1
|
Wu M, Guan G, Yin H, Niu Q. A Review of the Bromodomain and Extraterminal Domain Epigenetic Reader Proteins: Function on Virus Infection and Cancer. Viruses 2024; 16:1096. [PMID: 39066258 PMCID: PMC11281655 DOI: 10.3390/v16071096] [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: 05/21/2024] [Revised: 06/28/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
The BET (bromodomain and extraterminal domain) family of proteins, particularly BRD4 (bromodomain-containing protein 4), plays a crucial role in transcription regulation and epigenetic mechanisms, impacting key cellular processes such as proliferation, differentiation, and the DNA damage response. BRD4, the most studied member of this family, binds to acetylated lysines on both histones and non-histone proteins, thereby regulating gene expression and influencing diverse cellular functions such as the cell cycle, tumorigenesis, and immune responses to viral infections. Given BRD4's involvement in these fundamental processes, it is implicated in various diseases, including cancer and inflammation, making it a promising target for therapeutic development. This review comprehensively explores the roles of the BET family in gene transcription, DNA damage response, and viral infection, discussing the potential of targeted small-molecule compounds and highlighting BET proteins as promising candidates for anticancer therapy.
Collapse
Affiliation(s)
- Mengli Wu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China; (M.W.); (G.G.); (H.Y.)
- African Swine Fever Regional Laboratory of China (Lanzhou), Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Guiquan Guan
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China; (M.W.); (G.G.); (H.Y.)
- African Swine Fever Regional Laboratory of China (Lanzhou), Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Hong Yin
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China; (M.W.); (G.G.); (H.Y.)
- African Swine Fever Regional Laboratory of China (Lanzhou), Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Qingli Niu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China; (M.W.); (G.G.); (H.Y.)
- African Swine Fever Regional Laboratory of China (Lanzhou), Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| |
Collapse
|
2
|
Garg S, Ni W, Chowdhury B, Weisberg EL, Sattler M, Griffin JD. BRD9 regulates normal human hematopoietic stem cell function and lineage differentiation. Cell Death Differ 2024; 31:868-880. [PMID: 38816579 PMCID: PMC11239944 DOI: 10.1038/s41418-024-01306-5] [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: 02/26/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024] Open
Abstract
Bromodomain containing protein 9 (BRD9), a member of the non-canonical BRG1/BRM-associated factor (ncBAF) chromatin remodeling complex, has been implicated as a synthetic lethal target in AML but its function in normal human hematopoiesis is unknown. In hematopoietic stem and progenitor cells (HSPC) genomic or chemical inhibition of BRD9 led to a proliferative disadvantage and loss of stem cells in vitro. Human HSPCs with reduced BRD9 protein levels produced lower numbers of immature mixed multipotent GEMM colonies in semi-solid media. In lineage-promoting culture conditions, cells with reduced BRD9 levels failed to differentiate into the megakaryocytic lineage and showed delayed differentiation into erythroid cells but enhanced terminal myeloid differentiation. HSPCs with BRD9 knock down (KD) had reduced long-term multilineage engraftment in a xenotransplantation assay. An increased number of downregulated genes in RNAseq analysis after BRD9 KD coupled with a gain in chromatin accessibility at the promoters of several repressive transcription factors (TF) suggest that BRD9 functions in the maintenance of active transcription during HSC differentiation. In particular, the hematopoietic master regulator GATA1 was identified as one of the core TFs regulating the gene networks modulated by BRD9 loss in HSPCs. BRD9 inhibition reduced a GATA1-luciferase reporter signal, further suggesting a role for BRD9 in regulating GATA1 activity. BRD9 is therefore an additional example of epigenetic regulation of human hematopoiesis.
Collapse
Affiliation(s)
- Swati Garg
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Wei Ni
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Basudev Chowdhury
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Ellen L Weisberg
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - Martin Sattler
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA
| | - James D Griffin
- Dana-Farber Cancer Institute, Dept. of Medical Oncology, Boston, MA, 02215, USA.
- Harvard Medical School, Dept. of Medicine, Boston, MA, 02215, USA.
| |
Collapse
|
3
|
Viviano M, Cipriano A, Fabbrizi E, Feoli A, Castellano S, Sbardella G, Mai A, Milite C, Rotili D. Successes and challenges in the development of BD1-selective BET inhibitors: a patent review. Expert Opin Ther Pat 2024; 34:529-545. [PMID: 38465537 DOI: 10.1080/13543776.2024.2327300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/01/2024] [Indexed: 03/12/2024]
Abstract
INTRODUCTION Bromodomain and ExtraTerminal (BET) domain proteins are transcriptional cofactors that, recognizing acetylated lysines of histone and non-histone proteins, can modulate gene expression. The BET family consists of four members, each of which contains two bromodomains (BD1 and BD2) able to recognize the acetylated mark. Pan-BET inhibitors (BETi) have shown a promising anticancer potential in many clinical trials; however, their further development has been in part hampered by the side effects due to their lack of selectivity. Mounting evidence suggests that BD1 is primarily involved in cancer and that its selective inhibition can phenocopy the anticancer effects of pan-BETi with increased tolerability. Therefore, the development of BD1 selective inhibitors is highly pursed in both academia and industry. AREAS COVERED This review aims at giving an overview of the patent literature of BD1-selective BETi between 2014 and 2023. WIPO, USPTO, EPO, and SciFinder® databases were used for the search of patents. EXPERT OPINION The development of BD1-selective BETi, despite challenging, is highly desirable as it could have a great impact on the development of new safer anticancer therapeutics. Several strategies could be applied to discover potent and selective compounds with limited side effects.
Collapse
Affiliation(s)
- Monica Viviano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano, SA, Italy
| | - Alessandra Cipriano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano, SA, Italy
| | - Emanuele Fabbrizi
- Department of Drug Chemistry & Technologies, Sapienza University of Rome, Rome, Italy
| | - Alessandra Feoli
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano, SA, Italy
| | - Sabrina Castellano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano, SA, Italy
| | - Gianluca Sbardella
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano, SA, Italy
| | - Antonello Mai
- Department of Drug Chemistry & Technologies, Sapienza University of Rome, Rome, Italy
| | - Ciro Milite
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Fisciano, SA, Italy
| | - Dante Rotili
- Department of Drug Chemistry & Technologies, Sapienza University of Rome, Rome, Italy
| |
Collapse
|
4
|
Seifritz T, Brunner M, Camarillo Retamosa E, Maciukiewicz M, Krošel M, Moser L, Züllig T, Tomšič M, Distler O, Ospelt C, Klein K. BRD3 Regulates the Inflammatory and Stress Response in Rheumatoid Arthritis Synovial Fibroblasts. Biomedicines 2023; 11:3188. [PMID: 38137409 PMCID: PMC10741099 DOI: 10.3390/biomedicines11123188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/18/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND Individual functions of members of the bromodomain (BRD) and extra-terminal (BET) protein family underlying the anti-inflammatory effects of BET inhibitors in rheumatoid arthritis (RA) are incompletely understood. Here, we aimed to analyze the regulatory functions of BRD3, an understudied member of the BET protein family, in RA synovial fibroblasts (FLS). METHODS BRD3 was silenced in FLS prior to stimulation with TNF. Alternatively, FLS were treated with I-BET. Transcriptomes were analyzed by RNA sequencing (RNAseq), followed by pathway enrichment analysis. We confirmed results for selective target genes by real-time PCR, ELISA, and Western blotting. RESULTS BRD3 regulates the expression of several cytokines and chemokines in FLS, and positively correlates with inflammatory scores in the RA synovium. In addition, RNAseq pointed to a profound role of BRD3 in regulating FLS proliferation, metabolic adaption, and response to stress, including oxidative stress, and autophagy. CONCLUSIONS BRD3 acts as an upstream regulatory factor that integrates the response to inflammatory stimuli and stress conditions in FLS and executes many functions of BET proteins that have previously been identified using pan-BET inhibitors.
Collapse
Affiliation(s)
- Tanja Seifritz
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland (E.C.R.)
| | - Matthias Brunner
- Department of Rheumatology and Immunology, Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Eva Camarillo Retamosa
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland (E.C.R.)
| | - Malgorzata Maciukiewicz
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland (E.C.R.)
- Department of Rheumatology and Immunology, Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Monika Krošel
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland (E.C.R.)
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Larissa Moser
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland (E.C.R.)
| | - Thomas Züllig
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland (E.C.R.)
| | - Matija Tomšič
- Department of Rheumatology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Oliver Distler
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland (E.C.R.)
| | - Caroline Ospelt
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland (E.C.R.)
| | - Kerstin Klein
- Department of Rheumatology and Immunology, Inselspital, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| |
Collapse
|
5
|
Elmaidomy AH, El Zawily A, Salem AK, Altemani FH, Algehainy NA, Altemani AH, Rateb ME, Abdelmohsen UR, Shady NH. New cytotoxic dammarane type saponins from Ziziphus spina-christi. Sci Rep 2023; 13:20612. [PMID: 37996449 PMCID: PMC10667233 DOI: 10.1038/s41598-023-46841-2] [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: 06/30/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023] Open
Abstract
Cancer is the world's second-leading cause of death. Drug development efforts frequently focus on medicinal plants since they are a valuable source of anticancer medications. A phytochemical investigation of the edible Ziziphus spina-christi (F. Rhamnaceae) leaf extract afforded two new dammarane type saponins identified as christinin E and F (1, 2), along with the known compound christinin A (3). Different cancer cell lines, such as lung cancer (A549), glioblastoma (U87), breast cancer (MDA-MB-231), and colorectal carcinoma (CT-26) cell lines, were used to investigate the extracted compounds' cytotoxic properties. Our findings showed significant effects on all the tested cell lines at varying concentrations (1, 5, 10, and 20 µg/mL). The three compounds exhibited potent activity at low concentrations (< 10 μg/mL), as evidenced by their low IC50 values. To further investigate the complex relationships between these identified cancer-relevant biological targets and to identify critical targets in the pathogenesis of the disease, we turned to network pharmacology and in silico-based investigations. Following this, in silico-based analysis (e.g., inverse docking, ΔG calculation, and molecular dynamics simulation) was performed on the structures of the isolated compounds to identify additional potential targets for these compounds and their likely interactions with various signalling pathways relevant to this disease. Based on our findings, Z. spina-christi's compounds showed promise as potential anti-cancer therapeutic leads in the future.
Collapse
Affiliation(s)
- Abeer H Elmaidomy
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt
| | - Amr El Zawily
- Department of Plant and Microbiology, Faculty of Science, Damanhour University, Damanhour, 22511, Egypt.
- Division of Pharmaceutics and Translational Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA, 52242, USA.
| | - Aliasger K Salem
- Division of Pharmaceutics and Translational Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA, 52242, USA
| | - Faisal H Altemani
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, 71491, Tabuk, Saudi Arabia
| | - Naseh A Algehainy
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, 71491, Tabuk, Saudi Arabia
| | - Abdullah H Altemani
- Department of Family and Community Medicine, Faculty of Medicine, University of Tabuk, 71491, Tabuk, Saudi Arabia
| | - Mostafa E Rateb
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt.
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, New Minia, 61111, Egypt.
| | - Nourhan Hisham Shady
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, New Minia, 61111, Egypt
| |
Collapse
|
6
|
Wang ZQ, Zhang ZC, Wu YY, Pi YN, Lou SH, Liu TB, Lou G, Yang C. Bromodomain and extraterminal (BET) proteins: biological functions, diseases, and targeted therapy. Signal Transduct Target Ther 2023; 8:420. [PMID: 37926722 PMCID: PMC10625992 DOI: 10.1038/s41392-023-01647-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/23/2023] [Accepted: 09/12/2023] [Indexed: 11/07/2023] Open
Abstract
BET proteins, which influence gene expression and contribute to the development of cancer, are epigenetic interpreters. Thus, BET inhibitors represent a novel form of epigenetic anticancer treatment. Although preliminary clinical trials have shown the anticancer potential of BET inhibitors, it appears that these drugs have limited effectiveness when used alone. Therefore, given the limited monotherapeutic activity of BET inhibitors, their use in combination with other drugs warrants attention, including the meaningful variations in pharmacodynamic activity among chosen drug combinations. In this paper, we review the function of BET proteins, the preclinical justification for BET protein targeting in cancer, recent advances in small-molecule BET inhibitors, and preliminary clinical trial findings. We elucidate BET inhibitor resistance mechanisms, shed light on the associated adverse events, investigate the potential of combining these inhibitors with diverse therapeutic agents, present a comprehensive compilation of synergistic treatments involving BET inhibitors, and provide an outlook on their future prospects as potent antitumor agents. We conclude by suggesting that combining BET inhibitors with other anticancer drugs and innovative next-generation agents holds great potential for advancing the effective targeting of BET proteins as a promising anticancer strategy.
Collapse
Affiliation(s)
- Zhi-Qiang Wang
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Zhao-Cong Zhang
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Yu-Yang Wu
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Ya-Nan Pi
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Sheng-Han Lou
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Tian-Bo Liu
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China
| | - Ge Lou
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China.
| | - Chang Yang
- Department of Gynecology Oncology, Harbin Medical University Cancer Hospital, Harbin, 150086, China.
| |
Collapse
|
7
|
Mohammed A, Waddell MB, Sutkeviciute I, Danda A, Philips SJ, Lang W, Slavish PJ, Kietlinska SJ, Kaulage M, Sourav D, Ansari AZ. Domain-Selective BET Ligands Yield Next-Generation Synthetic Genome Readers/Regulators with Nonidentical Cellular Functions. J Am Chem Soc 2023. [PMID: 37923569 DOI: 10.1021/jacs.3c06297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
SynTEF1, a prototype synthetic genome reader/regulator (SynGR), was designed to target GAA triplet repeats and restore the expression of frataxin (FXN) in Friedreich's ataxia patients. It achieves this complex task by recruiting BRD4, via a pan-BET ligand (JQ1), to the GAA repeats by using a sequence-selective DNA-binding polyamide. When bound to specific genomic loci in this way, JQ1 functions as a chemical prosthetic for acetyl-lysine residues that are natural targets of the two tandem bromodomains (BD1 and BD2) in bromo- and extra-terminal domain (BET) proteins. As next-generation BET ligands were disclosed, we tested a select set with improved physicochemical, pharmacological, and bromodomain-selective properties as substitutes for JQ1 in the SynGR design. Here, we report two unexpected findings: (1) SynGRs bearing pan-BET or BD2-selective ligands license transcription at the FXN locus, whereas those bearing BD1-selective ligands do not, and (2) rather than being neutral or inhibitory, an untethered BD1-selective ligand (GSK778) substantively enhances the activity of all active SynGRs. The failure of BD1-selective SynGRs to recruit BRD4/BET proteins suggests that rather than functioning as "epigenetic/chromatin mimics," active SynGRs mimic the functions of natural transcription factors in engaging BET proteins through BD2 binding. Moreover, the enhanced activity of SynGRs upon cotreatment with the BD1-selective ligand suggests that natural transcription factors compete for a limited pool of nonchromatin-bound BET proteins, and blocking BD1 directs pan-BET ligands to more effectively engage BD2. Taken together, SynGRs as chemical probes provide unique insights into the molecular recognition principles utilized by natural factors to precisely regulate gene expression, and they guide the design of more sophisticated synthetic gene regulators with greater therapeutic potential.
Collapse
Affiliation(s)
- Ashraf Mohammed
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - M Brett Waddell
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Ieva Sutkeviciute
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Adithi Danda
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Steven J Philips
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Walter Lang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - P Jake Slavish
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Sandra J Kietlinska
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Mangesh Kaulage
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Das Sourav
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Aseem Z Ansari
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| |
Collapse
|
8
|
Shi M, Zheng X, Zhou Y, Yin Y, Lu Z, Zou Z, Hu Y, Liang Y, Chen T, Yang Y, Jing M, Lei D, Yang P, Li X. Selectivity Mechanism of Pyrrolopyridone Analogues Targeting Bromodomain 2 of Bromodomain-Containing Protein 4 from Molecular Dynamics Simulations. ACS OMEGA 2023; 8:33658-33674. [PMID: 37744850 PMCID: PMC10515184 DOI: 10.1021/acsomega.3c03935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023]
Abstract
Bromodomain and extra-terminal domain (BET) proteins play an important role in epigenetic regulation and are linked to several diseases; therefore, they are interesting targets. BET has two bromodomains: bromodomain 1 (BD1) and BD2. Selective targeting of BD1 or BD2 may produce different activities and greater effects than pan-BD inhibitors. However, the selective mechanism of the specific core must be studied at the atomic level. This study determined the effectiveness of pyrrolopyridone analogues to selectively inhibit BD2 using a pan-BD inhibitor (ABBV-075) and a selective-BD2 inhibitor (ABBV-744). Molecular dynamics simulations and calculations of binding free energies were used to systematically study the selectivity of BD2 inhibition by the pyrrolopyridone analogues. Overall, the pyrrolopyridone analogue inhibitors targeting BD2 interacted mainly with the following amino acid pairs between bromodomain-containing protein 4 (BRD4)-BD1 and BRD4-BD2 complexes: I146/V439, N140/N433, D144/H437, P82/P375, V87/V380, D88/D381, and Y139/Y432. The pyrrolopyridone analogues targeting BRD4-BD2 were divided into five regions based on selectivity mechanism. These results suggest that the R3 and R5 regions of pyrrolopyridone analogues can be modified to improve the selectivity between BRD4-BD1 and BRD4-BD2. The selectivity of BD2 inhibition by pyrrolopyridone analogues can be used to design novel BD2 inhibitors based on a pyrrolopyridone core.
Collapse
Affiliation(s)
- Mingsong Shi
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
- Innovation
Center of Nursing Research, Nursing Key Laboratory of Sichuan Province,
West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Xueting Zheng
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yan Zhou
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yuan Yin
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Zhou Lu
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Zhiyan Zou
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yan Hu
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yuanyuan Liang
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Tingting Chen
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yuhan Yang
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Meng Jing
- Department
of Pathology, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of
China, Mianyang 621099, Sichuan, China
| | - Dan Lei
- School
of Life Science and Engineering, Southwest
University of Science and Technology, Mianyang 621010, Sichuan, China
| | - Pei Yang
- Department
of Hepatobiliary Surgery, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of
China, Mianyang 621099, Sichuan, China
| | - Xiaoan Li
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| |
Collapse
|
9
|
Yan Z, Lyu X, Lin D, Wu G, Gong Y, Ren X, Xiao J, Lou J, Huang H, Chen Y, Zhao Y. Selective degradation of cellular BRD3 and BRD4-L promoted by PROTAC molecules in six cancer cell lines. Eur J Med Chem 2023; 254:115381. [PMID: 37084596 DOI: 10.1016/j.ejmech.2023.115381] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/30/2023] [Accepted: 04/13/2023] [Indexed: 04/23/2023]
Abstract
Targeted degradation of BET family proteins BRD2/3/4 or only BRD4 with PROTAC molecules has been a promising strategy for the treatment of human cancer. Meanwhile, selective degradation of cellular BRD3 and BRD4-L remains a challenging task. We report herein a novel PROTAC molecule 24 that promoted selective degradation of cellular BRD3 and BRD4-L, but not BRD2 or BRD4-S, in a panel of six cancer cell lines. The observed target selectivity was partially attributed to differences in protein degradation kinetics and in types of cell lines. In a MM.1S mouse xenograft model, an optimized lead compound 28 promoted selective degradation of BRD3 and BRD4-L in vivo and exhibited robust antitumor activity. In summary, we have demonstrated that selective degradation of BRD3 and BRD4-L over BRD2 and BRD4-S is a feasible and robust approach in multiple cancer cell lines and an animal model, which could be helpful for further investigations on BRD3 and BRD4-L that ultimately benefitting cancer research and therapeutics.
Collapse
Affiliation(s)
- Ziqin Yan
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Xilin Lyu
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Dongze Lin
- Cancer Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Gaoxing Wu
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Yang Gong
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, China
| | - Xuelian Ren
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Jian Xiao
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China; Cancer Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Jianfeng Lou
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - He Huang
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China
| | - Yi Chen
- Cancer Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China.
| | - Yujun Zhao
- State Key Laboratory of Drug Research and Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd, Shanghai, 201203, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China; Shandong Provincial Key Laboratory of Biopharmaceuticals, Shandong Academy of Pharmaceutical Sciences, Jinan, 250101, China.
| |
Collapse
|
10
|
Regulation of Cell Plasticity by Bromodomain and Extraterminal Domain (BET) Proteins: A New Perspective in Glioblastoma Therapy. Int J Mol Sci 2023; 24:ijms24065665. [PMID: 36982740 PMCID: PMC10055343 DOI: 10.3390/ijms24065665] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
BET proteins are a family of multifunctional epigenetic readers, mainly involved in transcriptional regulation through chromatin modelling. Transcriptome handling ability of BET proteins suggests a key role in the modulation of cell plasticity, both in fate decision and in lineage commitment during embryonic development and in pathogenic conditions, including cancerogenesis. Glioblastoma is the most aggressive form of glioma, characterized by a very poor prognosis despite the application of a multimodal therapy. Recently, new insights are emerging about the glioblastoma cellular origin, leading to the hypothesis that several putative mechanisms occur during gliomagenesis. Interestingly, epigenome dysregulation associated with loss of cellular identity and functions are emerging as crucial features of glioblastoma pathogenesis. Therefore, the emerging roles of BET protein in glioblastoma onco-biology and the compelling demand for more effective therapeutic strategies suggest that BET family members could be promising targets for translational breakthroughs in glioblastoma treatment. Primarily, “Reprogramming Therapy”, which is aimed at reverting the malignant phenotype, is now considered a promising strategy for GBM therapy.
Collapse
|
11
|
Vermunt MW, Luan J, Zhang Z, Thrasher AJ, Huang A, Saari MS, Khandros E, Beagrie RA, Zhang S, Vemulamada P, Brilleman M, Lee K, Yano JA, Giardine BM, Keller CA, Hardison RC, Blobel GA. Gene silencing dynamics are modulated by transiently active regulatory elements. Mol Cell 2023; 83:715-730.e6. [PMID: 36868189 PMCID: PMC10719944 DOI: 10.1016/j.molcel.2023.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 12/05/2022] [Accepted: 02/03/2023] [Indexed: 03/05/2023]
Abstract
Transcriptional enhancers have been extensively characterized, but cis-regulatory elements involved in acute gene repression have received less attention. Transcription factor GATA1 promotes erythroid differentiation by activating and repressing distinct gene sets. Here, we study the mechanism by which GATA1 silences the proliferative gene Kit during murine erythroid cell maturation and define stages from initial loss of activation to heterochromatinization. We find that GATA1 inactivates a potent upstream enhancer but concomitantly creates a discrete intronic regulatory region marked by H3K27ac, short noncoding RNAs, and de novo chromatin looping. This enhancer-like element forms transiently and serves to delay Kit silencing. The element is ultimately erased via the FOG1/NuRD deacetylase complex, as revealed by the study of a disease-associated GATA1 variant. Hence, regulatory sites can be self-limiting by dynamic co-factor usage. Genome-wide analyses across cell types and species uncover transiently active elements at numerous genes during repression, suggesting that modulation of silencing kinetics is widespread.
Collapse
Affiliation(s)
- Marit W Vermunt
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Jing Luan
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhe Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Pennsylvania, Philadelphia, PA 19104, USA
| | - A Josephine Thrasher
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Anran Huang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Megan S Saari
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Eugene Khandros
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Robert A Beagrie
- Chromatin and Disease Group, Wellcome Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Shiping Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pranay Vemulamada
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Matilda Brilleman
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kiwon Lee
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jennifer A Yano
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Belinda M Giardine
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| |
Collapse
|
12
|
Dong J, Wang X. Identification of novel BRD4 inhibitors by pharmacophore screening, molecular docking, and molecular dynamics simulation. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
13
|
Zerio CJ, Sivinski J, Wijeratne EMK, Xu YM, Ngo DT, Ambrose AJ, Villa-Celis L, Ghadirian N, Clarkson MW, Zhang DD, Horton NC, Gunatilaka AAL, Fromme R, Chapman E. Physachenolide C is a Potent, Selective BET Inhibitor. J Med Chem 2023; 66:913-933. [PMID: 36577036 DOI: 10.1021/acs.jmedchem.2c01770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A pulldown using a biotinylated natural product of interest in the 17β-hydroxywithanolide (17-BHW) class, physachenolide C (PCC), identified the bromodomain and extra-terminal domain (BET) family of proteins (BRD2, BRD3, and BRD4), readers of acetyl-lysine modifications and regulators of gene transcription, as potential cellular targets. BROMOscan bromodomain profiling and biochemical assays support PCC as a BET inhibitor with increased selectivity for bromodomain (BD)-1 of BRD3 and BRD4, and X-ray crystallography and NMR studies uncovered specific contacts that underlie the potency and selectivity of PCC toward BRD3-BD1 over BRD3-BD2. PCC also displays characteristics of a molecular glue, facilitating proteasome-mediated degradation of BRD3 and BRD4. Finally, PCC is more potent than other withanolide analogues and gold-standard pan-BET inhibitor (+)-JQ1 in cytotoxicity assays across five prostate cancer (PC) cell lines regardless of androgen receptor (AR)-signaling status.
Collapse
Affiliation(s)
- Christopher J Zerio
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Jared Sivinski
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - E M Kithsiri Wijeratne
- College of Agriculture and Life Sciences, School of Natural Resources and the Environment, Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
| | - Ya-Ming Xu
- College of Agriculture and Life Sciences, School of Natural Resources and the Environment, Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
| | - Duc T Ngo
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Andrew J Ambrose
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Luis Villa-Celis
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Niloofar Ghadirian
- Department of Molecular and Cellular Biology, University of Arizona, 1007 E. Lowell Street, Tucson, Arizona 85721, United States
| | - Michael W Clarkson
- Department of Chemistry and Biochemistry, University of Arizona, 1041 E. Lowell Street, Tucson, Arizona 85719, United States
| | - Donna D Zhang
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| | - Nancy C Horton
- Department of Molecular and Cellular Biology, University of Arizona, 1007 E. Lowell Street, Tucson, Arizona 85721, United States
| | - A A Leslie Gunatilaka
- College of Agriculture and Life Sciences, School of Natural Resources and the Environment, Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
| | - Raimund Fromme
- School of Molecular Sciences, Biodesign Institute, Arizona State University, 1001 S. McAllister Avenue, Tempe, Arizona 85287, United States
| | - Eli Chapman
- College of Pharmacy, Department of Pharmacology and Toxicology, University of Arizona, 1703 E. Mabel Street, PO Box 210207, Tucson, Arizona 85721, United States
| |
Collapse
|
14
|
Shang S, Liu J, Hua F. Protein acylation: mechanisms, biological functions and therapeutic targets. Signal Transduct Target Ther 2022; 7:396. [PMID: 36577755 PMCID: PMC9797573 DOI: 10.1038/s41392-022-01245-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/27/2022] [Accepted: 11/06/2022] [Indexed: 12/30/2022] Open
Abstract
Metabolic reprogramming is involved in the pathogenesis of not only cancers but also neurodegenerative diseases, cardiovascular diseases, and infectious diseases. With the progress of metabonomics and proteomics, metabolites have been found to affect protein acylations through providing acyl groups or changing the activities of acyltransferases or deacylases. Reciprocally, protein acylation is involved in key cellular processes relevant to physiology and diseases, such as protein stability, protein subcellular localization, enzyme activity, transcriptional activity, protein-protein interactions and protein-DNA interactions. Herein, we summarize the functional diversity and mechanisms of eight kinds of nonhistone protein acylations in the physiological processes and progression of several diseases. We also highlight the recent progress in the development of inhibitors for acyltransferase, deacylase, and acylation reader proteins for their potential applications in drug discovery.
Collapse
Affiliation(s)
- Shuang Shang
- grid.506261.60000 0001 0706 7839CAMS Key Laboratory of Molecular Mechanism and Target Discovery of Metabolic Disorder and Tumorigenesis, State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 100050 Beijing, P.R. China
| | - Jing Liu
- grid.506261.60000 0001 0706 7839CAMS Key Laboratory of Molecular Mechanism and Target Discovery of Metabolic Disorder and Tumorigenesis, State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 100050 Beijing, P.R. China
| | - Fang Hua
- grid.506261.60000 0001 0706 7839CAMS Key Laboratory of Molecular Mechanism and Target Discovery of Metabolic Disorder and Tumorigenesis, State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 100050 Beijing, P.R. China
| |
Collapse
|
15
|
Pan P, Qin G, Wang B, Yu H, Chen J, Liu J, Bing K, Shen J, Ren D, Zhao Y, Xia W, Li H, Wu H, Zhou Y. HDAC5 Loss Enhances Phospholipid-Derived Arachidonic Acid Generation and Confers Sensitivity to cPLA2 Inhibition in Pancreatic Cancer. Cancer Res 2022; 82:4542-4554. [PMID: 36102738 PMCID: PMC9755957 DOI: 10.1158/0008-5472.can-21-4362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 07/13/2022] [Accepted: 09/08/2022] [Indexed: 01/24/2023]
Abstract
HDAC5 is a class IIa histone deacetylase member that is downregulated in multiple solid tumors, including pancreatic cancer, and loss of HDAC5 is associated with unfavorable prognosis. In this study, assessment of The Cancer Genome Atlas pancreatic adenocarcinoma dataset revealed that expression of HDAC5 correlates negatively with arachidonic acid (AA) metabolism, which has been implicated in inflammatory responses and cancer progression. Nontargeted metabolomics analysis revealed that HDAC5 knockdown resulted in a significant increase in AA and its downstream metabolites, such as eicosanoids and prostaglandins. HDAC5 negatively regulated the expression of the gene encoding calcium-dependent phospholipase A2 (cPLA2), the key enzyme in the production of AA from phospholipids. Mechanistically, HDAC5 repressed cPLA2 expression via deacetylation of GATA1. HDAC5 knockdown in cancer cells enhanced sensitivity to genetic or pharmacologic inhibition of cPLA2 in vitro and in vivo. Fatty acid supplementation in the diet reversed the sensitivity of HDAC5-deficient tumors to cPLA2 inhibition. These data indicate that HDAC5 loss in pancreatic cancer results in the hyperacetylation of GATA1, enabling the upregulation of cPLA2, which contributes to overproduction of AA. Dietary management plus cPLA2-targeted therapy could serve as a viable strategy for treating HDAC5-deficient pancreatic cancer patients. SIGNIFICANCE The HDAC5-GATA1-cPLA2-AA signaling axis regulates sensitivity to fat restriction plus cPLA2 inhibition in pancreatic ductal adenocarcinoma, proposing dietary management as a feasible strategy for treating a subset of patients with pancreatic cancer.
Collapse
Affiliation(s)
- Penglin Pan
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Gengdu Qin
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Bo Wang
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Haixin Yu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Jie Chen
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Jiaying Liu
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Kaijian Bing
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Jian Shen
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Dianyun Ren
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Yuhan Zhao
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Wentao Xia
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Hui Li
- Center for Human Genome Research, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, P.R. China
- Corresponding Authors: Yingke Zhou, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, P.R. China. Phone: 8618-1861-28171; E-mail: ; Hui Li, ; and Heshui Wu,
| | - Heshui Wu
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
- Corresponding Authors: Yingke Zhou, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, P.R. China. Phone: 8618-1861-28171; E-mail: ; Hui Li, ; and Heshui Wu,
| | - Yingke Zhou
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
- Sino-German Laboratory of Personalized Medicine for Pancreatic Cancer, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
- Corresponding Authors: Yingke Zhou, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, P.R. China. Phone: 8618-1861-28171; E-mail: ; Hui Li, ; and Heshui Wu,
| |
Collapse
|
16
|
Thibord F, Klarin D, Brody JA, Chen MH, Levin MG, Chasman DI, Goode EL, Hveem K, Teder-Laving M, Martinez-Perez A, Aïssi D, Daian-Bacq D, Ito K, Natarajan P, Lutsey PL, Nadkarni GN, de Vries PS, Cuellar-Partida G, Wolford BN, Pattee JW, Kooperberg C, Braekkan SK, Li-Gao R, Saut N, Sept C, Germain M, Judy RL, Wiggins KL, Ko D, O’Donnell CJ, Taylor KD, Giulianini F, De Andrade M, Nøst TH, Boland A, Empana JP, Koyama S, Gilliland T, Do R, Huffman JE, Wang X, Zhou W, Soria JM, Souto JC, Pankratz N, Haessler J, Hindberg K, Rosendaal FR, Turman C, Olaso R, Kember RL, Bartz TM, Lynch JA, Heckbert SR, Armasu SM, Brumpton B, Smadja DM, Jouven X, Komuro I, Clapham KR, Loos RJ, Willer CJ, Sabater-Lleal M, Pankow JS, Reiner AP, Morelli VM, Ridker PM, van Hylckama Vlieg A, Deleuze JF, Kraft P, Rader DJ, Lee KM, Psaty BM, Skogholt AH, Emmerich J, Suchon P, Rich SS, Vy HMT, Tang W, Jackson RD, Hansen JB, Morange PE, Kabrhel C, Trégouët DA, Damrauer SM, Johnson AD, Smith NL. Cross-Ancestry Investigation of Venous Thromboembolism Genomic Predictors. Circulation 2022; 146:1225-1242. [PMID: 36154123 PMCID: PMC10152894 DOI: 10.1161/circulationaha.122.059675] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/09/2022] [Indexed: 01/24/2023]
Abstract
BACKGROUND Venous thromboembolism (VTE) is a life-threatening vascular event with environmental and genetic determinants. Recent VTE genome-wide association studies (GWAS) meta-analyses involved nearly 30 000 VTE cases and identified up to 40 genetic loci associated with VTE risk, including loci not previously suspected to play a role in hemostasis. The aim of our research was to expand discovery of new genetic loci associated with VTE by using cross-ancestry genomic resources. METHODS We present new cross-ancestry meta-analyzed GWAS results involving up to 81 669 VTE cases from 30 studies, with replication of novel loci in independent populations and loci characterization through in silico genomic interrogations. RESULTS In our genetic discovery effort that included 55 330 participants with VTE (47 822 European, 6320 African, and 1188 Hispanic ancestry), we identified 48 novel associations, of which 34 were replicated after correction for multiple testing. In our combined discovery-replication analysis (81 669 VTE participants) and ancestry-stratified meta-analyses (European, African, and Hispanic), we identified another 44 novel associations, which are new candidate VTE-associated loci requiring replication. In total, across all GWAS meta-analyses, we identified 135 independent genomic loci significantly associated with VTE risk. A genetic risk score of the significantly associated loci in Europeans identified a 6-fold increase in risk for those in the top 1% of scores compared with those with average scores. We also identified 31 novel transcript associations in transcriptome-wide association studies and 8 novel candidate genes with protein quantitative-trait locus Mendelian randomization analyses. In silico interrogations of hemostasis and hematology traits and a large phenome-wide association analysis of the 135 GWAS loci provided insights to biological pathways contributing to VTE, with some loci contributing to VTE through well-characterized coagulation pathways and others providing new data on the role of hematology traits, particularly platelet function. Many of the replicated loci are outside of known or currently hypothesized pathways to thrombosis. CONCLUSIONS Our cross-ancestry GWAS meta-analyses identified new loci associated with VTE. These findings highlight new pathways to thrombosis and provide novel molecules that may be useful in the development of improved antithrombosis treatments.
Collapse
Affiliation(s)
- Florian Thibord
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, 73 Mt. Wayte Ave, Suite #2, Framingham, MA, 01702, USA
- The Framingham Heart Study, Boston University and NHLBI, 73 Mt. Wayte Ave, Suite #2, Framingham, MA, 01702, USA
| | - Derek Klarin
- Division of Vascular Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA
- VA Palo Alto Healthcare System, Palo Alto, CA, 94550, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, WA, 98101, USA
| | - Ming-Huei Chen
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, 73 Mt. Wayte Ave, Suite #2, Framingham, MA, 01702, USA
- The Framingham Heart Study, Boston University and NHLBI, 73 Mt. Wayte Ave, Suite #2, Framingham, MA, 01702, USA
| | - Michael G. Levin
- Division of Cardiovascular Medicine, Department of Medicine, University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA, 19104, USA
| | - Daniel I. Chasman
- Division of Preventive Medicine, Brigham and Women’s Hospital, 900 Commonwealth Ave, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Ellen L. Goode
- Department of Quantitative Health Sciences, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Kristian Hveem
- HUNT Research Center, Department of Public Health and Nursing, Norwegian University of Science and Technology, Forskningsvegen 2, Levanger, 7600, Norway
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Håkon Jarls gate 11, Trondheim, 7030, Norway
| | - Maris Teder-Laving
- Institute of Genomics, University of Tartu, Riia 23b, Tartu, Tartu, 51010, Estonia
| | - Angel Martinez-Perez
- Genomics of Complex Disease Unit, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), St Quinti 77-79, Barcelona, 8041, Spain
| | - Dylan Aïssi
- Bordeaux Population Health Research Center, University of Bordeaux, 146 rue Léo Saignat, Bordeaux, 33076, France
- UMR1219, INSERM, 146 rue Léo Saignat, Bordeaux, 33076, France
| | - Delphine Daian-Bacq
- Centre National de Recherche en Génomique Humaine, CEA, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Laboratory of Excellence on Medical Genomics, GenMed, France
| | - Kaoru Ito
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02446, USA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, 75 Ames St, Cambridge, MA, 02142, USA
- Department of Medicine, Harvard Medical School, Shattuck St, Boston, MA, 02115, USA
| | - Pamela L. Lutsey
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, 1300 South Second Street, Minneapolis, MN, 55454, USA
| | - Girish N. Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1 Gu stave L. Levy Pl, New York, NY, 10029, USA
- Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, 1200 Pressler St, Houston, TX, 77030, USA
| | | | - Brooke N. Wolford
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jack W. Pattee
- Division of Biostatistics, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN, 55455, USA
- Center for Innovative Design & Analysis and Department of Biostatistics & Informatics, Colorado School of Public Health, 13001 East 17th Place, Aurora, CO, 80045, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Sigrid K. Braekkan
- Thrombosis Research Center (TREC), UiT - The Arctic University of Norway, Universitetsvegen 57, Tromsø, 9037, Norway
- Division of internal medicine, University Hospital of North Norway, Tromsø, 9038, Norway
| | - Ruifang Li-Gao
- Clinical Epidemiology, Leiden University Medical Center, PO Box 9600, Leiden, 2300 RC, The Netherlands
| | - Noemie Saut
- Hematology Laboratory, La Timone University Hospital of Marseille, 264 Rue Saint-Pierre, Marseille, 13385, France
| | - Corriene Sept
- Department of Epidemiology, Harvard TH Chan Harvard School of Public Health, 655 Huntington Ave., Building II, Boston, MA, 02115, USA
| | - Marine Germain
- Bordeaux Population Health Research Center, University of Bordeaux, 146 rue Léo Saignat, Bordeaux, 33076, France
- UMR1219, INSERM, 146 rue Léo Saignat, Bordeaux, 33076, France
- Laboratory of Excellence on Medical Genomics, GenMed, France
| | - Renae L. Judy
- Surgery, University of Pennsylvania, 3401 Walnut Street, Philadelphia, PA, 19104, USA
| | - Kerri L. Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, WA, 98101, USA
| | - Darae Ko
- The Framingham Heart Study, Boston University and NHLBI, 73 Mt. Wayte Ave, Suite #2, Framingham, MA, 01702, USA
- Section of Cardiovascular Medicine, Boston University School of Medicine, 85 East Newton Street, Boston, MA, 02118, USA
| | - Christopher J. O’Donnell
- Cardiology Section, Department of Medicine, VA Boston Healthcare System, Boston, MA, 02132, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation, 1124 W Carson St., Torrance, CA, 90502, USA
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women’s Hospital, 900 Commonwealth Ave, Boston, MA, 02215, USA
| | - Mariza De Andrade
- Department of Quantitative Health Sciences, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Therese H. Nøst
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Håkon Jarls gate 11, Trondheim, 7030, Norway
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, CEA, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Laboratory of Excellence on Medical Genomics, GenMed, France
| | - Jean-Philippe Empana
- Integrative Epidemiology of cardiovascular diseases, Université Paris Cité, Paris Cardiovascular Research Center (PARCC), 56 rue Leblanc, Paris, 75015, France
- Department of Cardiology, APHP, Hopital Européen Georges Pompidou, 20 rue Leblanc, Paris, 75015, France
| | - Satoshi Koyama
- Laboratory for Cardiovascular Genomics and Informatics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Cardiovascular Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02446, USA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, 75 Ames St, Cambridge, MA, 02142, USA
| | - Thomas Gilliland
- Cardiovascular Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02446, USA
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, 75 Ames St, Cambridge, MA, 02142, USA
- Department of Medicine, Harvard Medical School, Shattuck St, Boston, MA, 02115, USA
| | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1 Gu stave L. Levy Pl, New York, NY, 10029, USA
- BioMe Phenomics Center, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
| | - Jennifer E. Huffman
- MAVERIC, VA Boston Heathcare System, 2 Avenue de Lafayette, Boston, MA, 02111, USA
| | - Xin Wang
- 23andMe, Inc., 223 N Mathilda Ave, Sunnyvale, CA, 94086, USA
| | - Wei Zhou
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
| | - Jose Manuel Soria
- Genomics of Complex Disease Unit, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), St Quinti 77-79, Barcelona, 8041, Spain
| | - Juan Carlos Souto
- Genomics of Complex Disease Unit, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), St Quinti 77-79, Barcelona, 8041, Spain
- Unit of Thrombosis and Hemostasis, Hospital de la Santa Creu i Sant Pau, St Quinti 89, Barcelona, 8041, Spain
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN, 55455, USA
| | - Jeffery Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Kristian Hindberg
- Thrombosis Research Center (TREC), UiT - The Arctic University of Norway, Universitetsvegen 57, Tromsø, 9037, Norway
| | - Frits R. Rosendaal
- Clinical Epidemiology, Leiden University Medical Center, PO Box 9600, Leiden, 2300 RC, The Netherlands
| | - Constance Turman
- Department of Epidemiology, Harvard TH Chan Harvard School of Public Health, 655 Huntington Ave., Building II, Boston, MA, 02115, USA
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine, CEA, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Laboratory of Excellence on Medical Genomics, GenMed, France
| | - Rachel L. Kember
- Psychiatry, University of Pennsylvania, 3401 Walnut Street, Philadelphia, PA, 19104, USA
| | - Traci M. Bartz
- Cardiovascular Health Research Unit, Departments of Biostatistics and Medicine, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, WA, 98101, USA
| | - Julie A. Lynch
- VA Informatics & Computing Infrastructure, VA Salt Lake City Healthcare System, 500 Foothills Drive, Salt Lake City, UT, 84148, USA
- Epidemiology, University of Utah, 500 Foothills Drive, Salt Lake City, UT, 84148, USA
| | - Susan R. Heckbert
- Department of Epidemiology, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, WA, 98101, USA
| | - Sebastian M. Armasu
- Department of Quantitative Health Sciences, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Ben Brumpton
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Håkon Jarls gate 11, Trondheim, 7030, Norway
| | - David M. Smadja
- Hematology Department and Biosurgical Research Lab (Carpentier Foundation), European Georges Pompidou Hospital, Assistance Publique Hôpitaux de Paris, 20 rue Leblanc, Paris, 75015, France
- Innovative Therapies in Haemostasis, INSERM, Université de Paris, 4 avenue de l’Observatoire, Paris, 75270, France
| | - Xavier Jouven
- Integrative Epidemiology of cardiovascular diseases, Université Paris Descartes, Sorbonne Paris Cité, 56 rue Leblanc, Paris, 75015, France
- Paris Cardiovascular Research Center, Inserm U970, Université Paris Descartes, Sorbonne Paris Cité, 20 rue Leblanc, Paris, 75015, France
| | - Issei Komuro
- Department of Cardiovascular Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Tokyo, 113-8655, Japan
| | - Katharine R. Clapham
- Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, 75 Ames St, Cambridge, MA, 02142, USA
- Department of Medicine, Harvard Medical School, Shattuck St, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, 900 Commonwealth Ave, Boston, MA, 02215, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
| | - Cristen J. Willer
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Maria Sabater-Lleal
- Genomics of Complex Disease Unit, Institut d’Investigació Biomèdica Sant Pau (IIB SANT PAU), St Quinti 77-79, Barcelona, 8041, Spain
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska Institutet, Center for Molecular Medicine, Stockholm, 17176, Sweden
| | - James S. Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, 1300 South Second Street, Minneapolis, MN, 55454, USA
| | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Department of Epidemiology, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, WA, 98101, USA
| | - Vania M. Morelli
- Thrombosis Research Center (TREC), UiT - The Arctic University of Norway, Universitetsvegen 57, Tromsø, 9037, Norway
- Division of internal medicine, University Hospital of North Norway, Tromsø, 9038, Norway
| | - Paul M. Ridker
- Division of Preventive Medicine, Brigham and Women’s Hospital, 900 Commonwealth Ave, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Astrid van Hylckama Vlieg
- Clinical Epidemiology, Leiden University Medical Center, PO Box 9600, Leiden, 2300 RC, The Netherlands
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, CEA, Université Paris-Saclay, 2 Rue Gaston Crémieux, Evry, 91057, France
- Laboratory of Excellence on Medical Genomics, GenMed, France
- Centre D’Etude du Polymorphisme Humain, Fondation Jean Dausset, 27 rue Juliette Dodu, Paris, 75010, France
| | - Peter Kraft
- Department of Epidemiology, Harvard TH Chan Harvard School of Public Health, 655 Huntington Ave., Building II, Boston, MA, 02115, USA
| | - Daniel J. Rader
- Departments of Medicine and Genetics and Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | | | | | | | | | | | - Kyung Min Lee
- VA Informatics & Computing Infrastructure, VA Salt Lake City Healthcare System, 500 Foothills Drive, Salt Lake City, UT, 84148, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, WA, 98101, USA
- Department of Epidemiology, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, WA, 98101, USA
- Department of Health Systems and Population Heath, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, WA, 98101, USA
| | - Anne Heidi Skogholt
- K.G. Jebsen Centre for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Håkon Jarls gate 11, Trondheim, 7030, Norway
| | - Joseph Emmerich
- Department of vascular medicine, Paris Saint-Joseph Hospital Group, University of Paris, 185 rue Raymond Losserand, Paris, 75674, France
- UMR1153, INSERM CRESS, 185 rue Raymond Losserand, Paris, 75674, France
| | - Pierre Suchon
- Hematology Laboratory, La Timone University Hospital of Marseille, 264 Rue Saint-Pierre, Marseille, 13385, France
- C2VN, INSERM, INRAE, Aix-Marseille University, 27, bd Jean Moulin, Marseille, 13385, France
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, 3242 West Complex, Charlottesville, VA, 22908-0717, USA
| | - Ha My T. Vy
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Pl, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1 Gu stave L. Levy Pl, New York, NY, 10029, USA
| | - Weihong Tang
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, 1300 South Second Street, Minneapolis, MN, 55454, USA
| | - Rebecca D. Jackson
- College of Medicine, Ohio State University, 376 W. 10th Ave, Columbus, OH, 43210, USA
| | - John-Bjarne Hansen
- Thrombosis Research Center (TREC), UiT - The Arctic University of Norway, Universitetsvegen 57, Tromsø, 9037, Norway
- Division of internal medicine, University Hospital of North Norway, Tromsø, 9038, Norway
| | - Pierre-Emmanuel Morange
- Hematology Laboratory, La Timone University Hospital of Marseille, 264 Rue Saint-Pierre, Marseille, 13385, France
- C2VN, INSERM, INRAE, Aix-Marseille University, 27, bd Jean Moulin, Marseille, 13385, France
| | - Christopher Kabrhel
- Emergency Medicine, Massachusetts General Hospital, Zero Emerson Place, Suite 3B, Boston, MA, 02114, USA
- Emergency Medicine, Harvard Medical School, Zero Emerson Place, Suite 3B, Boston, MA, 02114, USA
| | - David-Alexandre Trégouët
- Bordeaux Population Health Research Center, University of Bordeaux, 146 rue Léo Saignat, Bordeaux, 33076, France
- UMR1219, INSERM, 146 rue Léo Saignat, Bordeaux, 33076, France
- Laboratory of Excellence on Medical Genomics, GenMed, France
| | - Scott M. Damrauer
- Corporal Michael J. Crescenz Philadelphia VA Medical Center, 3900 Woodland Ave, Philadelphia, PA, 19104, USA
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Andrew D. Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, 73 Mt. Wayte Ave, Suite #2, Framingham, MA, 01702, USA
- The Framingham Heart Study, Boston University and NHLBI, 73 Mt. Wayte Ave, Suite #2, Framingham, MA, 01702, USA
| | - Nicholas L. Smith
- Department of Epidemiology, University of Washington, 1730 Minor Ave, Suite 1360, Seattle, WA, 98101, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA, 98101, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA, 98108, USA
| |
Collapse
|
17
|
Chen IP, Ott M. Viral Hijacking of BET Proteins. Viruses 2022; 14:v14102274. [PMID: 36298829 PMCID: PMC9609653 DOI: 10.3390/v14102274] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 11/29/2022] Open
Abstract
Proteins of the bromodomain and exterminal domain (BET) family mediate critical host functions such as cell proliferation, transcriptional regulation, and the innate immune response, which makes them preferred targets for viruses. These multidomain proteins are best known as transcriptional effectors able to read acetylated histone and non-histone proteins through their tandem bromodomains. They also contain other short motif-binding domains such as the extraterminal domain, which recognizes transcriptional regulatory proteins. Here, we describe how different viruses have evolved to hijack or disrupt host BET protein function through direct interactions with BET family members to support their own propagation. The network of virus-BET interactions emerges as highly intricate, which may complicate the use of small-molecule BET inhibitors-currently in clinical development for the treatment of cancer and cardiovascular diseases-to treat viral infections.
Collapse
Affiliation(s)
- Irene P. Chen
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Correspondence:
| |
Collapse
|
18
|
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.
Collapse
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,
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Vong P, Ouled-Haddou H, Garçon L. Histone Deacetylases Function in the Control of Early Hematopoiesis and Erythropoiesis. Int J Mol Sci 2022; 23:9790. [PMID: 36077192 PMCID: PMC9456231 DOI: 10.3390/ijms23179790] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Numerous studies have highlighted the role of post-translational modifications in the regulation of cell proliferation, differentiation and death. Among these modifications, acetylation modifies the physicochemical properties of proteins and modulates their activity, stability, localization and affinity for partner proteins. Through the deacetylation of a wide variety of functional and structural, nuclear and cytoplasmic proteins, histone deacetylases (HDACs) modulate important cellular processes, including hematopoiesis, during which different HDACs, by controlling gene expression or by regulating non-histone protein functions, act sequentially to provide a fine regulation of the differentiation process both in early hematopoietic stem cells and in more mature progenitors. Considering that HDAC inhibitors represent promising targets in cancer treatment, it is necessary to decipher the role of HDACs during hematopoiesis which could be impacted by these therapies. This review will highlight the main mechanisms by which HDACs control the hematopoietic stem cell fate, particularly in the erythroid lineage.
Collapse
Affiliation(s)
- Pascal Vong
- Université Picardie Jules Verne, HEMATIM UR4666, 80000 Amiens, France
| | | | - Loïc Garçon
- Université Picardie Jules Verne, HEMATIM UR4666, 80000 Amiens, France
- Service d’Hématologie Biologique, Centre Hospitalier Universitaire, CEDEX 1, 80054 Amiens, France
- Laboratoire de Génétique Constitutionnelle, Centre Hospitalier Universitaire, CEDEX 1, 80054 Amiens, France
| |
Collapse
|
21
|
Holley JM, Stanbouly S, Pecaut MJ, Willey JS, Delp M, Mao XW. Characterization of gene expression profiles in the mouse brain after 35 days of spaceflight mission. NPJ Microgravity 2022; 8:35. [PMID: 35948598 PMCID: PMC9365836 DOI: 10.1038/s41526-022-00217-4] [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] [Received: 01/10/2022] [Accepted: 07/15/2022] [Indexed: 11/25/2022] Open
Abstract
It has been proposed that neuroinflammatory response plays an important role in the neurovascular remodeling in the brain after stress. The goal of the present study was to characterize changes in the gene expression profiles associated with neuroinflammation, neuronal function, metabolism and stress in mouse brain tissue. Ten-week old male C57BL/6 mice were launched to the International Space Station (ISS) on SpaceX-12 for a 35-day mission. Within 38 ± 4 h of splashdown, mice were returned to Earth alive. Brain tissues were collected for analysis. A novel digital color-coded barcode counting technology (NanoStringTM) was used to evaluate gene expression profiles in the spaceflight mouse brain. A set of 54 differently expressed genes (p < 0.05) significantly segregates the habitat ground control (GC) group from flight (FLT) group. Many pathways associated with cellular stress, inflammation, apoptosis, and metabolism were significantly altered by flight conditions. A decrease in the expression of genes important for oligodendrocyte differentiation and myelin sheath maintenance was observed. Moreover, mRNA expression of many genes related to anti-viral signaling, reactive oxygen species (ROS) generation, and bacterial immune response were significantly downregulated. Here we report that significantly altered immune reactions may be closely associated with spaceflight-induced stress responses and have an impact on the neuronal function.
Collapse
Affiliation(s)
- Jacob M Holley
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University School of Medicine, Loma Linda, CA, 92350, USA
| | - Seta Stanbouly
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University School of Medicine, Loma Linda, CA, 92350, USA
| | - Michael J Pecaut
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University School of Medicine, Loma Linda, CA, 92350, USA
| | - Jeffrey S Willey
- Department of Radiation Oncology, Wake Forest University, School of Medicine, Winston-Salem, NC, 27101, USA
| | - Michael Delp
- Department of Nutrition, Food and Exercise Sciences, Florida State University, Tallahassee, FL, 32306, USA
| | - Xiao Wen Mao
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University School of Medicine, Loma Linda, CA, 92350, USA.
| |
Collapse
|
22
|
Miller GM, Flynn EM, Tom J, Song A, Cochran AG. Trifluoroacetyl Lysine as a Bromodomain Binding Mimic of Lysine Acetylation. ACS Chem Biol 2022; 17:1022-1029. [PMID: 35467836 DOI: 10.1021/acschembio.2c00016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genetic code expansion has proven invaluable to the elucidation of functions of defined protein modifications through the site-specific incorporation of noncanonical amino acids. The use of nonhydrolyzable derivatives of post-translational modifications can greatly increase site stoichiometry and half-life. Investigating acetyllysine reader domain (bromodomain) interactions with acetylated nonhistone proteins is challenging due to the limited tools available and dynamic nature of this post-translational modification. Here, we demonstrate that bromodomains bind acetyllysine peptides and those substituted with an acetyllysine derivative, trifluoroacetyllysine, with similar affinity and selectivity. Importantly, both trifluoroacetyllysine and acetyllysine can be site-specifically incorporated into proteins expressed in bacterial and mammalian cells, and the strong electron-withdrawing trifluoro substituent makes the latter resistant to deacetylation by sirtuins (SIRTs). The controlled expression of SIRT-resistant, site-specifically acetylated transcription factors expands the set of available tools for determining the function of acetylation, and it serves as a template for investigating bromodomain interactions with acetylated transcription factors.
Collapse
Affiliation(s)
- Gregory M. Miller
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco 94080, California, United States
| | - E. Megan Flynn
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco 94080, California, United States
| | - Jeffrey Tom
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco 94080, California, United States
| | - Aimin Song
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco 94080, California, United States
| | - Andrea G. Cochran
- Department of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco 94080, California, United States
| |
Collapse
|
23
|
Ludwig LS, Lareau CA, Bao EL, Liu N, Utsugisawa T, Tseng AM, Myers SA, Verboon JM, Ulirsch JC, Luo W, Muus C, Fiorini C, Olive ME, Vockley CM, Munschauer M, Hunter A, Ogura H, Yamamoto T, Inada H, Nakagawa S, Ohzono S, Subramanian V, Chiarle R, Glader B, Carr SA, Aryee MJ, Kundaje A, Orkin SH, Regev A, McCavit TL, Kanno H, Sankaran VG. Congenital anemia reveals distinct targeting mechanisms for master transcription factor GATA1. Blood 2022; 139:2534-2546. [PMID: 35030251 PMCID: PMC9029090 DOI: 10.1182/blood.2021013753] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/24/2021] [Indexed: 11/20/2022] Open
Abstract
Master regulators, such as the hematopoietic transcription factor (TF) GATA1, play an essential role in orchestrating lineage commitment and differentiation. However, the precise mechanisms by which such TFs regulate transcription through interactions with specific cis-regulatory elements remain incompletely understood. Here, we describe a form of congenital hemolytic anemia caused by missense mutations in an intrinsically disordered region of GATA1, with a poorly understood role in transcriptional regulation. Through integrative functional approaches, we demonstrate that these mutations perturb GATA1 transcriptional activity by partially impairing nuclear localization and selectively altering precise chromatin occupancy by GATA1. These alterations in chromatin occupancy and concordant chromatin accessibility changes alter faithful gene expression, with failure to both effectively silence and activate select genes necessary for effective terminal red cell production. We demonstrate how disease-causing mutations can reveal regulatory mechanisms that enable the faithful genomic targeting of master TFs during cellular differentiation.
Collapse
Affiliation(s)
- Leif S Ludwig
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA
- Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Caleb A Lareau
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA
- Department of Computer Science and
- Department of Genetics, Stanford University, Stanford, CA
| | - Erik L Bao
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA
- Harvard-MIT Health Sciences and Technology, Harvard Medical School, Boston, MA
| | - Nan Liu
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Taiju Utsugisawa
- Department of Transfusion Medicine and Cell Processing, Faculty of Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Alex M Tseng
- Department of Computer Science and
- Department of Genetics, Stanford University, Stanford, CA
| | - Samuel A Myers
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA
- La Jolla Institute for Immunology, La Jolla, CA
| | - Jeffrey M Verboon
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA
| | - Jacob C Ulirsch
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA
| | - Wendy Luo
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA
| | - Christoph Muus
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA
- John A. Paulson School of Engineering and Applied Sciences, Faculty of Arts and Sciences, Harvard University, Cambridge, MA
| | - Claudia Fiorini
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA
| | - Meagan E Olive
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA
| | - Christopher M Vockley
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA
| | - Mathias Munschauer
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz Center for Infection Research, Würzburg, Germany
- Infection and Immunity Department, Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | | | - Hiromi Ogura
- Department of Transfusion Medicine and Cell Processing, Faculty of Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | | | - Shinichiro Nakagawa
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Kurume, Japan
| | - Shuichi Ohzono
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Kurume, Japan
| | - Vidya Subramanian
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Bertil Glader
- Lucile Packard Children's Hospital, Stanford University, Palo Alto, CA
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA
| | - Martin J Aryee
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Anshul Kundaje
- Department of Computer Science and
- Department of Genetics, Stanford University, Stanford, CA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Aviv Regev
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA
- Howard Hughes Medical Institute, Chevy Chase, MD
- Department of Biology and
- Koch Institute of Integrative Cancer Research, MIT, Cambridge, MA; and
| | | | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing, Faculty of Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Vijay G Sankaran
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA
- Harvard Stem Cell Institute, Cambridge, MA
| |
Collapse
|
24
|
Tontsch-Grunt U, Traexler PE, Baum A, Musa H, Marzin K, Wang S, Trapani F, Engelhardt H, Solca F. Therapeutic impact of BET inhibitor BI 894999 treatment: backtranslation from the clinic. Br J Cancer 2022; 127:577-586. [PMID: 35444289 PMCID: PMC9346113 DOI: 10.1038/s41416-022-01815-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/24/2022] [Accepted: 03/31/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND BET inhibitors have been tested in several clinical trials where, despite encouraging preclinical results, substantial clinical benefit in monotherapy remains limited. This work illustrates the translational challenges and reports new data around the novel BET inhibitor, BI 894999. At clinically achievable concentrations, mechanistic studies were carried out to study pathway modulation and rational drug combinations. METHODS BRD-NUT fusions are oncogenic drivers in NUT carcinoma (NC). The effects of BI 894999 on proliferation, chromatin binding and pathway modulation were studied in NC in vitro. These studies were complemented by efficacy studies either as a single agent or in combination with the clinical p300/CBP inhibitor CCS1477. RESULTS Based on the modelling of preclinical and clinical data, we proposed and implemented a new clinical scheduling regimen. This led to plasma levels sufficient to fully dislodge BRD-NUT from chromatin and to sustained and pronounced pharmacodynamic (PD) modulation of HEXIM1 and HIST2H2BF. Platelet counts in patient blood samples were improved compared to previous schedules. Rational combination studies of BI 894999 performed at clinically meaningful concentrations led to tumour regressions in all NC xenograft models tested. CONCLUSIONS BI 894999 holds significant potential as a combination drug and CCS1477 p300/CBP inhibitor is a promising partner for future clinical trials.
Collapse
Affiliation(s)
| | | | - Anke Baum
- Boehringer Ingelheim RCV GmbH & Co KG, A-1120, Vienna, Austria
| | - Hanny Musa
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Kristell Marzin
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Shaonan Wang
- Boehringer Ingelheim Pharma GmbH & Co. KG, Ingelheim am Rhein, Germany
| | | | | | - Flavio Solca
- Boehringer Ingelheim RCV GmbH & Co KG, A-1120, Vienna, Austria
| |
Collapse
|
25
|
Ali HA, Li Y, Bilal AHM, Qin T, Yuan Z, Zhao W. A Comprehensive Review of BET Protein Biochemistry, Physiology, and Pathological Roles. Front Pharmacol 2022; 13:818891. [PMID: 35401196 PMCID: PMC8990909 DOI: 10.3389/fphar.2022.818891] [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: 12/17/2021] [Accepted: 01/26/2022] [Indexed: 11/13/2022] Open
Abstract
Epigenetic modifications, specifically acetylation of histone plays a decisive role in gene regulation and transcription of normal cellular mechanisms and pathological conditions. The bromodomain and extraterminal (BET) proteins (BRD2, BRD3, BRD4, and BRDT), being epigenetic readers, ligate to acetylated regions of histone and synchronize gene transcription. BET proteins are crucial for normal cellular processing as they control cell cycle progression, neurogenesis, differentiation, and maturation of erythroids and spermatogenesis, etc. Research-based evidence indicated that BET proteins (mainly BRD4) are associated with numeral pathological ailments, including cancer, inflammation, infections, renal diseases, and cardiac diseases. To counter the BET protein-related pathological conditions, there are some BET inhibitors developed and also under development. BET proteins are a topic of most research nowadays. This review, provides an ephemeral but comprehensive knowledge about BET proteins’ basic structure, biochemistry, physiological roles, and pathological conditions in which the role of BETs have been proven. This review also highlights the current and future approaches to pledge BET protein-related pathologies.
Collapse
Affiliation(s)
- Hafiz Akbar Ali
- Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China.,Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yalan Li
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Akram Hafiz Muhammad Bilal
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Tingting Qin
- Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Ziqiao Yuan
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Wen Zhao
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, China
| |
Collapse
|
26
|
Wells M, Steiner L. Epigenetic and Transcriptional Control of Erythropoiesis. Front Genet 2022; 13:805265. [PMID: 35330735 PMCID: PMC8940284 DOI: 10.3389/fgene.2022.805265] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/16/2022] [Indexed: 12/21/2022] Open
Abstract
Erythropoiesis is a process of enormous magnitude, with the average person generating two to three million red cells every second. Erythroid progenitors start as large cells with large nuclei, and over the course of three to four cell divisions they undergo a dramatic decrease in cell size accompanied by profound nuclear condensation, which culminates in enucleation. As maturing erythroblasts are undergoing these dramatic phenotypic changes, they accumulate hemoglobin and express high levels of other erythroid-specific genes, while silencing much of the non-erythroid transcriptome. These phenotypic and gene expression changes are associated with distinct changes in the chromatin landscape, and require close coordination between transcription factors and epigenetic regulators, as well as precise regulation of RNA polymerase II activity. Disruption of these processes are associated with inherited anemias and myelodysplastic syndromes. Here, we review the epigenetic mechanisms that govern terminal erythroid maturation, and their role in human disease.
Collapse
Affiliation(s)
- Maeve Wells
- Department of Pediatrics, University of Rochester, Rochester, NY, United States
| | - Laurie Steiner
- Department of Pediatrics, University of Rochester, Rochester, NY, United States
| |
Collapse
|
27
|
Chen J, Tang P, Wang Y, Wang J, Yang C, Li Y, Yang G, Wu F, Zhang J, Ouyang L. Targeting Bromodomain-Selective Inhibitors of BET Proteins in Drug Discovery and Development. J Med Chem 2022; 65:5184-5211. [PMID: 35324195 DOI: 10.1021/acs.jmedchem.1c01835] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Blocking the interactions between bromodomain and extraterminal (BET) proteins and acetylated lysines of histones by small molecules has important implications for the treatment of cancers and other diseases. Many pan-BET inhibitors have shown satisfactory results in clinical trials, but their potential for poor tolerability and toxicity persist. However, recently reported studies illustrate that some BET bromodomain (BET-BD1 or BET-BD2)-selective inhibitors have advantage over pan-inhibitors, including reduced toxicity concerns. Furthermore, some selective BET inhibitors have similar or even better therapeutic efficacy in inflammatory diseases or cancers. Therefore, the development of selective BET inhibitors has become a hot spot for medicinal chemists. Here, we summarize the known selective BET-BD1 and BET-BD2 inhibitors and review the methods for enhancing the selectivity and potency of these inhibitors based on their different modes of interactions with BET-BD1 or BET-BD2. Finally, we discuss prospective strategies that selectively target the bromodomains of BET proteins.
Collapse
Affiliation(s)
- Juncheng Chen
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Pan Tang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yuxi Wang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China.,Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Chengcan Yang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yang Li
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Gaoxia Yang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Fengbo Wu
- Department of Pharmacy, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Jifa Zhang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| |
Collapse
|
28
|
Chetry M, Bhandari A, Lin Y. Prognostic role of overexpressed Bromodomain and extra-terminal family in ovarian cancer. J Cancer 2022; 13:1695-1705. [PMID: 35371325 PMCID: PMC8965123 DOI: 10.7150/jca.69574] [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: 11/30/2021] [Accepted: 02/25/2022] [Indexed: 02/05/2023] Open
Abstract
Background: BET family proteins have a role as epigenetic readers to accelerate the transcription of target genes. Several studies have shown that the BET protein family played important roles in several biological processes. Although, the prognostic influence of individual BET genes family in ovarian cancer patients remains unclear. Methods: We investigated BET mRNA prognostic roles subtypes in ovarian cancer patients by means of the KM plotter database. The BET mRNA expression and protein in cancer and normal ovarian cells was determined using qRTPCR and western blot. We used the HPA database to look at the protein expression profiles in normal and cancer tissues for this study. Results: Among BET members, mRNA expression BRD2 showed improve OS in all the ovarian malignancy patients, serous patients, stage III and IV, grade II and grade III, TP53 mutated ovarian cancer patients, as well as all patients treated with Platin based chemotherapy. As for BRD3, we found that BRD3 expression was related to better OS in endometrioid ovarian carcinoma and stage III+IV ovarian carcinoma patients, as well as all patients managed with Taxol and concurrent Taxol+Platin based chemotherapy. In addition, BRDT was associated with better OS in all ovarian carcinoma patients, grade I and grade III, all clinical stage (I+II, III+IV) patients, as well as all patients cured with Taxol and concurrent Taxol+Platin chemotherapy. Conclusion: We conclude that high expression of BRD2, BRD3, and BRDT predicted a better prognosis. mRNA expression of BET family is considerably associated with the prognosis of ovarian carcinoma and individual BET family gene could act as a predictive prognostic indicator in ovarian carcinoma.
Collapse
Affiliation(s)
- Mandika Chetry
- Department of Oncology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Adheesh Bhandari
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- Department of General Surgery, Breast and Thyroid Unit, Primera Hospital, Kathmandu, Nepal
| | - Yue Lin
- Department of Reproductive Medicine Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, 325000, China
| |
Collapse
|
29
|
Lay CS, Thomas DA, Evans JP, Campbell M, McCombe K, Phillipou AN, Gordon LJ, Jones EJ, Riching K, Mahmood M, Messenger C, Carver CE, Gatfield KM, Craggs PD. Development of an intracellular quantitative assay to measure compound binding kinetics. Cell Chem Biol 2022; 29:287-299.e8. [PMID: 34520747 DOI: 10.1016/j.chembiol.2021.07.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 06/09/2021] [Accepted: 07/23/2021] [Indexed: 02/08/2023]
Abstract
Contemporary drug discovery typically quantifies the effect of a molecule on a biological target using the equilibrium-derived measurements of IC50, EC50, or KD. Kinetic descriptors of drug binding are frequently linked with the effectiveness of a molecule in modulating a disease phenotype; however, these parameters are yet to be fully adopted in early drug discovery. Nanoluciferase bioluminescence resonance energy transfer (NanoBRET) can be used to measure interactions between fluorophore-conjugated probes and luciferase fused target proteins. Here, we describe an intracellular NanoBRET competition assay that can be used to quantify cellular kinetic rates of compound binding to nanoluciferase-fused bromodomain and extra-terminal (BET) proteins. Comparative rates are generated using a cell-free NanoBRET assay and by utilizing orthogonal recombinant protein-based methodologies. A screen of known pan-BET inhibitors is used to demonstrate the value of this approach in the investigation of kinetic selectivity between closely related proteins.
Collapse
Affiliation(s)
- Charles S Lay
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Daniel A Thomas
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK; Arctoris, Oxford OX14 4SA, UK
| | - John P Evans
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Matthew Campbell
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Kristopher McCombe
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK; Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Alexander N Phillipou
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Laurie J Gordon
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Emma J Jones
- Protein and Cellular Sciences, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | | | - Mahnoor Mahmood
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Cassie Messenger
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Charlotte E Carver
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Kelly M Gatfield
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK
| | - Peter D Craggs
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK; GSK-Francis Crick Institute Linklabs, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK.
| |
Collapse
|
30
|
Cai M, Dong J, Li H, Qin JJ. Recent Developments in Targeting Bromodomain and Extra Terminal Domain Proteins for Cancer Therapeutics. Curr Med Chem 2022; 29:4391-4409. [PMID: 35152859 DOI: 10.2174/0929867329666220211091806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/04/2021] [Accepted: 12/14/2021] [Indexed: 11/22/2022]
Abstract
Abstract:
Bromodomain and extra-terminal domain (BET) proteins are a well-studied family of proteins associated with a variety of diseases including malignancy and chronic inflammation. Currently, numerous pan BET inhibitors have exhibited potent efficacy in several in vivo preclinical models and entered clinical trials, but have largely stalled due to their adverse events. Therefore, the development of new selective inhibitors and PROTACs (Proteolysis Targeting Chimeras) targeting BET is urgently needed. In the present review, we summarize the BET protein structure, the recent development of BET inhibitors, focusing mainly on BRD4-selective inhibitors and PROTAC degraders.
Collapse
Affiliation(s)
- Maohua Cai
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, China
| | - Jinyun Dong
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Haobin Li
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, China
| | - Jiang-Jiang Qin
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, China
| |
Collapse
|
31
|
Shvedunova M, Akhtar A. Modulation of cellular processes by histone and non-histone protein acetylation. Nat Rev Mol Cell Biol 2022; 23:329-349. [PMID: 35042977 DOI: 10.1038/s41580-021-00441-y] [Citation(s) in RCA: 265] [Impact Index Per Article: 132.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2021] [Indexed: 12/12/2022]
Abstract
Lysine acetylation is a widespread and versatile protein post-translational modification. Lysine acetyltransferases and lysine deacetylases catalyse the addition or removal, respectively, of acetyl groups at both histone and non-histone targets. In this Review, we discuss several features of acetylation and deacetylation, including their diversity of targets, rapid turnover, exquisite sensitivity to the concentrations of the cofactors acetyl-CoA, acyl-CoA and NAD+, and tight interplay with metabolism. Histone acetylation and non-histone protein acetylation influence a myriad of cellular and physiological processes, including transcription, phase separation, autophagy, mitosis, differentiation and neural function. The activity of lysine acetyltransferases and lysine deacetylases can, in turn, be regulated by metabolic states, diet and specific small molecules. Histone acetylation has also recently been shown to mediate cellular memory. These features enable acetylation to integrate the cellular state with transcriptional output and cell-fate decisions.
Collapse
Affiliation(s)
- Maria Shvedunova
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
| |
Collapse
|
32
|
Cui H, Divakaran A, Hoell ZJ, Ellingson MO, Scholtz CR, Zahid H, Johnson JA, Griffith EC, Gee CT, Lee AL, Khanal S, Shi K, Aihara H, Shah VH, Lee RE, Harki DA, Pomerantz WCK. A Structure-based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical Probes. J Med Chem 2022; 65:2342-2360. [PMID: 35007061 DOI: 10.1021/acs.jmedchem.1c01779] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Chemical probes for epigenetic proteins are essential tools for dissecting the molecular mechanisms for gene regulation and therapeutic development. The bromodomain and extra-terminal (BET) proteins are master transcriptional regulators. Despite promising therapeutic targets, selective small molecule inhibitors for a single bromodomain remain an unmet goal due to their high sequence similarity. Here, we address this challenge via a structure-activity relationship study using 1,4,5-trisubstituted imidazoles against the BRD4 N-terminal bromodomain (D1). Leading compounds 26 and 30 have 15 and 18 nM affinity against BRD4 D1 and over 500-fold selectivity against BRD2 D1 and BRD4 D2 via ITC. Broader BET selectivity was confirmed by fluorescence anisotropy, thermal shift, and CETSA. Despite BRD4 engagement, BRD4 D1 inhibition was unable to reduce c-Myc expression at low concentration in multiple myeloma cells. Conversely, for inflammation, IL-8 and chemokine downregulation were observed. These results provide new design rules for selective inhibitors of an individual BET bromodomain.
Collapse
Affiliation(s)
- Huarui Cui
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Anand Divakaran
- Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth Street SE, Minneapolis, Minnesota 55455, United States
| | - Zachariah J Hoell
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Mikael O Ellingson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Cole R Scholtz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Huda Zahid
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Jorden A Johnson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Elizabeth C Griffith
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS1000, Memphis, Tennessee 38105, United States
| | - Clifford T Gee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS1000, Memphis, Tennessee 38105, United States
| | - Amani L Lee
- GI Research Unit, Guggenheim 1034 Mayo Clinic, 200 First Street SW Rochester, Minnesota 55902, United States
| | - Shalil Khanal
- GI Research Unit, Guggenheim 1034 Mayo Clinic, 200 First Street SW Rochester, Minnesota 55902, United States
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| | - Vijay H Shah
- GI Research Unit, Guggenheim 1034 Mayo Clinic, 200 First Street SW Rochester, Minnesota 55902, United States
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS1000, Memphis, Tennessee 38105, United States
| | - Daniel A Harki
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States.,Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth Street SE, Minneapolis, Minnesota 55455, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States.,Department of Medicinal Chemistry, University of Minnesota, 2231 Sixth Street SE, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
33
|
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.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Qiang Fu
- Correspondence: ; Tel.: +86-771-3237124
| |
Collapse
|
34
|
Yang J, Song C, Zhan X. The role of protein acetylation in carcinogenesis and targeted drug discovery. Front Endocrinol (Lausanne) 2022; 13:972312. [PMID: 36171897 PMCID: PMC9510633 DOI: 10.3389/fendo.2022.972312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/23/2022] [Indexed: 12/01/2022] Open
Abstract
Protein acetylation is a reversible post-translational modification, and is involved in many biological processes in cells, such as transcriptional regulation, DNA damage repair, and energy metabolism, which is an important molecular event and is associated with a wide range of diseases such as cancers. Protein acetylation is dynamically regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs) in homeostasis. The abnormal acetylation level might lead to the occurrence and deterioration of a cancer, and is closely related to various pathophysiological characteristics of a cancer, such as malignant phenotypes, and promotes cancer cells to adapt to tumor microenvironment. Therapeutic modalities targeting protein acetylation are a potential therapeutic strategy. This article discussed the roles of protein acetylation in tumor pathology and therapeutic drugs targeting protein acetylation, which offers the contributions of protein acetylation in clarification of carcinogenesis, and discovery of therapeutic drugs for cancers, and lays the foundation for precision medicine in oncology.
Collapse
Affiliation(s)
- Jingru Yang
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Cong Song
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Xianquan Zhan
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
- *Correspondence: Xianquan Zhan,
| |
Collapse
|
35
|
Karr JP, Ferrie JJ, Tjian R, Darzacq X. The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer-promoter communication. Genes Dev 2022; 36:7-16. [PMID: 34969825 PMCID: PMC8763055 DOI: 10.1101/gad.349160.121] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
How distal cis-regulatory elements (e.g., enhancers) communicate with promoters remains an unresolved question of fundamental importance. Although transcription factors and cofactors are known to mediate this communication, the mechanism by which diffusible molecules relay regulatory information from one position to another along the chromosome is a biophysical puzzle-one that needs to be revisited in light of recent data that cannot easily fit into previous solutions. Here we propose a new model that diverges from the textbook enhancer-promoter looping paradigm and offer a synthesis of the literature to make a case for its plausibility, focusing on the coactivator p300.
Collapse
Affiliation(s)
- Jonathan P Karr
- University of California at Berkeley, Berkeley, California 94720, USA
| | - John J Ferrie
- University of California at Berkeley, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, Berkeley, California 94720, USA
| | - Robert Tjian
- University of California at Berkeley, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, Berkeley, California 94720, USA
| | - Xavier Darzacq
- University of California at Berkeley, Berkeley, California 94720, USA
| |
Collapse
|
36
|
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.
Collapse
|
37
|
Andrieu GP, Kohn M, Simonin M, Smith CL, Cieslak A, Dourthe MÉ, Charbonnier G, Graux C, Huguet F, Lhéritier V, Dombret H, Spicuglia S, Rousselot P, Boissel N, Asnafi V. PRC2 loss of function confers a targetable vulnerability to BET proteins in T-ALL. Blood 2021; 138:1855-1869. [PMID: 34125178 PMCID: PMC9642784 DOI: 10.1182/blood.2020010081] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 05/21/2021] [Indexed: 11/20/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a group of aggressive hematological cancers with dismal outcomes that are in need of new therapeutic options. Polycomb repressor complex 2 (PRC2) loss-of-function alterations were reported in pediatric T-ALL, yet their clinical relevance and functional consequences remain elusive. Here, we extensively analyzed PRC2 alterations in a large series of 218 adult T-ALL patients. We found that PRC2 genetic lesions are frequent events in T-ALL and are not restricted to early thymic precursor ALL. PRC2 loss of function associates with activating mutations of the IL7R/JAK/STAT pathway. PRC2-altered T-ALL patients respond poorly to prednisone and have low bone marrow blast clearance and persistent minimal residual disease. Furthermore, we identified that PRC2 loss of function profoundly reshapes the genetic and epigenetic landscapes, leading to the reactivation of stem cell programs that cooperate with bromodomain and extraterminal (BET) proteins to sustain T-ALL. This study identifies BET proteins as key mediators of the PRC2 loss of function-induced remodeling. Our data have uncovered a targetable vulnerability to BET inhibition that can be exploited to treat PRC2-altered T-ALL patients.
Collapse
Affiliation(s)
- Guillaume P Andrieu
- Institut Necker Enfants-Malades, Team 2, INSERM Unité1151, Paris, France
- Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université de Paris, Paris, France
| | - Milena Kohn
- Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Department of Hematology and Oncology, Centre Hospitalier de Versailles, Le Chesnay, France
| | - Mathieu Simonin
- Institut Necker Enfants-Malades, Team 2, INSERM Unité1151, Paris, France
- Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université de Paris, Paris, France
| | - Charlotte L Smith
- Institut Necker Enfants-Malades, Team 2, INSERM Unité1151, Paris, France
- Université de Paris, Paris, France
| | - Agata Cieslak
- Institut Necker Enfants-Malades, Team 2, INSERM Unité1151, Paris, France
- Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Marie-Émilie Dourthe
- Institut Necker Enfants-Malades, Team 2, INSERM Unité1151, Paris, France
- Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université de Paris, Paris, France
| | - Guillaume Charbonnier
- Aix-Marseille University, Theories and Approaches of Genomic Complexity (TAGC), INSERM Unité Mixte de Recherche (UMR)1090 13288 Marseille, France
| | - Carlos Graux
- Université Catholique de Louvain, Centre Hospitalier Universitaire UCLouvaine Namur-Godinne, Service d'Hématologie, Yvoir, Belgium
| | | | | | - Hervé Dombret
- Université Paris Diderot, Institut Universitaire d'Hématologie, EA-3518, Assistance Publique-Hôpitaux de Paris, University Hospital Saint-Louis, Paris, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Theories and Approaches of Genomic Complexity (TAGC), INSERM Unité Mixte de Recherche (UMR)1090 13288 Marseille, France
| | - Philippe Rousselot
- Department of Hematology and Oncology, Centre Hospitalier de Versailles, Le Chesnay, France
| | - Nicolas Boissel
- Université Paris Diderot, Institut Universitaire d'Hématologie, EA-3518, Assistance Publique-Hôpitaux de Paris, University Hospital Saint-Louis, Paris, France
| | - Vahid Asnafi
- Institut Necker Enfants-Malades, Team 2, INSERM Unité1151, Paris, France
- Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université de Paris, Paris, France
| |
Collapse
|
38
|
BET Proteins as Attractive Targets for Cancer Therapeutics. Int J Mol Sci 2021; 22:ijms222011102. [PMID: 34681760 PMCID: PMC8538173 DOI: 10.3390/ijms222011102] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/04/2021] [Accepted: 10/08/2021] [Indexed: 12/15/2022] Open
Abstract
Transcriptional dysregulation is a hallmark of cancer and can be an essential driver of cancer initiation and progression. Loss of transcriptional control can cause cancer cells to become dependent on certain regulators of gene expression. Bromodomain and extraterminal domain (BET) proteins are epigenetic readers that regulate the expression of multiple genes involved in carcinogenesis. BET inhibitors (BETis) disrupt BET protein binding to acetylated lysine residues of chromatin and suppress the transcription of various genes, including oncogenic transcription factors. Phase I and II clinical trials demonstrated BETis’ potential as anticancer drugs against solid tumours and haematological malignancies; however, their clinical success was limited as monotherapies. Emerging treatment-associated toxicities, drug resistance and a lack of predictive biomarkers limited BETis’ clinical progress. The preclinical evaluation demonstrated that BETis synergised with different classes of compounds, including DNA repair inhibitors, thus supporting further clinical development of BETis. The combination of BET and PARP inhibitors triggered synthetic lethality in cells with proficient homologous recombination. Mechanistic studies revealed that BETis targeted multiple essential homologous recombination pathway proteins, including RAD51, BRCA1 and CtIP. The exact mechanism of BETis’ anticancer action remains poorly understood; nevertheless, these agents provide a novel approach to epigenome and transcriptome anticancer therapy.
Collapse
|
39
|
Zhang L, Cai T, Lin X, Huang X, Bui MH, Plotnik JP, Bellin RJ, Faivre EJ, Kuruvilla VM, Lam LT, Lu X, Zha Z, Feng W, Hessler P, Uziel T, Zhang Q, Cavazos A, Han L, Ferguson DC, Mehta G, Shanmugavelandy SS, Magoc TJ, Rowe J, Goodwin NC, Dorritie KA, Boyiadzis M, Albert DH, McDaniel KF, Kati WM, Konopleva M, Shen Y. Selective Inhibition of the Second Bromodomain of BET Family Proteins Results in Robust Antitumor Activity in Preclinical Models of Acute Myeloid Leukemia. Mol Cancer Ther 2021; 20:1809-1819. [PMID: 34253595 DOI: 10.1158/1535-7163.mct-21-0029] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/31/2021] [Accepted: 06/29/2021] [Indexed: 11/16/2022]
Abstract
Dual bromodomain BET inhibitors that bind with similar affinities to the first and second bromodomains across BRD2, BRD3, BRD4, and BRDT have displayed modest activity as monotherapy in clinical trials. Thrombocytopenia, closely followed by symptoms characteristic of gastrointestinal toxicity, have presented as dose-limiting adverse events that may have prevented escalation to higher dose levels required for more robust efficacy. ABBV-744 is a highly selective inhibitor for the second bromodomain of the four BET family proteins. In contrast to the broad antiproliferative activities observed with dual bromodomain BET inhibitors, ABBV-744 displayed significant antiproliferative activities largely although not exclusively in cancer cell lines derived from acute myeloid leukemia and androgen receptor positive prostate cancer. Studies in acute myeloid leukemia xenograft models demonstrated antitumor efficacy for ABBV-744 that was comparable with the pan-BET inhibitor ABBV-075 but with an improved therapeutic index. Enhanced antitumor efficacy was also observed with the combination of ABBV-744 and the BCL-2 inhibitor, venetoclax compared with monotherapies of either agent alone. These results collectively support the clinical evaluation of ABBV-744 in AML (Clinical Trials.gov identifier: NCT03360006).
Collapse
MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Apoptosis
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- Cell Proliferation
- Drug Therapy, Combination
- Female
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Proteins/antagonists & inhibitors
- Proto-Oncogene Proteins c-bcl-2/antagonists & inhibitors
- Pyridines/pharmacology
- Pyrroles/pharmacology
- Sulfonamides/pharmacology
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
Collapse
Affiliation(s)
- Lu Zhang
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois
| | - Tianyu Cai
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiaoyu Lin
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois
| | - Xiaoli Huang
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois
| | - Mai H Bui
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois
| | | | | | - Emily J Faivre
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois
| | - Vinitha M Kuruvilla
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lloyd T Lam
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois
| | - Xin Lu
- Genomic Research Center, AbbVie Inc., North Chicago, Illinois
| | - Zheng Zha
- Cyteir Therapeutics, 128 Spring Street, Lexington, Massachusetts
| | - Weiguo Feng
- Genomic Research Center, AbbVie Inc., North Chicago, Illinois
| | | | - Tamar Uziel
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois
| | - Qi Zhang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Antonio Cavazos
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lina Han
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Gaurav Mehta
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois
| | | | - Terrance J Magoc
- Cyteir Therapeutics, 128 Spring Street, Lexington, Massachusetts
| | - Jenny Rowe
- Charles River Laboratories, Wilmington, Massachusetts
| | | | - Kathleen A Dorritie
- Division of Hematology/Oncology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Michael Boyiadzis
- Division of Hematology/Oncology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | | | - Warren M Kati
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois
| | - Marina Konopleva
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Yu Shen
- Oncology Discovery, AbbVie Inc., North Chicago, Illinois.
| |
Collapse
|
40
|
Yan B, Yang J, Kim MY, Luo H, Cesari N, Yang T, Strouboulis J, Zhang J, Hardison R, Huang S, Qiu Y. HDAC1 is required for GATA-1 transcription activity, global chromatin occupancy and hematopoiesis. Nucleic Acids Res 2021; 49:9783-9798. [PMID: 34450641 PMCID: PMC8464053 DOI: 10.1093/nar/gkab737] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 08/05/2021] [Accepted: 08/16/2021] [Indexed: 12/20/2022] Open
Abstract
The activity of hematopoietic factor GATA-1 is modulated through p300/CBP-mediated acetylation and FOG-1 mediated indirect interaction with HDAC1/2 containing NuRD complex. Although GATA-1 acetylation is implicated in GATA-1 activation, the role of deacetylation is not studied. Here, we found that the FOG-1/NuRD does not deacetylate GATA-1. However, HDAC1/2 can directly bind and deacetylate GATA-1. Two arginine residues within the GATA-1 linker region mediates direct interaction with HDAC1. The arginine to alanine mutation (2RA) blocks GATA-1 deacetylation and fails to induce erythroid differentiation. Gene expression profiling and ChIP-seq analysis further demonstrate the importance of GATA-1 deacetylation for gene activation and chromatin recruitment. GATA-12RA knock-in (KI) mice suffer mild anemia and thrombocytopenia with accumulation of immature erythrocytes and megakaryocytes in bone marrow and spleen. Single cell RNA-seq analysis of Lin- cKit+ (LK) cells further reveal a profound change in cell subpopulations and signature gene expression patterns in HSC, myeloid progenitors, and erythroid/megakaryocyte clusters in KI mice. Thus, GATA-1 deacetylation and its interaction with HDAC1 modulates GATA-1 chromatin binding and transcriptional activity that control erythroid/megakaryocyte commitment and differentiation.
Collapse
Affiliation(s)
- Bowen Yan
- Department of Cellular and Molecular Physiology, Hershey, PA 17033, USA
| | - Jennifer Yang
- Department of Cellular and Molecular Physiology, Hershey, PA 17033, USA
| | - Min Young Kim
- Department of Cellular and Molecular Physiology, Hershey, PA 17033, USA
| | - Huacheng Luo
- Department of Pediatrics, Hershey, PA 17033, USA
| | | | - Tao Yang
- Department of Cellular and Molecular Physiology, Hershey, PA 17033, USA
| | - John Strouboulis
- Comprehensive Cancer Center, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London SE5 9NU, UK
| | - Jiwang Zhang
- Department of Pathology, Loyola University Medical Center, Maywood, IL 60153, USA
| | - Ross Hardison
- Departments of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Suming Huang
- Department of Pediatrics, Hershey, PA 17033, USA
- Penn State Cancer Institute, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Yi Qiu
- To whom correspondence should be addressed. Tel: +1 717 531 0003 (Ext 321489); Fax: +1 717 531 7667;
| |
Collapse
|
41
|
Guo J, Liu Y, Lv J, Zou B, Chen Z, Li K, Feng J, Cai Z, Wei L, Liu M, Pang X. BCL6 confers KRAS-mutant non-small-cell lung cancer resistance to BET inhibitors. J Clin Invest 2021; 131:133090. [PMID: 33393503 DOI: 10.1172/jci133090] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/29/2020] [Indexed: 02/05/2023] Open
Abstract
The bromodomain and extra-terminal domain (BET) proteins are promising therapeutic targets to treat refractory solid tumors; however, inherent resistance remains a major challenge in the clinic. Recently, the emerging role of the oncoprotein B cell lymphoma 6 (BCL6) in tumorigenesis and stress response has been unveiled. Here, we demonstrate that BCL6 was upregulated upon BET inhibition in KRAS-mutant cancers, including non-small-cell lung cancer (NSCLC). We further found that BRD3, not BRD2 or BRD4, directly interacted with BCL6 and maintained the negative autoregulatory circuit of BCL6. Disrupting this negative autoregulation by BET inhibitors (BETi) resulted in a striking increase in BCL6 transcription, which further activated the mTOR signaling pathway through repression of the tumor suppressor death-associated protein kinase 2. Importantly, pharmacological inhibition of either BCL6 or mTOR improved the tumor response and enhanced the sensitivity of KRAS-mutant NSCLC to BETi in both in vitro and in vivo settings. Overall, our findings identify a mechanism of BRD3-mediated BCL6 autoregulation and further develop an effective combinatorial strategy to circumvent BETi resistance in KRAS-driven NSCLC.
Collapse
Affiliation(s)
- Jiawei Guo
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.,Department of Thoracic Surgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Yanan Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jing Lv
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Bin Zou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zhi Chen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.,Medical Research Institute, Wuhan University, Wuhan, China
| | - Kun Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Juanjuan Feng
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Zhenyu Cai
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Xiufeng Pang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| |
Collapse
|
42
|
Robinson J, Raguseo F, Nuccio SP, Liano D, Di Antonio M. DNA G-quadruplex structures: more than simple roadblocks to transcription? Nucleic Acids Res 2021; 49:8419-8431. [PMID: 34255847 PMCID: PMC8421137 DOI: 10.1093/nar/gkab609] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 12/12/2022] Open
Abstract
It has been >20 years since the formation of G-quadruplex (G4) secondary structures in gene promoters was first linked to the regulation of gene expression. Since then, the development of small molecules to selectively target G4s and their cellular application have contributed to an improved understanding of how G4s regulate transcription. One model that arose from this work placed these non-canonical DNA structures as repressors of transcription by preventing polymerase processivity. Although a considerable number of studies have recently provided sufficient evidence to reconsider this simplistic model, there is still a misrepresentation of G4s as transcriptional roadblocks. In this review, we will challenge this model depicting G4s as simple 'off switches' for gene expression by articulating how their formation has the potential to alter gene expression at many different levels, acting as a key regulatory element perturbing the nature of epigenetic marks and chromatin architecture.
Collapse
Affiliation(s)
- Jenna Robinson
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
- Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
| | - Federica Raguseo
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
- Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
| | - Sabrina Pia Nuccio
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
- Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
| | - Denise Liano
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
- Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
| | - Marco Di Antonio
- Imperial College London, Chemistry Department, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
- Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London W12 0BZ, UK
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| |
Collapse
|
43
|
Wang Q, Shao X, Leung ELH, Chen Y, Yao X. Selectively targeting individual bromodomain: Drug discovery and molecular mechanisms. Pharmacol Res 2021; 172:105804. [PMID: 34450309 DOI: 10.1016/j.phrs.2021.105804] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 12/21/2022]
Abstract
Bromodomain-containing proteins include bromodomain and extra-terminal (BET) and non-BET families. Due to the conserved bromodomain (BD) module between BD-containing proteins, and especially BETs with each member having two BDs (BD1 and BD2), the high degree of structural similarity makes BD-selective inhibitors much difficult to be designed. However, increasing evidences emphasized that individual BDs had distinct functions and different cellular phenotypes after pharmacological inhibition, and selectively targeting one of the BDs could result in a different efficacy and tolerability profile. This review is to summarize the pioneering progress of BD-selective inhibitors targeting BET and non-BET proteins, focusing on their structural features, biological activity, therapeutic application and experimental/theoretical mechanisms. The present proteolysis targeting chimeras (PROTAC) degraders targeting BDs, and clinical status of BD-selective inhibitors were also analyzed, providing a new insight into future direction of bromodomain-selective drug discovery.
Collapse
Affiliation(s)
- Qianqian Wang
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China
| | - Xiaomin Shao
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China
| | - Elaine Lai Han Leung
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau(SAR) 999078, China
| | - Yingqing Chen
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China.
| | - Xiaojun Yao
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau(SAR) 999078, China.
| |
Collapse
|
44
|
Lara-Ureña N, García-Domínguez M. Relevance of BET Family Proteins in SARS-CoV-2 Infection. Biomolecules 2021; 11:1126. [PMID: 34439792 PMCID: PMC8391731 DOI: 10.3390/biom11081126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/14/2022] Open
Abstract
The recent pandemic we are experiencing caused by the coronavirus disease 2019 (COVID-19) has put the world's population on the rack, with more than 191 million cases and more than 4.1 million deaths confirmed to date. This disease is caused by a new type of coronavirus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A massive proteomic analysis has revealed that one of the structural proteins of the virus, the E protein, interacts with BRD2 and BRD4 proteins of the Bromodomain and Extra Terminal domain (BET) family of proteins. BETs are essential to cell cycle progression, inflammation and immune response and have also been strongly associated with infection by different types of viruses. The fundamental role BET proteins play in transcription makes them appropriate targets for the propagation strategies of some viruses. Recognition of histone acetylation by BET bromodomains is essential for transcription control. The development of drugs mimicking acetyl groups, and thereby able to displace BET proteins from chromatin, has boosted interest on BETs as attractive targets for therapeutic intervention. The success of these drugs against a variety of diseases in cellular and animal models has been recently enlarged with promising results from SARS-CoV-2 infection studies.
Collapse
Affiliation(s)
| | - Mario García-Domínguez
- Andalusian Centre for Molecular Biology and Regenerative Medicine (CABIMER), CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Av. Américo Vespucio 24, 41092 Seville, Spain;
| |
Collapse
|
45
|
García-Gutiérrez P, García-Domínguez M. BETting on a Transcriptional Deficit as the Main Cause for Cornelia de Lange Syndrome. Front Mol Biosci 2021; 8:709232. [PMID: 34386522 PMCID: PMC8353280 DOI: 10.3389/fmolb.2021.709232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Cornelia de Lange Syndrome (CdLS) is a human developmental syndrome with complex multisystem phenotypic features. It has been traditionally considered a cohesinopathy together with other phenotypically related diseases because of their association with mutations in subunits of the cohesin complex. Despite some overlap, the clinical manifestations of cohesinopathies vary considerably and, although their precise molecular mechanisms are not well defined yet, the potential pathomechanisms underlying these diverse developmental defects have been theoretically linked to alterations of the cohesin complex function. The cohesin complex plays a critical role in sister chromatid cohesion, but this function is not affected in CdLS. In the last decades, a non-cohesion-related function of this complex on transcriptional regulation has been well established and CdLS pathoetiology has been recently associated to gene expression deregulation. Up to 70% of CdLS cases are linked to mutations in the cohesin-loading factor NIPBL, which has been shown to play a prominent function on chromatin architecture and transcriptional regulation. Therefore, it has been suggested that CdLS can be considered a transcriptomopathy. Actually, CdLS-like phenotypes have been associated to mutations in chromatin-associated proteins, as KMT2A, AFF4, EP300, TAF6, SETD5, SMARCB1, MAU2, ZMYND11, MED13L, PHIP, ARID1B, NAA10, BRD4 or ANKRD11, most of which have no known direct association with cohesin. In the case of BRD4, a critical highly investigated transcriptional coregulator, an interaction with NIPBL has been recently revealed, providing evidence on their cooperation in transcriptional regulation of developmentally important genes. This new finding reinforces the notion of an altered gene expression program during development as the major etiological basis for CdLS. In this review, we intend to integrate the recent available evidence on the molecular mechanisms underlying the clinical manifestations of CdLS, highlighting data that favors a transcription-centered framework, which support the idea that CdLS could be conceptualized as a transcriptomopathy.
Collapse
Affiliation(s)
- Pablo García-Gutiérrez
- Andalusian Centre for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Seville, Spain
| | - Mario García-Domínguez
- Andalusian Centre for Molecular Biology and Regenerative Medicine-CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide, Seville, Spain
| |
Collapse
|
46
|
Lines KE, Gluck AK, Thongjuea S, Bountra C, Thakker RV, Gorvin CM. The bromodomain inhibitor JQ1+ reduces calcium-sensing receptor activity in pituitary cell lines. J Mol Endocrinol 2021; 67:83-94. [PMID: 34223822 PMCID: PMC8345903 DOI: 10.1530/jme-21-0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 12/05/2022]
Abstract
Corticotrophinomas represent 10% of all surgically removed pituitary adenomas, however, current treatment options are often not effective, and there is a need for improved pharmacological treatments. Recently, JQ1+, a bromodomain inhibitor that promotes gene transcription by binding acetylated histone residues and recruiting transcriptional machinery, has been shown to reduce proliferation in a murine corticotroph cell line, AtT20. RNA-Seq analysis of AtT20 cells following treatment with JQ1+ identified the calcium-sensing receptor (CaSR) gene as significantly downregulated, which was subsequently confirmed using real-time PCR and Western blot analysis. CaSR is a G protein-coupled receptor that plays a central role in calcium homeostasis but can elicit non-calcitropic effects in multiple tissues, including the anterior pituitary where it helps regulate hormone secretion. However, in AtT20 cells, CaSR activates a tumour-specific cAMP pathway that promotes ACTH and PTHrP hypersecretion. We hypothesised that the Casr promoter may harbour binding sites for BET proteins, and using chromatin immunoprecipitation (ChIP)-sequencing demonstrated that the BET protein Brd3 binds to the promoter of the Casr gene. Assessment of CaSR signalling showed that JQ1+ significantly reduced Ca2+e-mediated increases in intracellular calcium (Ca2+i) mobilisation and cAMP signalling. However, the CaSR-negative allosteric modulator, NPS-2143, was unable to reduce AtT20 cell proliferation, indicating that reducing CaSR expression rather than activity is likely required to reduce pituitary cell proliferation. Thus, these studies demonstrate that reducing CaSR expression may be a viable option in the treatment of pituitary tumours. Moreover, current strategies to reduce CaSR activity, rather than protein expression for cancer treatments, may be ineffective.
Collapse
Affiliation(s)
- Kate E Lines
- Academic Endocrine Unit, Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford,UK
- Correspondence should be addressed to K E Lines or C M Gorvin: or
| | - Anna K Gluck
- Academic Endocrine Unit, Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford,UK
| | - Supat Thongjuea
- Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Chas Bountra
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Rajesh V Thakker
- Academic Endocrine Unit, Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford,UK
| | - Caroline M Gorvin
- Academic Endocrine Unit, Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford,UK
- Institute of Metabolism and Systems Research and Centre for Endocrinology, Diabetes and Metabolism, University of Birmingham, Birmingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK
- Correspondence should be addressed to K E Lines or C M Gorvin: or
| |
Collapse
|
47
|
Kim SK, Liu X, Park J, Um D, Kilaru G, Chiang CM, Kang M, Huber KM, Kang K, Kim TK. Functional coordination of BET family proteins underlies altered transcription associated with memory impairment in fragile X syndrome. SCIENCE ADVANCES 2021; 7:7/21/eabf7346. [PMID: 34138732 PMCID: PMC8133748 DOI: 10.1126/sciadv.abf7346] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/30/2021] [Indexed: 05/07/2023]
Abstract
Bromodomain and extraterminal proteins (BET) are epigenetic readers that play critical roles in gene regulation. Pharmacologic inhibition of the bromodomain present in all BET family members is a promising therapeutic strategy for various diseases, but its impact on individual family members has not been well understood. Using a transcriptional induction paradigm in neurons, we have systematically demonstrated that three major BET family proteins (BRD2/3/4) participated in transcription with different recruitment kinetics, interdependency, and sensitivity to a bromodomain inhibitor, JQ1. In a mouse model of fragile X syndrome (FXS), BRD2/3 and BRD4 showed oppositely altered expression and chromatin binding, correlating with transcriptional dysregulation. Acute inhibition of CBP/p300 histone acetyltransferase (HAT) activity restored the altered binding patterns of BRD2 and BRD4 and rescued memory impairment in FXS. Our study emphasizes the importance of understanding the BET coordination controlled by a balanced action between HATs with different substrate specificity.
Collapse
Affiliation(s)
- Seung-Kyoon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Korea
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xihui Liu
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jongmin Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Korea
| | - Dahun Um
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Korea
| | - Gokhul Kilaru
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cheng-Ming Chiang
- Simmons Comprehensive Cancer Center, Department of Biochemistry, and Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mingon Kang
- Department of Computer Science, University of Nevada, Las Vegas, NV 89154, USA
| | - Kimberly M Huber
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Keunsoo Kang
- Department of Microbiology, Dankook University, Cheonan 31116, Korea.
| | - Tae-Kyung Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Korea.
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
48
|
Engelberg IA, Foley CA, James LI, Frye SV. Improved methods for targeting epigenetic reader domains of acetylated and methylated lysine. Curr Opin Chem Biol 2021; 63:132-144. [PMID: 33852996 DOI: 10.1016/j.cbpa.2021.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 01/20/2023]
Abstract
Responsible for interpreting histone post-translational modifications, epigenetic reader proteins have emerged as novel therapeutic targets for a wide range of diseases. Chemical probes have been critical in enabling target validation studies and have led to translational advances in cancer and inflammation-related pathologies. Here, we present the most recently reported probes of reader proteins that recognize acylated and methylated lysine. We will discuss challenges associated with achieving potent antagonism of reader domains and review ongoing efforts to overcome these hurdles, focusing on targeting strategies including the use of peptidomimetic ligands, allosteric modulators, and protein degraders.
Collapse
Affiliation(s)
- Isabelle A Engelberg
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Caroline A Foley
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Stephen V Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States.
| |
Collapse
|
49
|
Patel K, Solomon PD, Walshe JL, Ford DJ, Wilkinson-White L, Payne RJ, Low JKK, Mackay JP. BET-Family Bromodomains Can Recognize Diacetylated Sequences from Transcription Factors Using a Conserved Mechanism. Biochemistry 2021; 60:648-662. [PMID: 33620209 DOI: 10.1021/acs.biochem.0c00816] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Almost all eukaryotic proteins receive diverse post-translational modifications (PTMs) that modulate protein activity. Many histone PTMs are well characterized, heavily influence gene regulation, and are often predictors of distinct transcriptional programs. Although our understanding of the histone PTM network has matured, much is yet to be understood about the roles of transcription factor (TF) PTMs, which might well represent a similarly complex and dynamic network of functional regulation. Members of the bromodomain and extra-terminal domain (BET) family of proteins recognize acetyllysine residues and relay the signals encoded by these modifications. Here, we have investigated the acetylation dependence of several functionally relevant BET-TF interactions in vitro using surface plasmon resonance, nuclear magnetic resonance, and X-ray crystallography. We show that motifs known to be acetylated in TFs E2F1 and MyoD1 can interact with all bromodomains of BRD2, BRD3, and BRD4. The interactions are dependent on diacetylation of the motifs and show a preference for the first BET bromodomain. Structural mapping of the interactions confirms a conserved mode of binding for the two TFs to the acetyllysine binding pocket of the BET bromodomains, mimicking that of other already established functionally important histone- and TF-BET interactions. We also examined a motif from the TF RelA that is known to be acetylated but were unable to observe any interaction, regardless of the acetylation state of the sequence. Our findings overall advance our understanding of BET-TF interactions and suggest a physical link between the important diacetylated motifs found in E2F1 and MyoD1 and the BET-family proteins.
Collapse
Affiliation(s)
- Karishma Patel
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Paul D Solomon
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - James L Walshe
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Daniel J Ford
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | | | - Richard J Payne
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| |
Collapse
|
50
|
Tang P, Zhang J, Liu J, Chiang CM, Ouyang L. Targeting Bromodomain and Extraterminal Proteins for Drug Discovery: From Current Progress to Technological Development. J Med Chem 2021; 64:2419-2435. [PMID: 33616410 DOI: 10.1021/acs.jmedchem.0c01487] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bromodomain and extraterminal (BET) proteins bind acetylated lysine residues in histones and nonhistone proteins via tandem bromodomains and regulate chromatin dynamics, cellular processes, and disease procession. Thus targeting BET proteins is a promising strategy for treating various diseases, especially malignant tumors and chronic inflammation. Many pan-BET small-molecule inhibitors have been described, and some of them are in clinical evaluation. Nevertheless, the limited clinical efficacy of the current BET inhibitors is also evident and has inspired the development of new technologies to improve their clinical outcomes and minimize unwanted side effects. In this Review, we summarize the latest protein characteristics and biological functions of BRD4 as an example of BET proteins, analyze the clinical development status and preclinical resistance mechanisms, and discuss recent advances in BRD4-selective inhibitors, dual-target BET inhibitors, proteolysis targeting chimera degraders, and protein-protein interaction inhibitors.
Collapse
Affiliation(s)
- Pan Tang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Jifa Zhang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Jie Liu
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Cheng-Ming Chiang
- Simmons Comprehensive Cancer Center, Department of Pharmacology, and Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital of Sichuan University, Chengdu 610041, China
| |
Collapse
|