(s)
- Qingji Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Qianying Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Jia Hao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Yuan Yue
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Xiaodong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Jianhui Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China
| | - Lei An
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P.R. China.
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12
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Zhang J, Li Y, Fan TY, Liu D, Zou WD, Li H, Li YK. Identification of bromodomain-containing proteins prognostic value and expression significance based on a genomic landscape analysis of ovarian serous cystadenocarcinoma. Front Oncol 2022; 12:1021558. [PMID: 36276071 PMCID: PMC9579433 DOI: 10.3389/fonc.2022.1021558] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/15/2022] [Indexed: 12/24/2022] Open
Abstract
BackgroundOvarian serous cystadenocarcinoma (OSC), a common gynecologic tumor, is characterized by high mortality worldwide. Bromodomain (BRD)-containing proteins are a series of evolutionarily conserved proteins that bind to acetylated Lys residues of histones to regulate the transcription of multiple genes. The ectopic expression of BRDs is often observed in multiple cancer types, but the role of BRDs in OSC is still unclear.MethodsWe performed the differential expression, GO enrichment, GSEA, immune infiltration, risk model, subtype classification, stemness feature, DNA alteration, and epigenetic modification analysis for these BRDs based on multiple public databases.ResultsMost BRDs were dysregulated in OSC tissues compared to normal ovary tissues. These BRDs were positively correlated with each other in OSC patients. Gene alteration and epigenetic modification were significant for the dysregulation of BRDs in OSC patients. GO enrichment suggested that BRDs played key roles in histone acetylation, viral carcinogenesis, and transcription coactivator activity. Two molecular subtypes were classified by BRDs for OSC, which were significantly correlated with stemness features, m6A methylation, ferroptosis, drug sensitivity, and immune infiltration. The risk model constructed by LASSO regression with BRDs performed moderately well in prognostic predictions for OSC patients. Moreover, BRPF1 plays a significant role in these BRDs for the development and progression of OSC patients.ConclusionBRDs are potential targets and biomarkers for OSC patients, especially BRPF1.
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Affiliation(s)
- Juan Zhang
- Department of Assisted Reproductive Centre, Zhuzhou Central Hospital, Xiangya Hospital Zhuzhou Central South University, Central South University, Zhuzhou, China
| | - Yan Li
- Department of Assisted Reproductive Centre, Zhuzhou Central Hospital, Xiangya Hospital Zhuzhou Central South University, Central South University, Zhuzhou, China
| | - Ting-yu Fan
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, China
| | - Dan Liu
- Department of Assisted Reproductive Centre, Zhuzhou Central Hospital, Xiangya Hospital Zhuzhou Central South University, Central South University, Zhuzhou, China
| | - Wen-da Zou
- Department of Assisted Reproductive Centre, Zhuzhou Central Hospital, Xiangya Hospital Zhuzhou Central South University, Central South University, Zhuzhou, China
| | - Hui Li
- Department of Assisted Reproductive Centre, Zhuzhou Central Hospital, Xiangya Hospital Zhuzhou Central South University, Central South University, Zhuzhou, China
- *Correspondence: Hui Li, ; Yu-kun Li,
| | - Yu-kun Li
- Department of Assisted Reproductive Centre, Zhuzhou Central Hospital, Xiangya Hospital Zhuzhou Central South University, Central South University, Zhuzhou, China
- *Correspondence: Hui Li, ; Yu-kun Li,
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13
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Abstract
Transcription elongation by RNA polymerase II (Pol II) has emerged as a regulatory hub in gene expression. A key control point occurs during early transcription elongation when Pol II pauses in the promoter-proximal region at the majority of genes in mammalian cells and at a large set of genes in Drosophila. An increasing number of trans-acting factors have been linked to promoter-proximal pausing. Some factors help to establish the pause, whereas others are required for the release of Pol II into productive elongation. A dysfunction of this elongation control point leads to aberrant gene expression and can contribute to disease development. The BET bromodomain protein BRD4 has been implicated in elongation control. However, only recently direct BRD4-specific functions in Pol II transcription elongation have been uncovered. This mainly became possible with technological advances that allow selective and rapid ablation of BRD4 in cells along with the availability of approaches that capture the immediate consequences on nascent transcription. This review sheds light on the experimental breakthroughs that led to the emerging view of BRD4 as a general regulator of transcription elongation.
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Affiliation(s)
- Elisabeth Altendorfer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Yelizaveta Mochalova
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Andreas Mayer
- Otto-Warburg-Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
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14
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Kalra P, Zahid H, Ayoub A, Dou Y, Pomerantz WCK. Alternative Mechanisms for DNA Engagement by BET Bromodomain-Containing Proteins. Biochemistry 2022; 61:1260-1272. [PMID: 35748495 PMCID: PMC9682295 DOI: 10.1021/acs.biochem.2c00157] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Epigenetic reader domains regulate chromatin structure and modulate gene expression through the recognition of post-translational modifications on histones. Recently, reader domains have also been found to harbor double-stranded (ds) DNA-binding activity, which is as functionally critical as histone association. Here, we explore the dsDNA recognition of the N-terminal bromodomain of the bromodomain and extra-terminal (BET) protein, BRD4. Using protein-observed 19F NMR, 1H-15N HSQC NMR, electrophoretic mobility shift assays (EMSA), and competitive-inhibition assays, we establish the binding surface of dsDNA and find it to be largely overlapping with the acetylated histone (KAc)-binding site. Rather than engaging in electrostatic contacts, we find dsDNA to interact competitively within the KAc-binding pocket. These interactions are distinct from the highly homologous BET bromodomain, BRDT. Nine additional bromodomains have also been characterized for interacting with dsDNA, including tandem BET bromodomains. Together, these studies help establish a binding model for dsDNA interactions with BRD4 bromodomains and elucidate the chromatin-recognition mechanisms of the BRD4 protein for regulating gene expression.
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Affiliation(s)
- Prakriti Kalra
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Huda Zahid
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Alex Ayoub
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yali Dou
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089, United States
| | - William C. K. Pomerantz
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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15
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Doherty J, Mandati V, González-Rodriguez MA, Troutman S, Shepard A, Harbaugh D, Brody R, Miller DC, Kareta MS, Kissil JL. Validation of BET proteins as therapeutic targets in Neurofibromatosis type 2. Neurooncol Adv 2022; 4:vdac072. [PMID: 35855490 PMCID: PMC9278623 DOI: 10.1093/noajnl/vdac072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background Neurofibromatosis type 2 (NF2) is an autosomal dominant genetic disease characterized by development of schwannomas on the VIIIth (vestibular) cranial nerves. Bromodomain and extra-terminal domain (BET) proteins regulate gene transcription and their activity is required in a variety of cancers including malignant peripheral nerve sheath tumors. The use of BET inhibitors as a therapeutic option to treat NF2 schwannomas has not been explored and is the focus of this study. Methods A panel of normal and NF2-null Schwann and schwannoma cell lines were used to characterize the impact of the BET inhibitor JQ1 in vitro and in vivo. The mechanism of action was explored by chromatin immunoprecipitation of the BET BRD4, phospho-kinase arrays and immunohistochemistry (IHC) of BRD4 in vestibular schwannomas. Results JQ1 inhibited proliferation of NF2-null schwannoma and Schwann cell lines in vitro and in vivo. Further, loss of NF2 by CRISPR deletion or siRNA knockdown increased sensitivity of cells to JQ1. Loss of function experiments identified BRD4, and to a lesser extent BRD2, as BET family members mediating the majority of JQ1 effects. IHC demonstrated elevated levels of BRD4 protein in human vestibular schwannomas. Analysis of signaling pathways effected by JQ1 treatment suggests that the effects of JQ1 treatment are mediated, at least in part, via inhibition of PI3K/Akt signaling. Conclusions NF2-deficient Schwann and schwannoma cells are sensitive to BET inhibition, primarily mediated by BRD4, which is overexpressed in human vestibular schwannomas. Our results suggest BRD4 regulates PI3K signaling and likely impedes NF2 schwannoma growth via this inhibition. These findings implicate BET inhibition as a therapeutic option for NF2-deficient schwannomas.
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Affiliation(s)
- Joanne Doherty
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida, USA
| | - Vinay Mandati
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida, USA
| | | | - Scott Troutman
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center, Tampa, Florida
| | - Alyssa Shepard
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida, USA
| | - David Harbaugh
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, Florida, USA
| | - Rachel Brody
- Department of Pathology, Molecular, and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Douglas C Miller
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO, USA
| | - Michael S Kareta
- Genetics and Genomics Group, Sanford Research, Sioux Falls, South Dakota, 57104, USA
| | - Joseph L Kissil
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center, Tampa, Florida
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16
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Zhou N, Zhang Y, Lei G, Chen Y, Lin T, Liu Q, Zhao Y, Mao J, Jiang Y, Mao R. Inhibition of BETs prevents heat shock-induced cell death via upregulating HSPs in SV40 large T antigen transfected cells. Genes Genomics 2022; 44:1259-1269. [PMID: 35175516 DOI: 10.1007/s13258-022-01228-x] [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: 08/19/2021] [Accepted: 01/31/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Heat shock response is a protected mechanism against environmental changes for the organism, which must be tightly regulated. Bromodomain and extra terminal-containing protein family (BETs) regulate numerous gene expression in many physiological and pathological conditions, including viral infection. SV40 is considered as a highly human disease-associated virus. OBJECTIVE We aimed to explore whether BETs play a role in heat shock in SV40 large T antigen transfected cells. METHODS SV40LTA was transfected in HeLa cells using the Lipofectamine 8000. BETs inhibitor JQ1 and I-BET-762 was employed to treat transfected cells and HEK-293 T cells. Heat shock treatment was performed to determine the effect of JQ1 and I-BET-762 on these cells. Western blot and quantitative RT-PCR were carried out to assess the expression of HSP70 and other HSPs. RESULTS We found that inhibition of BETs by JQ1 and I-BET-762 protects cells from heat shock-induced death in HEK293T cells. Both JQ1 and I-BET-762 induce the expression of HSPs and HSF1 in HEK-293 T cells. However, neither JQ1 nor I-BET-762 fail to induce the expression of HSPs in either HeLa or HBL-1 cells. When SV40 large T antigen was transfected into HeLa cells, the induction of HSP70 expressing and the protection of heat shock-induced cell death are reproduced by JQ1 and IBET treatment in these transfected cells. CONCLUSIONS Inhibition of BETs by JQ1 and I-BET-762 prevents heat shock-induced cell death via upregulating HSPs in SV40 large T antigen transfected cells. Our data indicate a novel function of BETs in SV40 large T antigen transformed cells, affecting HSPs and HSF1 as well as its function on heat shock response.
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Affiliation(s)
- Nan Zhou
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China
| | - Ye Zhang
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China
| | - Gongyun Lei
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China
| | - Yifan Chen
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China
| | - Ting Lin
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China
| | - Qin Liu
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China
| | - Yinshuang Zhao
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China.,Department of Pediatric Surgery, Affiliated Hospital of Nantong University, Nantong University, Nantong, 226001, Jiangsu, People's Republic of China
| | - Jiahui Mao
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China
| | - Yongying Jiang
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China.
| | - Renfang Mao
- Department of Pathophysiology, School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, People's Republic of China.
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Chen L, Liu Z, Li X. Recent Advances in Dual BRD4-Kinase Inhibitors Base on Polypharmacology. ChemMedChem 2022; 17:e202100731. [PMID: 35146935 DOI: 10.1002/cmdc.202100731] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/08/2022] [Indexed: 11/11/2022]
Abstract
Epigenetic reader BRD4 is involved in chromatin remodeling and transcriptional regulation, making it a promising therapeutic target. However, during the past decades, the results of many BRD4 inhibitors that have entered clinical trials were, in the main, unsatisfactory, due to some therapeutic limitations such as off-target effects and drug resistance. Combining a BRD4 inhibitor with another drug was expected to be an ideal option to overcome these "bottlenecks" and achieve improved therapeutic outcomes. However, combination therapy might trigger toxicity caused by drug-drug interaction, complex pharmacokinetic and additive effects. Recently, the application of dual-target drugs targeting BRD4 and other kinases has emerged to be an attractive approach to remedy defects of a single BRD4 inhibitor. Herein, this review focuses on recent advances in the discovery of dual BRD4-kinase inhibitors, with emphasis on their co-crystal structures and structure-activity relationships (SARs), as well as perspective prospects in the field.
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Affiliation(s)
- Li Chen
- Shandong University Cheeloo College of Medicine, Medicinal chemistry, West Wenhua Road 44, 250012, Jinnan, CHINA
| | - Zhaopeng Liu
- Institute of Medicinal Chemistry, Department of Organic Chemistry, School of Pharmaceutical Sciences, Shandong Un, No.44 WhenHua XiLu, 250012, Jinan, CHINA
| | - Xun Li
- Shandong First Medical University, Institute of Materia Medica, CHINA
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18
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Gong ZG, Zhao Y, Wang ZY, Fan RF, Liu ZP, Wang L. Epigenetic regulator BRD4 is involved in cadmium-induced acute kidney injury via contributing to lysosomal dysfunction, autophagy blockade and oxidative stress. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127110. [PMID: 34523489 DOI: 10.1016/j.jhazmat.2021.127110] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/23/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Cadmium (Cd) is a known nephrotoxic heavy metal and proximal tubules are the major target of Cd-induced acute kidney injury (AKI). We previously demonstrated that lysosomal dysfunction and dysregulated autophagy contribute to Cd-induced AKI. Recent studies have revealed that bromodomain-containing protein 4 (BRD4) is a transcriptional repressor of autophagy and lysosomal function. Hence, in vivo and in vitro studies were performed to clarify the role of BRD4 in Cd-induced AKI. Firstly, Cd has no effect on BRD4 expression levels, but increases H4K16 acetylation. Resultantly, Cd promotes the recruitment of BRD4 to lysosomal gene promoter regions to make it as a transcriptional regulator. Pharmacological and genetic inhibition of BRD4 alleviates Cd-inhibited lysosomal gene transcript levels and lysosomal function, leading to the alleviation of Cd-induced autophagy inhibition. Moreover, inhibition of BRD4 relieves Cd-induced oxidative stress and concurrent cytotoxicity, which is counteracted by the inhibition of autophagy via Atg5 knockdown, indicating that alleviation of oxidative stress by BRD4 inhibition is ascribed to its restoration of autophagic flux. Collectively, these results demonstrate that BRD4 acts as a transcriptional repressor to mediate lysosomal dysfunction, autophagy blockade and oxidative stress during Cd exposure, which may be a potential therapeutic target for Cd-induced AKI.
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Affiliation(s)
- Zhong-Gui Gong
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China; College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu Province 225009, People's Republic of China
| | - Yuan Zhao
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China
| | - Zhen-Yong Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China
| | - Rui-Feng Fan
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China
| | - Zong-Ping Liu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, Jiangsu Province 225009, People's Republic of China.
| | - Lin Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province 271018, People's Republic of China.
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19
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Cai T, Yao W, Qiu L, Zhu AR, Shi Z, Du Y. PLEK2 promotes the proliferation and migration of non-small cell lung cancer cells in a BRD4-dependent manner. Mol Biol Rep 2022; 49:3693-3704. [DOI: 10.1007/s11033-022-07209-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/27/2022] [Indexed: 12/24/2022]
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20
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Zhang J, Huang L, Zhang P, Huang X, Yang W, Liu R, Sun Q, Lu Y, Zhang M, Fu Q. Genomic Identification, Evolution, and Expression Analysis of Bromodomain Genes Family in Buffalo. Genes (Basel) 2022; 13:genes13010103. [PMID: 35052443 PMCID: PMC8774554 DOI: 10.3390/genes13010103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 02/05/2023] Open
Abstract
Bromodomain (BRD) is an evolutionarily conserved protein-protein interaction module that is critical in gene regulation, cellular homeostasis, and epigenetics. This study aimed to conduct an identification, evolution, and expression analysis of the BRD gene family in the swamp buffalo (Bubalus bubalis). A total of 101 BRD protein sequences deduced from 22 BRD genes were found in the buffalo genome. The BRD proteins were classified into six groups based on phylogenetic relationships, conserved motifs, and conserved domains. The BRD genes were irregularly distributed in 13 chromosomes. Collinearity analysis revealed 20 BRD gene pairs that had remarkable homologous relationships between the buffalo and cattle, although no tandem or segmental duplication event was found in the buffalo BRD genes. Comparative transcriptomics using a 10x sequencing platform analysis showed that 22 BRD genes were identified in the Sertoli cells (SCs) at different developmental stages of buffalo. Further, the mRNA expression levels of bromodomain and the extraterminal (BET) family in SCs at the pubertal stage were higher than that at the prepubertal stage of buffalo. However, the SMARCA2, PHIP, BRD9, and TAF1 genes exhibited the opposite trend. The maturation process of SCs may be regulated by the BRD family members expressed differentially in SCs at different developmental stages of buffalo. In summary, our findings provide an understanding of the evolutionary, structural, and functional properties of the buffalo BRD family members, and further characterize the function of the BRD family in the maturation of SCs. It also provides a theoretical basis for further understanding in the future of the mechanism of SCs regulating spermatogenesis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Qiang Fu
- Correspondence: ; Tel.: +86-771-3237124
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21
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Progress in the development of domain selective inhibitors of the bromo and extra terminal domain family (BET) proteins. Eur J Med Chem 2021; 226:113853. [PMID: 34547507 DOI: 10.1016/j.ejmech.2021.113853] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/04/2021] [Accepted: 09/11/2021] [Indexed: 12/13/2022]
Abstract
Dysfunction of the bromo and extra terminal domain (BET) family proteins is associated with many human diseases, therefore the BET family proteins have been considered as promising targets for drug development. Numerous small molecular compounds targeting the N-terminal two tandem bromodomains BD1 and BD2 of the BET family proteins have been reported, and a number of them have been advanced into clinical trials. Most of the BET inhibitors entered clinical trials are pan-BET inhibitors which show poor selectivity among BET members and bind to the BD1 and BD2 of the BET family proteins with comparable binding affinities. In order to elucidate the distinct functions of BD1s and BD2s, many BD1 and BD2 selective BET inhibitors have also been developed. In this review, we summarized the recent progress in the development of BD1 and BD2 selective BET inhibitors, and provided the perspectives for future studies of BET inhibitors.
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22
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Gokani S, Bhatt LK. Bromodomains: A novel target for the anticancer therapy. Eur J Pharmacol 2021; 911:174523. [PMID: 34563497 DOI: 10.1016/j.ejphar.2021.174523] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 02/02/2023]
Abstract
Bromodomains are a group of structurally diverse proteins characterized as readers of post-translational modifications. They bear unique structural topology and are known to have diverse cellular functions. As epigenetic readers of histone acetylation, bromodomains appear to have both physiological and pathological implications. Among the various types of bromodomain-containing proteins, BRD2 and BRD4 proteins are expressed ubiquitously and act as critical regulators of the cell cycle in normal mammalian cells. Therefore, they are increasingly involved in the process of oncogenesis. Bromodomains are the emerging novel epigenetic targets for the treatment of cancer. Various small molecules are proposed to target the bromodomain proteins as the readers of acetyl-lysine residues. In recent years, inhibiting the interaction of acetyl-lysine residues and bromodomain proteins on chromatin has served as an interesting target to regulate the expression of various pathological genes, including BCL-2, MYC, and NF-κB. The review summarizes bromodomains as potential targets in cancer and various bromodomain inhibitors in the early stages of the clinical trial.
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Affiliation(s)
- Shivani Gokani
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (West), Mumbai, India
| | - Lokesh Kumar Bhatt
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Vile Parle (West), Mumbai, India.
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23
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Barman S, Roy A, Bardhan I, Kandasamy T, Shivani S, Sudhamalla B. Insights into the Molecular Mechanisms of Histone Code Recognition by the BRPF3 Bromodomain. Chem Asian J 2021; 16:3404-3412. [PMID: 34448544 DOI: 10.1002/asia.202100793] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/24/2021] [Indexed: 01/16/2023]
Abstract
Bromodomains are evolutionarily conserved reader modules that recognize acetylated lysine residues on the histone tails to facilitate gene transcription. The bromodomain and PHD finger containing protein 3 (BRPF3) is a scaffolding protein that forms a tetrameric complex with HBO1 histone acetyltransferase (HAT) and two other subunits, which is known to regulate the HAT activity and substrate specificity. However, its molecular mechanism, histone ligands, and biological functions remain unknown. Herein, we identify mono- (H4K5ac) and di- (H4K5acK12ac) acetylated histone peptides as novel interacting partners of the BRPF3 bromodomain. Consistent with this, pull-down assays on purified histones from human cells confirm the interaction of BRPF3 bromodomain with acetylated histone H4. Further, MD simulation studies highlight the binding mode of acetyllysine (Kac) and the stability of bromodomain-histone peptide complexes. Collectively, our findings provide a key insight into how histone targets of the BRPF3 bromodomain direct the recruitment of HBO1 complex to chromatin for downstream transcriptional regulation.
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Affiliation(s)
- Soumen Barman
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, Nadia, West Bengal, India
| | - Anirban Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, Nadia, West Bengal, India
| | - Ishita Bardhan
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, Nadia, West Bengal, India
| | - Thirukumaran Kandasamy
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, Nadia, West Bengal, India
| | - Shivani Shivani
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, Nadia, West Bengal, India
| | - Babu Sudhamalla
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, Nadia, West Bengal, India
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24
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Liang Y, Tian J, Wu T. BRD4 in physiology and pathology: ''BET'' on its partners. Bioessays 2021; 43:e2100180. [PMID: 34697817 DOI: 10.1002/bies.202100180] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/07/2021] [Accepted: 10/07/2021] [Indexed: 12/20/2022]
Abstract
Bromodomain-containing 4 (BRD4), a member of Bromo and Extra-Terminal (BET) family, recognizes acetylated histones and is of importance in transcription, replication, and DNA repair. It also binds non-histone proteins, DNA and RNA, contributing to development, tissue growth, and various physiological processes. Additionally, BRD4 has been implicated in driving diverse diseases, ranging from cancer, viral infection, inflammation to neurological disorders. Inhibiting its functions with BET inhibitors (BETis) suppresses the progression of several types of cancer, creating an impetus for translating these chemicals to the clinic. The diverse roles of BRD4 are largely dependent on its interaction partners in different contexts. In this review we discuss the molecular mechanisms of BRD4 with its interacting partners in physiology and pathology. Current development of BETis is also summarized. Further understanding the functions of BRD4 and its partners will facilitate resolving the liabilities of present BETis and accelerate their clinical translation.
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Affiliation(s)
- Yin Liang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Jieyi Tian
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Tao Wu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Carcinogenesis and Intervention, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
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25
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Paradise CR, De La Vega RE, Galvan ML, Carrasco ME, Thaler R, van Wijnen AJ, Dudakovic A. Brd4 Inactivation Increases Adenoviral Delivery of BMP2 for Paracrine Stimulation of Osteogenic Differentiation as a Gene Therapeutic Concept to Enhance Bone Healing. JBMR Plus 2021; 5:e10520. [PMID: 34693189 PMCID: PMC8520065 DOI: 10.1002/jbm4.10520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 05/19/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
Bromodomain (BRD) proteins are histone code interpreters that recognize acetylated lysines and link the dynamic state of chromatin with the transcriptional machinery. Here, we demonstrate that ablation of the Brd4 gene in primary mouse bone marrow–derived mesenchymal stem cells via a conditional Brd4fl/fl allele suppresses osteogenic lineage commitment. Remarkably, loss of Brd4 function also enhances expression of genes in engineered adenoviral vectors, including Cre recombinase and green fluorescent protein (GFP). Similarly, vector‐based expression of BMP2 mRNA and protein levels are enhanced upon Brd4 depletion in cells transduced with an adenoviral vector that expresses BMP2 (Ad‐BMP2). Importantly, Brd4 depletion in MC3T3‐E1 and human adipose‐derived mesenchymal stem cells (AMSCs) transduced with Ad‐BMP2 enhances osteogenic differentiation of naïve MC3T3‐E1 cells via paracrine mechanisms based on transwell and conditioned medium studies. Our studies indicate that Brd4 depletion enhances adenoviral transgene expression in mammalian cells, which can be leveraged as a therapeutic strategy to improve viral vector‐based gene therapies. © 2021 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Christopher R Paradise
- Department of Orthopedic Surgery Mayo Clinic Rochester MN USA.,Center for Regenerative Medicine Mayo Clinic Rochester MN USA
| | - Rodolfo E De La Vega
- Musculosketal Gene Therapy Research Laboratory, Rehabilitation Medicine Research Center Mayo Clinic Rochester MN USA.,Department cBITE, MERLN Institute for Technology-Inspired Regenerative Medicine Maastricht University Maastricht The Netherlands.,Department IBE, MERLN Institute for Technology-Inspired Regenerative Medicine Maastricht University Maastricht The Netherlands
| | - M Lizeth Galvan
- Department of Orthopedic Surgery Mayo Clinic Rochester MN USA
| | | | - Roman Thaler
- Department of Orthopedic Surgery Mayo Clinic Rochester MN USA
| | - Andre J van Wijnen
- Department of Orthopedic Surgery Mayo Clinic Rochester MN USA.,Center for Regenerative Medicine Mayo Clinic Rochester MN USA.,Department of Biochemistry and Molecular Biology Mayo Clinic Rochester MN USA
| | - Amel Dudakovic
- Department of Orthopedic Surgery Mayo Clinic Rochester MN USA.,Department of Biochemistry and Molecular Biology Mayo Clinic Rochester MN USA
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26
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Feng L, Wang G, Chen Y, He G, Liu B, Liu J, Chiang CM, Ouyang L. Dual-target inhibitors of bromodomain and extra-terminal proteins in cancer: A review from medicinal chemistry perspectives. Med Res Rev 2021; 42:710-743. [PMID: 34633088 DOI: 10.1002/med.21859] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 07/14/2021] [Accepted: 09/26/2021] [Indexed: 02/05/2023]
Abstract
Bromodomain-containing protein 4 (BRD4), as the most studied member of the bromodomain and extra-terminal (BET) family, is a chromatin reader protein interpreting epigenetic codes through binding to acetylated histones and non-histone proteins, thereby regulating diverse cellular processes including cell cycle, cell differentiation, and cell proliferation. As a promising drug target, BRD4 function is closely related to cancer, inflammation, cardiovascular disease, and liver fibrosis. Currently, clinical resistance to BET inhibitors has limited their applications but synergistic antitumor effects have been observed when used in combination with other tumor inhibitors targeting additional cellular components such as PLK1, HDAC, CDK, and PARP1. Therefore, designing dual-target inhibitors of BET bromodomains is a rational strategy in cancer treatment to increase potency and reduce drug resistance. This review summarizes the protein structures and biological functions of BRD4 and discusses recent advances of dual BET inhibitors from a medicinal chemistry perspective. We also discuss the current design and discovery strategies for dual BET inhibitors, providing insight into potential discovery of additional dual-target BET inhibitors.
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Affiliation(s)
- Lu Feng
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Yi Chen
- State Key Laboratory of Biotherapy and Cancer Center and Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Gu He
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Bo Liu
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Jie Liu
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
| | - Cheng-Ming Chiang
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, China
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27
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Lu J, Qian C, Ji Y, Bao Q, Lu B. Gene Signature Associated With Bromodomain Genes Predicts the Prognosis of Kidney Renal Clear Cell Carcinoma. Front Genet 2021; 12:643935. [PMID: 34149798 PMCID: PMC8206647 DOI: 10.3389/fgene.2021.643935] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Bromodomain (BRD) proteins exhibit a variety of activities, such as histone modification, transcription factor recruitment, chromatin remodeling, and mediator or enhancer complex assembly, that affect transcription initiation and elongation. These proteins also participate in epigenetic regulation. Although specific epigenetic regulation plays an important role in the occurrence and development of cancer, the characteristics of the BRD family in renal clear cell carcinoma (KIRC) have not been determined. In this study, we investigated the expression of BRD family genes in KIRC at the transcriptome level and examined the relationship of the expression of these genes with patient overall survival. mRNA levels of tumor tissues and adjacent tissues were extracted from The Cancer Genome Atlas (TCGA) database. Seven BRD genes (KAT2A, KAT2B, SP140, BRD9, BRPF3, SMARCA2, and EP300) were searched by using LASSO Cox regression and the model with prognostic risk integration. The patients were divided into two groups: high risk and low risk. The combined analysis of these seven BRD genes showed a significant association with the high-risk groups and lower overall survival (OS). This analysis demonstrated that total survival could be predicted well in the low-risk group according to the time-dependent receiver operating characteristic (ROC) curve. The prognosis was determined to be consistent with that obtained using an independent dataset from TCGA. The relevant biological functions were identified using Gene Set Enrichment Analysis (GSEA). In summary, this study provides an optimized survival prediction model and promising data resources for further research investigating the role of the expression of BRD genes in KIRC.
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Affiliation(s)
- Junwan Lu
- Protein Quality Control and Diseases Laboratory, Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | | | - Yongan Ji
- Protein Quality Control and Diseases Laboratory, Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qiyu Bao
- Protein Quality Control and Diseases Laboratory, Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Bin Lu
- Protein Quality Control and Diseases Laboratory, Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
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28
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Quinlan RBA, Brennan PE. Chemogenomics for drug discovery: clinical molecules from open access chemical probes. RSC Chem Biol 2021; 2:759-795. [PMID: 34458810 PMCID: PMC8341094 DOI: 10.1039/d1cb00016k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
In recent years chemical probes have proved valuable tools for the validation of disease-modifying targets, facilitating investigation of target function, safety, and translation. Whilst probes and drugs often differ in their properties, there is a belief that chemical probes are useful for translational studies and can accelerate the drug discovery process by providing a starting point for small molecule drugs. This review seeks to describe clinical candidates that have been inspired by, or derived from, chemical probes, and the process behind their development. By focusing primarily on examples of probes developed by the Structural Genomics Consortium, we examine a variety of epigenetic modulators along with other classes of probe.
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Affiliation(s)
- Robert B A Quinlan
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Old Road Campus Oxford OX3 7FZ UK
| | - Paul E Brennan
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Old Road Campus Oxford OX3 7FZ UK
- Alzheimer's Research (UK) Oxford Drug Discovery Institute, Nuffield Department of Medicine, University of Oxford Oxford OX3 7FZ UK
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29
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Noguchi T, Hidaka K, Kobayashi S, Matsumoto K, Yoshioka M, Hu X, Maloney DJ, Yang SM, Kato S. A quinazoline-based bromodomain inhibitor, CN210, ameliorates indomethacin-induced ileitis in mice by inhibiting inflammatory cytokine expression. Drug Dev Res 2021; 82:1235-1246. [PMID: 34075610 DOI: 10.1002/ddr.21838] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/22/2021] [Accepted: 05/22/2021] [Indexed: 12/24/2022]
Abstract
Inhibitors of bromodomain and extra-terminal motif (BET) proteins are emerging epigenetic therapeutics that suppress gene expressions that drive cancer and inflammation. The present study examined anti-inflammatory effects of a quinazoline-based BET inhibitor, CN210, in a murine ileitis model. CN210 was given orally 30 min before and 24 h after a subcutaneous administration of indomethacin. Macroscopic and histological evidences of ileitis, mucosal myeloperoxidase (MPO) activity and cytokine expressions were evaluated 48 h after the indomethacin administration. To further characterize the anti-inflammatory pathways modulated by CN210, its effects on RAW264 cells treated with lipopolysaccharide (LPS) were investigated. Competitive ligand binding and docking studies of CN210 to CREB-binding protein (CBP) and p300 were also performed. Oral administration of CN210 significantly reduced the severity of ileitis, normalized both proinflammatory MPO activity and concomitant cytokine expressions induced by indomethacin administration. Furthermore, CN210 attenuated the expression of cytokines and reversed the activation of nuclear factor κB (NF-κB) and mitogen-activated protein kinases (MAPK) induced by LPS. Competitive ligand binding assays showed that CN210 bound to the bromodomains of two paralogous histone acetyltransferases, CBP and p300, in addition to the bromodomains of BET proteins. Docking studies of CN210 to the bromodomains of CBP and p300 showed a similarity to the binding mode of SGC-CBP30, a specific CBP/p300 inhibitor. CN210 ameliorates indomethacin-induced ileitis by inhibiting the expression of inflammatory cytokines through the attenuation of NF-κB and MAPK pathways. CN210 thus represents a new mode of therapy for non-steroidal anti-inflammatory drug-induced ileitis and inflammatory bowel disease.
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Affiliation(s)
- Takehisa Noguchi
- Division of Pathological Sciences, Department of Pharmacology and Experimental Therapeutics, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Kyosuke Hidaka
- Division of Pathological Sciences, Department of Pharmacology and Experimental Therapeutics, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Satsuki Kobayashi
- Division of Pathological Sciences, Department of Pharmacology and Experimental Therapeutics, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Kenjiro Matsumoto
- Division of Pathological Sciences, Department of Pharmacology and Experimental Therapeutics, Kyoto Pharmaceutical University, Kyoto, Japan
| | | | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - David J Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Shyh-Ming Yang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Shinichi Kato
- Division of Pathological Sciences, Department of Pharmacology and Experimental Therapeutics, Kyoto Pharmaceutical University, Kyoto, Japan
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30
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Che-1/AATF-induced transcriptionally active chromatin promotes cell proliferation in multiple myeloma. Blood Adv 2021; 4:5616-5630. [PMID: 33186461 DOI: 10.1182/bloodadvances.2020002566] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/28/2020] [Indexed: 12/18/2022] Open
Abstract
Multiple myeloma (MM) is a hematologic malignancy produced by a clonal expansion of plasma cells and characterized by abnormal production and secretion of monoclonal antibodies. This pathology exhibits an enormous heterogeneity resulting not only from genetic alterations but also from several epigenetic dysregulations. Here we provide evidence that Che-1/AATF (Che-1), an interactor of RNA polymerase II, promotes MM proliferation by affecting chromatin structure and sustaining global gene expression. We found that Che-1 depletion leads to a reduction of "active chromatin" by inducing a global decrease of histone acetylation. In this context, Che-1 directly interacts with histones and displaces histone deacetylase class I members from them. Strikingly, transgenic mice expressing human Che-1 in plasma cells develop MM with clinical features resembling those observed in the human disease. Finally, Che-1 downregulation decreases BRD4 chromatin accumulation to further sensitize MM cells to bromodomain and external domain inhibitors. These findings identify Che-1 as a promising target for MM therapy, alone or in combination with bromodomain and external domain inhibitors.
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31
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Wang L, Wang Y, Yang Z, Xu S, Li H. Binding Selectivity of Inhibitors toward Bromodomains BAZ2A and BAZ2B Uncovered by Multiple Short Molecular Dynamics Simulations and MM-GBSA Calculations. ACS OMEGA 2021; 6:12036-12049. [PMID: 34056358 PMCID: PMC8154142 DOI: 10.1021/acsomega.1c00687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
Two Bromodomain-Containing proteins BAZ2A and BAZ2B are responsible for remodeling chromatin and regulating noncoding RNAs. As for our current studies, integration of multiple short molecular dynamics simulations (MSMDSs) with molecular mechanics generalized Born surface area (MM-GBSA) method is adopted for insights into binding selectivity of three small molecules D8Q, D9T and UO1 to BAZ2A against BAZ2B. The calculations of MM-GBSA unveil that selectivity of inhibitors toward BAZ2A and BAZ2B highly depends on the enthalpy changes and the details uncover that D8Q has better selectivity toward BAZ2A than BAZ2B, D9T more favorably bind to BAZ2B than BAZ2A, and UO1 does not show obvious selectivity toward these two proteins. The analysis of interaction network between residues and inhibitors indicates that seven residues are mainly responsible for the selectivity of D8Q, six residues for D9T and four residues provide significant contributions to associations of UO1 with two proteins. Moreover the analysis of interaction network not only reveals warm spots of inhibitor bindings to BAZ2A and BAZ2B but also unveils that common residue pairs, including (W1816, W1887), (P1817, P1888), (F1818, F1889), (V1822, V1893), (N1823, N1894),(L1826, L1897), (V1827, V1898), (F1872, F1943), (N1873, N1944) and (V1879, I1950) belonging to (BAZ2A, BAZ2B), induce mainly binding differences of inhibitors to BAZ2A and BAZ2B. Hence, insights from our current studies offer useful dynamics information relating with conformational alterations and structure-affinity relationship at atomistic levels for novel therapeutic strategies toward BAZ2A and BAZ2B.
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Affiliation(s)
- Lifei Wang
- School
of Science, Shandong Jiaotong University, 5001 Haitang Road, Changqing District, Jinan, Shandong Province 250357, China
| | - Yan Wang
- School
of Science, Shandong Jiaotong University, 5001 Haitang Road, Changqing District, Jinan, Shandong Province 250357, China
| | - Zhiyong Yang
- Department
of Physics, Jiangxi Agricultural University, 1101 Zhimin Road, Economic and Technological
Development Zone, Nanchang, Jiangxi Province 330045, China
| | - Shuobo Xu
- School
of Information Science and Electrical Engineering, Shandong Jiaotong University, 5001 Haitang Road, Changqing District, Jinan, Shandong Province 250357, China
| | - Hongyun Li
- School
of Science, Shandong Jiaotong University, 5001 Haitang Road, Changqing District, Jinan, Shandong Province 250357, China
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The poly(ADP-ribosyl)ation of BRD4 mediated by PARP1 promoted pathological cardiac hypertrophy. Acta Pharm Sin B 2021; 11:1286-1299. [PMID: 34094834 PMCID: PMC8148063 DOI: 10.1016/j.apsb.2020.12.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/18/2020] [Accepted: 10/13/2020] [Indexed: 12/02/2022] Open
Abstract
The bromodomain and extraterminal (BET) family member BRD4 is pivotal in the pathogenesis of cardiac hypertrophy. BRD4 induces hypertrophic gene expression by binding to the acetylated chromatin, facilitating the phosphorylation of RNA polymerases II (Pol II) and leading to transcription elongation. The present study identified a novel post-translational modification of BRD4: poly(ADP-ribosyl)ation (PARylation), that was mediated by poly(ADP-ribose)polymerase-1 (PARP1) in cardiac hypertrophy. BRD4 silencing or BET inhibitors JQ1 and MS417 prevented cardiac hypertrophic responses induced by isoproterenol (ISO), whereas overexpression of BRD4 promoted cardiac hypertrophy, confirming the critical role of BRD4 in pathological cardiac hypertrophy. PARP1 was activated in ISO-induced cardiac hypertrophy and facilitated the development of cardiac hypertrophy. BRD4 was involved in the prohypertrophic effect of PARP1, as implied by the observations that BRD4 inhibition or silencing reversed PARP1-induced hypertrophic responses, and that BRD4 overexpression suppressed the anti-hypertrophic effect of PARP1 inhibitors. Interactions of BRD4 and PARP1 were observed by co-immunoprecipitation and immunofluorescence. PARylation of BRD4 induced by PARP1 was investigated by PARylation assays. In response to hypertrophic stimuli like ISO, PARylation level of BRD4 was elevated, along with enhanced interactions between BRD4 and PARP1. By investigating the PARylation of truncation mutants of BRD4, the C-terminal domain (CTD) was identified as the PARylation modification sites of BRD4. PARylation of BRD4 facilitated its binding to the transcription start sites (TSS) of hypertrophic genes, resulting in enhanced phosphorylation of RNA Pol II and transcription activation of hypertrophic genes. The present findings suggest that strategies targeting inhibition of PARP1-BRD4 might have therapeutic potential for pathological cardiac hypertrophy.
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Key Words
- ANP, atrial natriuretic peptide
- BET, bromodomain and extraterminal domain
- BNP, brain natriuretic polypeptide
- BRD4
- BW, body weight
- CDK9, cyclin-dependent kinase 9
- Cardiac hypertrophy
- EF, ejection fraction
- FBS, fetal bovine serum
- FS, fractional shortening
- HATs, histone acetyltransferases
- HDACs, histone deacetylases
- HE, hematoxylin-eosin
- HW, heart weight
- Hypertrophic genes
- IF, immunofluorescence
- ISO, isoproterenol
- Isoproterenol
- LVAW, left ventricular anterior wall thickness
- LVID, left ventricular internal diameter
- LVPW, left ventricular posterior wall thickness
- NC, negative control
- NRCMs, neonatal rat cardiomyocytes
- NS, normal saline
- PARP1
- PARP1, poly(ADP-ribose)polymerase-1
- PARylation
- PBS, phosphate buffer solution
- PSR, picrosirius red
- RNA Pol II
- RNA Pol II, RNA polymerases II
- SD, Sprague–Dawley
- TL, tibia length
- TSS, transcription start sites
- Transcription activation
- WGA, wheat germ agglutinin
- co-IP, co-immunoprecipitation
- siRNA, small-interfering RNA
- β-AR, β-adrenergic receptor
- β-MHC, β-myosin heavy chain
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The BET inhibitor attenuates the inflammatory response and cell migration in human microglial HMC3 cell line. Sci Rep 2021; 11:8828. [PMID: 33893325 PMCID: PMC8065145 DOI: 10.1038/s41598-021-87828-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/01/2021] [Indexed: 11/08/2022] Open
Abstract
Microglia, resident macrophages of the brain that act as primary immune cells, play essential roles in innate immunity and neuroinflammatory pathologies. Microglial cells are rapidly activated in response to infection and inflammation/injury, associated with the expression of proinflammatory genes and secretion of cytokines. The bromodomain and extra-terminal (BET) inhibitor JQ1 has been shown to be an epigenetic agent that reduces inflammation. In this study, we investigated the mechanisms underlying the anti-inflammatory and anti-migratory functions of JQ1 and the genes targeted by JQ1 in lipopolysaccharide (LPS)-activated human microglial clone 3 (HMC3) cells using RNA-sequencing (RNA-seq). We analyzed the pattern of inflammation-related genes (chemokines, cytokines, and interferon-stimulated genes) and migration-related genes with JQ1 treatment from differentially expressed genes analysis in HMC3 cells. We found that LPS-induced IRF1 directly regulated inflammation- and migration-related genes and that JQ1 significantly reduced IRF1 and its target genes. Additionally, IRF1 attenuation significantly downregulated target genes and inhibited microglial migration. Our data suggest that the BET inhibitor JQ1 can modulate the inflammatory response and migration through the regulation of LPS-induced IRF1 in human microglia.
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34
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Feng L, Yin YY, Liu CH, Xu KR, Li QR, Wu JR, Zeng R. Proteome-wide data analysis reveals tissue-specific network associated with SARS-CoV-2 infection. J Mol Cell Biol 2021; 12:946-957. [PMID: 32642770 PMCID: PMC7454804 DOI: 10.1093/jmcb/mjaa033] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/04/2020] [Accepted: 06/11/2020] [Indexed: 12/14/2022] Open
Abstract
For patients with COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the damages to multiple organs have been clinically observed. Since most of current investigations for virus–host interaction are based on cell level, there is an urgent demand to probe tissue-specific features associated with SARS-CoV-2 infection. Based on collected proteomic datasets from human lung, colon, kidney, liver, and heart, we constructed a virus-receptor network, a virus-interaction network, and a virus-perturbation network. In the tissue-specific networks associated with virus–host crosstalk, both common and different key hubs are revealed in diverse tissues. Ubiquitous hubs in multiple tissues such as BRD4 and RIPK1 would be promising drug targets to rescue multi-organ injury and deal with inflammation. Certain tissue-unique hubs such as REEP5 might mediate specific olfactory dysfunction. The present analysis implies that SARS-CoV-2 could affect multi-targets in diverse host tissues, and the treatment of COVID-19 would be a complex task.
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Affiliation(s)
- Li Feng
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Mollecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan-Yuan Yin
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Mollecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cong-Hui Liu
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Mollecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ke-Ren Xu
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Mollecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing-Run Li
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Mollecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jia-Rui Wu
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Mollecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,CAS Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
| | - Rong Zeng
- CAS Key Laboratory of Systems Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Mollecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.,CAS Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 310024, China
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35
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Sato M, Kondo T, Kohno Y, Seto S. Discovery of benzo[f]pyrido[4,3-b][1,4]oxazepin-10-one derivatives as orally available bromodomain and extra-terminal domain (BET) inhibitors with efficacy in an in vivo psoriatic animal model. Bioorg Med Chem 2021; 34:116015. [PMID: 33549905 DOI: 10.1016/j.bmc.2021.116015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/03/2021] [Accepted: 01/07/2021] [Indexed: 11/25/2022]
Abstract
Bromodomain and extra-terminal domain (BET) protein plays an important role in epigenetic regulation, and the regulation of disruption contributes to the pathogenesis of cancer and inflammatory disease. With the goal of discovering novel BET inhibitors, especially BRD4 inhibitors, we designed and synthesized several compounds starting from our previously reported pyrido-benzodiazepinone derivative 4 to enhance BRD4 inhibitory activity while avoiding hERG inhibition. Molecular docking studies and structure-activity relationship studies led to the identification of 9-fluorobenzo[f]pyrido[4,3-b][1,4]oxazepin-10-one derivative 43, which exhibited potent BRD4 inhibitory activity with excellent potency in imiquimod-induced psoriasis model mice.
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Affiliation(s)
- Masanori Sato
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co., Ltd., 1848, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Takekazu Kondo
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co., Ltd., 1848, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Yasushi Kohno
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co., Ltd., 1848, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan
| | - Shigeki Seto
- Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co., Ltd., 1848, Nogi, Nogi-machi, Shimotsuga-gun, Tochigi 329-0114, Japan.
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36
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Shen H, Li J, Xie X, Yang H, Zhang M, Wang B, Kent KC, Plutzky J, Guo LW. BRD2 regulation of sigma-2 receptor upon cholesterol deprivation. Life Sci Alliance 2021; 4:e201900540. [PMID: 33234676 PMCID: PMC7723276 DOI: 10.26508/lsa.201900540] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/17/2022] Open
Abstract
The sigma-2 receptor (S2R) has long been pharmacologically targeted for antipsychotic treatment and tumor imaging. Only recently was it known for its coding gene and for its role implicated in cholesterol homeostasis. Here, we have investigated the transcriptional control of S2R by the Bromo/ExtraTerminal epigenetic reader family (BETs, including BRD2, 3, and 4) upon cholesterol perturbation. Cholesterol deprivation was induced in ARPE19 cells using a blocker of lysosomal cholesterol export. This condition up-regulated S2R mRNA and protein, and also SREBP2 but not SREBP1, both transcription factors key to cholesterol/fatty acid metabolism. Silencing BRD2 but not BRD3 or BRD4 (though widely deemed a master regulator) averted S2R up-regulation that was induced by cholesterol deprivation. Silencing SREBP2 but not SREBP1 diminished S2R expression. Furthermore, endogenous BRD2 co-immunoprecipitated with the transcription-active N-terminal half of SREBP2, and chromatin immunoprecipitation-qPCR signified co-occupancy of BRD2, H3K27ac (histone acetylation), and SREBP2Nterm at the S2R gene promoter. In summary, this study reveals a previously unrecognized BRD2/SREBP2 cooperative regulation of S2R transcription, thus shedding new light on signaling in response to cholesterol deprivation.
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Affiliation(s)
- Hongtao Shen
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Jing Li
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Xiujie Xie
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Huan Yang
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Mengxue Zhang
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Bowen Wang
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - K Craig Kent
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Jorge Plutzky
- Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lian-Wang Guo
- Department of Surgery, School of Medicine, University of Virginia, Charlottesville, VA, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
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37
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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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38
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Shapiro GI, LoRusso P, Dowlati A, T Do K, Jacobson CA, Vaishampayan U, Weise A, Caimi PF, Eder JP, French CA, Labriola-Tompkins E, Boisserie F, Pierceall WE, Zhi J, Passe S, DeMario M, Kornacker M, Armand P. A Phase 1 study of RO6870810, a novel bromodomain and extra-terminal protein inhibitor, in patients with NUT carcinoma, other solid tumours, or diffuse large B-cell lymphoma. Br J Cancer 2020; 124:744-753. [PMID: 33311588 PMCID: PMC7884382 DOI: 10.1038/s41416-020-01180-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 10/19/2020] [Accepted: 11/05/2020] [Indexed: 01/09/2023] Open
Abstract
Background Bromodomain and extra-terminal (BET) proteins are epigenetic readers that can drive carcinogenesis and therapy resistance. RO6870810 is a novel, small-molecule BET inhibitor. Methods We conducted a Phase 1 study of RO6870810 administered subcutaneously for 21 or 14 days of 28- or 21-day cycles, respectively, in patients with the nuclear protein of the testis carcinoma (NC), other solid tumours, or diffuse large B-cell lymphoma (DLBCL) with MYC deregulation. Results Fatigue (42%), decreased appetite (35%) and injection-site erythema (35%) were the most common treatment-related adverse events. Pharmacokinetic parameters demonstrated linearity over the dose range tested and support once-daily dosing. Pharmacodynamic assessments demonstrated sustained decreases in CD11b levels in peripheral blood mononuclear cells. Objective response rates were 25% (2/8), 2% (1/47) and 11% (2/19) for patients with NC, other solid tumours and DLBCL, respectively. Responding tumours had evidence of deregulated MYC expression. Conclusions This trial establishes the safety, favourable pharmacokinetics, evidence of target engagement and preliminary single-agent activity of RO6870810. Responses in patients with NC, other solid tumours and DLBCL provide proof-of-principle for BET inhibition in MYC-driven cancers. The results support further exploration of RO6870810 as monotherapy and in combinations. Clinical trials registration NCT01987362.
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Affiliation(s)
- Geoffrey I Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute, and Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Patricia LoRusso
- Early Phase Clinical Trials Program, Yale University Medical Center, New Haven, CT, USA
| | - Afshin Dowlati
- Department of Medicine-Hematology and Oncology, University Hospitals Seidman Cancer Center, Cleveland, OH, USA
| | - Khanh T Do
- Department of Medical Oncology, Dana-Farber Cancer Institute, and Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Caron A Jacobson
- Department of Medical Oncology, Dana-Farber Cancer Institute, and Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Amy Weise
- Medical Oncology, Karmanos Cancer Institute, Detroit, MI, USA
| | - Paolo F Caimi
- Department of Medicine-Hematology and Oncology, University Hospitals Seidman Cancer Center, Cleveland, OH, USA
| | - Joseph Paul Eder
- Early Phase Clinical Trials Program, Yale University Medical Center, New Haven, CT, USA
| | - Christopher A French
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Emily Labriola-Tompkins
- Roche Pharma Research and Early Development, Roche Innovation Center New York, New York, NY, USA
| | - Frédéric Boisserie
- Roche Pharma Research and Early Development, Roche Innovation Center New York, New York, NY, USA
| | - William E Pierceall
- Roche Pharma Research and Early Development, Roche Innovation Center New York, New York, NY, USA
| | - Jianguo Zhi
- Roche Pharma Research and Early Development, Roche Innovation Center New York, New York, NY, USA
| | - Sharon Passe
- Roche Pharma Research and Early Development, Roche Innovation Center New York, New York, NY, USA
| | - Mark DeMario
- Roche Pharma Research and Early Development, Roche Innovation Center New York, New York, NY, USA
| | - Martin Kornacker
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Philippe Armand
- Department of Medical Oncology, Dana-Farber Cancer Institute, and Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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39
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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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40
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BRD4 inhibition sensitizes renal cell carcinoma cells to the PI3K/mTOR dual inhibitor VS-5584. Aging (Albany NY) 2020; 12:19147-19158. [PMID: 33051401 PMCID: PMC7732329 DOI: 10.18632/aging.103723] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 06/29/2020] [Indexed: 01/24/2023]
Abstract
Activation of the PI3K/AKT/mTOR pathway promotes the progression of renal cell carcinoma (RCC). This study tested the anti-RCC cell activity of the PI3K/mTOR dual inhibitor, VS-5584. We show that VS-5584 inhibited PI3K/AKT/mTORC1/2 activation in established (786-O and A498 lines) and primary RCC cells, thereby suppressing cell survival, proliferation, migration and cell cycle progression. VS-5584 induced significant apoptosis in RCC cells. A daily single oral dose of VS-5584 (20 mg/kg) significantly inhibited 786-O tumor growth in vivo. VS-5584 treatment of 786-O tumor xenografts and RCC cells resulted in feedback upregulation of bromodomain-containing protein 4 (BRD4). Furthermore, BRD4 inhibition (by JQ1 and CPI203), knockdown or complete knockout potentiated VS-5584-induced RCC cell death and apoptosis. Conversely, forced overexpression of BRD4 attenuated the cytotoxicity of VS-5584 in 786-O cells. Collectively, VS-5584 potently inhibits RCC cell proliferation and survival. Its anti-tumor activity is further enhanced by the targeted inhibition of BRD4.
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41
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Kannan-Sundhari A, Abad C, Maloof ME, Ayad NG, Young JI, Liu XZ, Walz K. Bromodomain Protein BRD4 Is Essential for Hair Cell Function and Survival. Front Cell Dev Biol 2020; 8:576654. [PMID: 33015071 PMCID: PMC7509448 DOI: 10.3389/fcell.2020.576654] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/18/2020] [Indexed: 12/13/2022] Open
Abstract
Hair cells (HCs) play crucial roles in perceiving sound, acceleration, and fluid motion. The tonotopic architecture of the sensory epithelium recognizes mechanical stimuli and convert them into electrical signals. The expression and regulation of the genes in the inner ear is very important to keep the sensory organ functional. Our study is the first to investigate the role of the epigenetic reader Brd4 in the mouse inner ear. We demonstrate that HC specific deletion of Brd4 in vivo in the mouse inner ear is sufficient to cause profound hearing loss (HL), degeneration of stereocilia, nerve fibers and HC loss postnatally in mouse; suggesting an important role in hearing function and maintenance.
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Affiliation(s)
- Abhiraami Kannan-Sundhari
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, FL, United States.,The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, United States
| | - Clemer Abad
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, United States
| | - Marie E Maloof
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Nagi G Ayad
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Juan I Young
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, United States.,John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, United States
| | - Xue Zhong Liu
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, FL, United States.,The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, United States.,John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, United States
| | - Katherina Walz
- The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, United States.,John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, United States
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Pavlova II, Tsvetkov VB, Isaakova EA, Severov VV, Khomyakova EA, Lacis IA, Lazarev VN, Lagarkova MA, Pozmogova GE, Varizhuk AM. Transcription-facilitating histone chaperons interact with genomic and synthetic G4 structures. Int J Biol Macromol 2020; 160:1144-1157. [PMID: 32454109 DOI: 10.1016/j.ijbiomac.2020.05.173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/11/2020] [Accepted: 05/21/2020] [Indexed: 01/26/2023]
Abstract
Affinity for G-quadruplex (G4) structures may be a common feature of transcription-facilitating histone chaperons (HCs). This assumption is based on previous unmatched studies of HCs FACT, nucleolin (NCL), BRD3, and ATRX. We verified this assumption and considered its implications for the therapeutic applications of synthetic (exogenous) G4s and the biological significance of genomic G4s. First, we questioned whether exogenous G4s that recognize cell-surface NCL and could trap other HCs in the nucleus are usable as anticancer agents. We performed in vitro binding assays and selected leading multi-targeted G4s. They exhibited minor effects on cell viability. The presumed NCL-regulated intracellular transport of G4s was inefficient or insufficient for tumor-specific G4 delivery. Next, to clarify whether G4s in the human genome could recruit HCs, we compared available HC ChIP-seq data with G4-seq/G4-ChIP-seq data. Several G4s, including the well-known c-Myc quadruplex structure, were found to be colocalized with HC occupancy sites in cancer cell lines. As evidenced by our molecular modeling data, c-Myc G4 might interfere with the HC function of BRD3 but is unlikely to prevent the BRD3-driven assembly of the chromatin remodeling complex. The c-Myc case illustrates the intricate role of genomic G4s in chromatin remodeling, nucleosome remodeling, and transcription.
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Affiliation(s)
- Iulia I Pavlova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Vladimir B Tsvetkov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Computational Oncology Group, I.M. Sechenov First Moscow State Medical University, Trubetskaya str, 8/2, Moscow 119146, Russia; A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky prospect str. 29, Moscow 119991, Russia
| | - Ekaterina A Isaakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Vyacheslav V Severov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Ekaterina A Khomyakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Ivan A Lacis
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Vassilii N Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Maria A Lagarkova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Galina E Pozmogova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia
| | - Anna M Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia.; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia; Engelhardt Institute of Molecular Biology, Vavilova str. 32, Moscow 119991, Russia.
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Kulikowski E, Rakai BD, Wong NCW. Inhibitors of bromodomain and extra-terminal proteins for treating multiple human diseases. Med Res Rev 2020; 41:223-245. [PMID: 32926459 PMCID: PMC7756446 DOI: 10.1002/med.21730] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/17/2022]
Abstract
Clinical development of bromodomain and extra‐terminal (BET) protein inhibitors differs from the traditional course of drug development. These drugs are simultaneously being evaluated for treating a wide spectrum of human diseases due to their novel mechanism of action. BET proteins are epigenetic “readers,” which play a primary role in transcription. Here, we briefly describe the BET family of proteins, of which BRD4 has been studied most extensively. We discuss BRD4 activity at latent enhancers as an example of BET protein function. We examine BRD4 redistribution and enhancer reprogramming in embryonic development, cancer, cardiovascular, autoimmune, and metabolic diseases, presenting hallmark studies that highlight BET proteins as attractive targets for therapeutic intervention. We review the currently available approaches to targeting BET proteins, methods of selectively targeting individual bromodomains, and review studies that compare the effects of selective BET inhibition to those of pan‐BET inhibition. Lastly, we examine the current clinical landscape of BET inhibitor development.
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44
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Prieto-Martínez FD, Medina-Franco JL. Current advances on the development of BET inhibitors: insights from computational methods. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:127-180. [PMID: 32951810 DOI: 10.1016/bs.apcsb.2020.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Epigenetics was coined almost 70 years ago for the description of heritable phenotype without altering DNA sequences. Research on the field has uncovered significant roles of such mechanisms, that account for the biogenesis of several diseases. Further studies have led the way for drug development which targets epi-enzymes, mainly for cancer treatment. Of the numerous epi-targets involved with histone acetylation, bromodomains have captured the spotlight of drug discovery focused on novel therapies. However, due to high sequence identity, the development of potent and selective inhibitors poses a significant challenge. Herein, we discuss recent computational developments on BET inhibitors and other methods that may be applied for drug discovery in general. As a proof-of-concept, we discuss a virtual screening to identify novel BET inhibitors based on coumarin derivatives. From public data, we identified putative structure-activity relationships of coumarin scaffold and propose R-group modifications for BET selectivity. Results showed that the optimization and design of novel coumarins could be further explored.
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Affiliation(s)
- Fernando D Prieto-Martínez
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
| | - José L Medina-Franco
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
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45
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Abstract
PURPOSE OF REVIEW Emerging evidence has shown that epigenetic derangements might drive and promote tumorigenesis in various types of malignancies and is prevalent in both B cell and T cell lymphomas. The purpose of this review is to explain how the epigenetic derangements result in a chromatin-remodeled state in lymphoma and contribute to the biology and clinical features of these tumors. RECENT FINDINGS Studies have explored on the functional role of epigenetic derangements in chromatin remodeling and lymphomagenesis. For example, the haploinsufficiency of CREBBP facilitates malignant transformation in mice and directly implicates the importance to re-establish the physiologic acetylation level. New findings identified 4 prominent DLBCL subtypes, including EZB-GC-DLBCL subtype that enriched in mutations of CREBBP, EP300, KMT2D, and SWI/SNF complex genes. EZB subtype has a worse prognosis than other GCB-tumors. Moreover, the action of the histone modifiers as well as chromatin-remodeling factors (e.g., SWI/SNF complex) cooperates to influence the chromatin state resulting in transcription repression. Drugs that alter the epigenetic landscape have been approved in T cell lymphoma. In line with this finding, epigenetic lesions in histone modifiers have recently been uncovered in this disease, further confirming the vulnerability to the therapies targeting epigenetic derangements. Modulating the chromatin state by epigenetic-modifying agents provides precision-medicine opportunities to patients with lymphomas that depend on this biology.
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Affiliation(s)
- Yuxuan Liu
- Division of Hematology and Oncology, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, USA
| | - Yulissa Gonzalez
- Division of Hematology and Oncology, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, USA
| | - Jennifer E Amengual
- Division of Hematology and Oncology, Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, USA.
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46
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Targeting bromodomain-containing proteins to prevent spontaneous preterm birth. Clin Sci (Lond) 2020; 133:2379-2400. [PMID: 31750510 DOI: 10.1042/cs20190919] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 12/16/2022]
Abstract
Preterm birth is a global healthcare challenge. Spontaneous preterm birth (sPTB) is commonly caused by inflammation, yet there are currently no effective therapies available. The Bromodomain and Extra-Terminal motif (BET) proteins, Bromodomain-containing protein (Brd) 2 (Brd2), Brd3 and Brd4 regulate inflammation in non-gestational tissues. The roles of Brd2-4 in human pregnancy are unknown. Using human and mouse models, the present study has identified the Brd proteins part of the process by which inflammation induces parturition. Using human clinical samples, we demonstrate that labor and infection increase the expression of Brds in the uterus and fetal membranes. In primary human myometrial, amnion and decidual cells, we found that global Brd protein inhibition, as well as selective inhibition of Brds, suppressed inflammation-induced expression of mediators involved in myometrial contractions and rupture of fetal membranes. Importantly, studies in the mouse model demonstrate that the pan-Brd inhibitor JQ1 reduced intrauterine inflammation induced by bacterial endotoxin LPS as well as decreasing the effectiveness of LPS to induce parturition. These results implicate BET proteins as novel therapeutic targets for reducing inflammation associated with spontaneous preterm labor.
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47
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Olp MD, Sprague DJ, Goetz CJ, Kathman SG, Wynia-Smith SL, Shishodia S, Summers SB, Xu Z, Statsyuk AV, Smith BC. Covalent-Fragment Screening of BRD4 Identifies a Ligandable Site Orthogonal to the Acetyl-Lysine Binding Sites. ACS Chem Biol 2020; 15:1036-1049. [PMID: 32149490 DOI: 10.1021/acschembio.0c00058] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BRD4, a member of the bromodomain and extraterminal domain (BET) family, has emerged as a promising epigenetic target in cancer and inflammatory disorders. All reported BET family ligands bind within the bromodomain acetyl-lysine binding sites and competitively inhibit BET protein interaction with acetylated chromatin. Alternative chemical probes that act orthogonally to the highly conserved acetyl-lysine binding sites may exhibit selectivity within the BET family and avoid recently reported toxicity in clinical trials of BET bromodomain inhibitors. Here, we report the first identification of a ligandable site on a bromodomain outside the acetyl-lysine binding site. Inspired by our computational prediction of hotspots adjacent to nonhomologous cysteine residues within the C-terminal BRD4 bromodomain (BRD4-BD2), we performed a midthroughput mass spectrometry screen to identify cysteine-reactive fragments that covalently and selectively modify BRD4. Subsequent mass spectrometry, NMR, and computational docking analyses of electrophilic fragment hits revealed a novel ligandable site near Cys356 that is unique to BRD4 among human bromodomains. This site is orthogonal to the BRD4-BD2 acetyl-lysine binding site as Cys356 modification did not impact binding of the pan-BET bromodomain inhibitor JQ1 in fluorescence polarization assays nor an acetylated histone peptide in AlphaScreen assays. Finally, we tethered our top-performing covalent fragment to JQ1 and performed NanoBRET assays to provide proof of principle that this orthogonal site can be covalently targeted in intact human cells. Overall, we demonstrate the potential of targeting sites orthogonal to bromodomain acetyl-lysine binding sites to develop bivalent and covalent inhibitors that displace BRD4 from chromatin.
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Affiliation(s)
- Michael D. Olp
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Daniel J. Sprague
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Christopher J. Goetz
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Stefan G. Kathman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Sarah L. Wynia-Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Shifali Shishodia
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Steven B. Summers
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Ziyang Xu
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Alexander V. Statsyuk
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- College of Pharmacy, University of Houston, Houston, Texas 77004, United States
| | - Brian C. Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
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Wisniewski A, Georg GI. BET proteins: Investigating BRDT as a potential target for male contraception. Bioorg Med Chem Lett 2020; 30:126958. [PMID: 32019712 PMCID: PMC7023680 DOI: 10.1016/j.bmcl.2020.126958] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/01/2020] [Accepted: 01/02/2020] [Indexed: 02/06/2023]
Abstract
While many contraception options are available for women, birth control methods for men are limited to condoms and vasectomy. Past research into male contraceptives has focused on hormonal options but the associated side effects have thus far precluded this method from reaching the market. Non-hormonal male contraceptives and vas occlusion have also been explored, but to date no method has progressed past clinical testing. Recent interest in epigenetic research has unveiled a new potential non-hormonal male contraceptive target: the testis-specific bromodomain BRDT. Potent inhibitors for bromodomain-containing proteins are described in the literature, but a BRDT-specific compound has yet to be designed, prepared and tested. The high similarity between bromodomain proteins of the BET family makes development of selective and specific inhibitors both difficult and necessary. Selective inhibition of BRDT by a small molecule is an exciting new target in the search for a new non-hormonal male contraceptive.
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Affiliation(s)
- Andrea Wisniewski
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55414, United States
| | - Gunda I Georg
- Department of Medicinal Chemistry and Institute for Therapeutics Discovery and Development, College of Pharmacy, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN 55414, United States.
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49
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Tonini C, Colardo M, Colella B, Di Bartolomeo S, Berardinelli F, Caretti G, Pallottini V, Segatto M. Inhibition of Bromodomain and Extraterminal Domain (BET) Proteins by JQ1 Unravels a Novel Epigenetic Modulation to Control Lipid Homeostasis. Int J Mol Sci 2020; 21:ijms21041297. [PMID: 32075110 PMCID: PMC7072965 DOI: 10.3390/ijms21041297] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/08/2020] [Accepted: 02/13/2020] [Indexed: 12/19/2022] Open
Abstract
The homeostatic control of lipid metabolism is essential for many fundamental physiological processes. A deep understanding of its regulatory mechanisms is pivotal to unravel prospective physiopathological factors and to identify novel molecular targets that could be employed to design promising therapies in the management of lipid disorders. Here, we investigated the role of bromodomain and extraterminal domain (BET) proteins in the regulation of lipid metabolism. To reach this aim, we used a loss-of-function approach by treating HepG2 cells with JQ1, a powerful and selective BET inhibitor. The main results demonstrated that BET inhibition by JQ1 efficiently decreases intracellular lipid content, determining a significant modulation of proteins involved in lipid biosynthesis, uptake and intracellular trafficking. Importantly, the capability of BET inhibition to slow down cell proliferation is dependent on the modulation of cholesterol metabolism. Taken together, these data highlight a novel epigenetic mechanism involved in the regulation of lipid homeostasis.
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Affiliation(s)
- Claudia Tonini
- Department of Science, University of Rome “Roma Tre”, Viale Marconi 446, 00146 Rome, Italy; (C.T.); (F.B.); (V.P.)
| | - Mayra Colardo
- Department of Bioscience and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche (Is), Italy; (M.C.); (B.C.); (S.D.B.)
| | - Barbara Colella
- Department of Bioscience and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche (Is), Italy; (M.C.); (B.C.); (S.D.B.)
| | - Sabrina Di Bartolomeo
- Department of Bioscience and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche (Is), Italy; (M.C.); (B.C.); (S.D.B.)
| | - Francesco Berardinelli
- Department of Science, University of Rome “Roma Tre”, Viale Marconi 446, 00146 Rome, Italy; (C.T.); (F.B.); (V.P.)
| | - Giuseppina Caretti
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy;
| | - Valentina Pallottini
- Department of Science, University of Rome “Roma Tre”, Viale Marconi 446, 00146 Rome, Italy; (C.T.); (F.B.); (V.P.)
| | - Marco Segatto
- Department of Bioscience and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche (Is), Italy; (M.C.); (B.C.); (S.D.B.)
- Correspondence:
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50
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Abstract
The epigenetic modifications of histones are versatile marks that are intimately connected to development and disease pathogenesis including human cancers. In this review, we will discuss the many different types of histone modifications and the biological processes with which they are involved. Specifically, we review the enzymatic machineries and modifications that are involved in cancer development and progression, and how to apply currently available small molecule inhibitors for histone modifiers as tool compounds to study the functional significance of histone modifications and their clinical implications.
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Affiliation(s)
- Zibo Zhao
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Simpson Querrey 7th Floor 303 E. Superior Street, Chicago, IL 60611 USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Simpson Querrey 7th Floor 303 E. Superior Street, Chicago, IL 60611 USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
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