1
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Hurd CA, Bush JT, Powell AJ, Walport LJ. mRNA Display in Cell Lysates Enables Identification of Cyclic Peptides Targeting the BRD3 Extraterminal Domain. Angew Chem Int Ed Engl 2024; 63:e202406414. [PMID: 38899853 DOI: 10.1002/anie.202406414] [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: 04/04/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 06/21/2024]
Abstract
mRNA display is a powerful technology to screen libraries of >1012 cyclic peptides against a protein target, enabling the rapid discovery of high affinity ligands. These cyclic peptides are particularly well suited to challenging protein targets that have been difficult to drug with small molecules. However, target choice can still be limited as screens are typically performed against purified proteins which often demands the use of isolated domains and precludes the use of aggregation-prone targets. Herein, we report a method to perform mRNA display selections in mammalian cell lysates without the need for prior target purification, vastly expanding the potential target scope of mRNA display. We have applied the methodology to identify low to sub-nanomolar peptide binders for two targets: a NanoLuc subunit (LgBiT) and full-length bromodomain-containing protein 3 (BRD3). Our cyclic peptides for BRD3 were found to bind to the extraterminal (ET) domain of BRD3 and the closely related BRD proteins, BRD2 and BRD4. While many chemical probes exist for the bromodomains of BRD proteins, the ET domain is relatively underexplored, making these peptides valuable additions to the BRD toolbox.
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Affiliation(s)
- Catherine A Hurd
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, W12 0BZ
- Crick-GSK Biomedical LinkLabs, The Francis Crick Institute, London, NW1 1AT
| | - Jacob T Bush
- Crick-GSK Biomedical LinkLabs, GSK, Gunnels Wood Road, Stevenage, SG1 2NY
| | - Andrew J Powell
- Crick-GSK Biomedical LinkLabs, GSK, Gunnels Wood Road, Stevenage, SG1 2NY
| | - Louise J Walport
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, W12 0BZ
- Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT
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2
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Zhang S, Roeder RG. Resistance of estrogen receptor function to BET bromodomain inhibition is mediated by transcriptional coactivator cooperativity. Nat Struct Mol Biol 2024:10.1038/s41594-024-01384-6. [PMID: 39251822 DOI: 10.1038/s41594-024-01384-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 08/01/2024] [Indexed: 09/11/2024]
Abstract
The bromodomain and extraterminal domain (BET) family of proteins are critical chromatin readers that bind to acetylated histones through their bromodomains to activate transcription. Here, we reveal that bromodomain inhibition fails to repress oncogenic targets of estrogen receptor because of an intrinsic transcriptional mechanism. While bromodomains are necessary for the transcription of many genes, bromodomain-containing protein 4 (BRD4) binds to estrogen receptor binding sites and activates transcription of critical oncogenes such as MYC, independently of its bromodomains. BRD4 associates with the Mediator complex and disruption of Mediator reduces BRD4's enhancer occupancy. Profiling changes of the post-initiation RNA polymerase II (Pol II)-associated factors revealed that BET proteins regulate interactions between Pol II and elongation factors SPT5, SPT6 and the polymerase-associated factor 1 complex, which associate with BET proteins independently of their bromodomains and mediate their transcription elongation effect. Our findings highlight the importance of bromodomain-independent functions and interactions of BET proteins in the development of future therapeutic strategies.
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Affiliation(s)
- Sicong Zhang
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA.
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY, USA.
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3
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Reid XJ, Zhong Y, Mackay JP. How does CHD4 slide nucleosomes? Biochem Soc Trans 2024:BST20230070. [PMID: 39221830 DOI: 10.1042/bst20230070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
Chromatin remodelling enzymes reposition nucleosomes throughout the genome to regulate the rate of transcription and other processes. These enzymes have been studied intensively since the 1990s, and yet the mechanism by which they operate has only very recently come into focus, following advances in cryoelectron microscopy and single-molecule biophysics. CHD4 is an essential and ubiquitous chromatin remodelling enzyme that until recently has received less attention than remodellers such as Snf2 and CHD1. Here we review what recent work in the field has taught us about how CHD4 reshapes the genome. Cryoelectron microscopy and single-molecule studies demonstrate that CHD4 shares a central remodelling mechanism with most other chromatin remodellers. At the same time, differences between CHD4 and other chromatin remodellers result from the actions of auxiliary domains that regulate remodeller activity by for example: (1) making differential interactions with nucleosomal epitopes such as the acidic patch and the N-terminal tail of histone H4, and (2) inducing the formation of distinct multi-protein remodelling complexes (e.g. NuRD vs ChAHP). Thus, although we have learned much about remodeller activity, there is still clearly much more waiting to be revealed.
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Affiliation(s)
- Xavier J Reid
- School of Life and Environmental Sciences, University of Sydney, Darlington, NSW 2006, Australia
| | - Yichen Zhong
- School of Life and Environmental Sciences, University of Sydney, Darlington, NSW 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Darlington, NSW 2006, Australia
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4
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Wei Q, Gan C, Sun M, Xie Y, Liu H, Xue T, Deng C, Mo C, Ye T. BRD4: an effective target for organ fibrosis. Biomark Res 2024; 12:92. [PMID: 39215370 PMCID: PMC11365212 DOI: 10.1186/s40364-024-00641-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Fibrosis is an excessive wound-healing response induced by repeated or chronic external stimuli to tissues, significantly impacting quality of life and primarily contributing to organ failure. Organ fibrosis is reported to cause 45% of all-cause mortality worldwide. Despite extensive efforts to develop new antifibrotic drugs, drug discovery has not kept pace with the clinical demand. Currently, only pirfenidone and nintedanib are approved by the FDA to treat pulmonary fibrotic illness, whereas there are currently no available antifibrotic drugs for hepatic, cardiac or renal fibrosis. The development of fibrosis is closely related to epigenetic alterations. The field of epigenetics primarily studies biological processes, including chromatin modifications, epigenetic readers, DNA transcription and RNA translation. The bromodomain and extra-terminal structural domain (BET) family, a class of epigenetic readers, specifically recognizes acetylated histone lysine residues and promotes the formation of transcriptional complexes. Bromodomain-containing protein 4 (BRD4) is one of the most well-researched proteins in the BET family. BRD4 is implicated in the expression of genes related to inflammation and pro-fibrosis during fibrosis. Inhibition of BRD4 has shown promising anti-fibrotic effects in preclinical studies; however, no BRD4 inhibitor has been approved for clinical use. This review introduces the structure and function of BET proteins, the research progress on BRD4 in organ fibrosis, and the inhibitors of BRD4 utilized in fibrosis. We emphasize the feasibility of targeting BRD4 as an anti-fibrotic strategy and discuss the therapeutic potential and challenges associated with BRD4 inhibitors in treating fibrotic diseases.
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Affiliation(s)
- Qun Wei
- Laboratory of Gastrointestinal Cancer and Liver Disease, Department of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Cailing Gan
- Laboratory of Gastrointestinal Cancer and Liver Disease, Department of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Meng Sun
- Laboratory of Gastrointestinal Cancer and Liver Disease, Department of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuting Xie
- Laboratory of Gastrointestinal Cancer and Liver Disease, Department of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hongyao Liu
- Laboratory of Gastrointestinal Cancer and Liver Disease, Department of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Taixiong Xue
- Laboratory of Gastrointestinal Cancer and Liver Disease, Department of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Conghui Deng
- Laboratory of Gastrointestinal Cancer and Liver Disease, Department of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Chunheng Mo
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
| | - Tinghong Ye
- Laboratory of Gastrointestinal Cancer and Liver Disease, Department of Gastroenterology and Hepatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Ningxia Medical University, Yin Chuan, 640100, China.
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5
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Ahmadpour Youshanlui M, Yari A, Bahojb Mahdavi SZ, Amini M, Baradaran B, Ahangar R, Pourbagherian O, Mokhtarzadeh AA. BRD4 expression and its regulatory interaction with miR-26a-3p, DLG5-AS1, and JMJD1C-AS1 lncRNAs in gastric cancer progression. Discov Oncol 2024; 15:356. [PMID: 39152304 PMCID: PMC11329449 DOI: 10.1007/s12672-024-01230-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Accepted: 08/12/2024] [Indexed: 08/19/2024] Open
Abstract
Gastric cancer remains a significant health challenge despite advancements in diagnosis and treatment. Early detection is critical to reducing mortality, necessitating the investigation of molecular mechanisms underlying gastric cancer progression. This study focuses on BRD4 expression and its correlation with miR-26a-3p, DLG5-AS1, and JMJD1C-AS1 lncRNAs in gastric cancer. Analysis of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets revealed significant upregulation of BRD4 in gastric cancer tissues compared to normal tissues, correlating negatively with miR-26a-3p and positively with DLG5-AS1 and JMJD1C-AS1 lncRNAs. Quantitative RT-PCR confirmed these findings in 25 gastric cancer tissue samples and 25 normal samples. BRD4's overexpression was associated with reduced survival rates and older patient age. MiR-26a-3p, a known tumor suppressor, showed decreased expression in gastric cancer tissues, with ROC analysis suggesting it, alongside BRD4, as a potential diagnostic biomarker. Additionally, bioinformatics predicted miR-26a-3p's interaction with BRD4 mRNA. Upregulated lncRNAs DLG5-AS1 and JMJD1C-AS1 likely act as competing endogenous RNAs, sponging miR-26a-3p, thus promoting BRD4 dysregulation. These lncRNAs have not been previously studied in gastric cancer. The findings propose a novel BRD4/lncRNA/miRNA regulatory axis in gastric cancer, highlighting the potential of BRD4, DLG5-AS1, and JMJD1C-AS1 as biomarkers for early diagnosis. Further studies with larger sample sizes and in vivo and in vitro experiments are needed to elucidate this regulatory mechanism's role in gastric cancer progression.
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Affiliation(s)
| | - Amirhossein Yari
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Mohammad Amini
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ramin Ahangar
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Omid Pourbagherian
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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6
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Kato T, Oyamatsu H, Hanamatsu Y, Huang H, Okado S, Imamura Y, Nomata Y, Watanabe H, Kadomatsu Y, Ueno H, Nakamura S, Mizuno T, Hase T, Takeuchi T, Chen-Yoshikawa TF. Transcriptomic profiling of a late recurrent nuclear protein in testis carcinoma of the lung 14 years after the initial operation: a case report. Transl Lung Cancer Res 2024; 13:1756-1762. [PMID: 39118893 PMCID: PMC11304145 DOI: 10.21037/tlcr-24-259] [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: 03/22/2024] [Accepted: 06/24/2024] [Indexed: 08/10/2024]
Abstract
Background Nuclear protein in testis (NUT) carcinoma (NC) of the lung is a rare cancer that occurs mainly in young adolescents and adults. NC is genetically characterized by NUTM1 rearrangements, which usually take the form of BRD4-NUT fusions. The prognosis for NC is dismal, and treatment with conventional chemotherapeutic regimens is ineffective. Case Description We herein describe the case of a 53-year-old woman with recurrent NC of the lung 14 years after surgery for nasal cavity cancer. Chest computed tomography revealed a 5.5-cm tumor in the lower lobe of the left lung. We completely resected the recurrent lung NC via thoracotomy. Immunohistochemistry (IHC) of the lung and nasal cavity cancers showed diffuse strong expression of NUT. RNA-seq of the lung NC revealed NUTM1 rearrangement, with a fusion of BRD4 exon 10 to NUTM1 exon 4. This breakpoint has never been reported before. In addition, IHC revealed elevated expression of parathyroid hormone-like hormone in the lung NC but not in the nasal cavity NC, indicating that the lung and nasal cavity NCs were metachronous multiple primary cancers. Conclusions We experienced a rare recurrence of lung NC 14 years after the initial surgery. The BRD4-NUT fusion consisted of a new breakpoint. Furthermore, the expression pattern of parathyroid hormone-like hormone (PTHLH) suggested that the NCs in the nasal cavity and lung may be metachronous multiple lung cancers. This extremely rare case highlighted the possibility of identifying less malignant NCs in patients with poorly differentiated tumors via fusion gene analysis and the need to develop more effective treatment strategies for this malignancy.
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Affiliation(s)
- Taketo Kato
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Yuki Hanamatsu
- Department of Pathology and Translational Research, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Heng Huang
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shoji Okado
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshito Imamura
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuji Nomata
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroki Watanabe
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuka Kadomatsu
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Harushi Ueno
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shota Nakamura
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tetsuya Mizuno
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tetsunari Hase
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tamotsu Takeuchi
- Department of Pathology and Translational Research, Gifu University Graduate School of Medicine, Gifu, Japan
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7
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Zhang S, Roeder RG. Resistance of estrogen receptor function to BET bromodomain inhibition is mediated by transcriptional coactivator cooperativity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.25.605008. [PMID: 39211208 PMCID: PMC11361192 DOI: 10.1101/2024.07.25.605008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The Bromodomain and Extra-Terminal Domain (BET) family of proteins are critical chromatin readers that bind to acetylated histones through their bromodomains to activate transcription. Here, we reveal that bromodomain inhibition fails to repress oncogenic targets of estrogen receptor due to an intrinsic transcriptional mechanism. While bromodomains are necessary for the transcription of many genes, BRD4 binds to estrogen receptor binding sites and activates transcription of critical oncogenes independently of its bromodomains. BRD4 associates with the Mediator complex and disruption of Mediator complex reduces BRD4's enhancer occupancy. Profiling changes in the post-initiation RNA polymerase II (Pol II)-associated factors revealed that BET proteins regulate interactions between Pol II and elongation factors SPT5, SPT6, and PAF1 complex, which associate with BET proteins independently of their bromodomains and mediate their transcription elongation effect. Our findings highlight the importance of bromodomain-independent functions and interactions of BET proteins in the development of future therapeutic strategies.
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8
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Zhang Y, Fong KW, Mao F, Wang R, Allison DB, Napier D, He D, Liu J, Zhang Y, Chen J, Kong Y, Li C, Li G, Liu J, Li Z, Zhu H, Wang C, Liu X. Elevating PLK1 overcomes BETi resistance in prostate cancer via triggering BRD4 phosphorylation-dependent degradation in mitosis. Cell Rep 2024; 43:114431. [PMID: 38968071 PMCID: PMC11334074 DOI: 10.1016/j.celrep.2024.114431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 04/20/2024] [Accepted: 06/18/2024] [Indexed: 07/07/2024] Open
Abstract
Bromodomain-containing protein 4 (BRD4) has emerged as a promising therapeutic target in prostate cancer (PCa). Understanding the mechanisms of BRD4 stability could enhance the clinical response to BRD4-targeted therapy. In this study, we report that BRD4 protein levels are significantly decreased during mitosis in a PLK1-dependent manner. Mechanistically, we show that BRD4 is primarily phosphorylated at T1186 by the CDK1/cyclin B complex, recruiting PLK1 to phosphorylate BRD4 at S24/S1100, which are recognized by the APC/CCdh1 complex for proteasome pathway degradation. We find that PLK1 overexpression lowers SPOP mutation-stabilized BRD4, consequently rendering PCa cells re-sensitized to BRD4 inhibitors. Intriguingly, we report that sequential treatment of docetaxel and JQ1 resulted in significant inhibition of PCa. Collectively, the results support that PLK1-phosphorylated BRD4 triggers its degradation at M phase. Sequential treatment of docetaxel and JQ1 overcomes BRD4 accumulation-associated bromodomain and extra-terminal inhibitor (BETi) resistance, which may shed light on the development of strategies to treat PCa.
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Affiliation(s)
- Yanquan Zhang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA.
| | - Ka-Wing Fong
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Fengyi Mao
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Ruixin Wang
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Derek B Allison
- Pathology & Laboratory Medicine, University of Kentucky, Lexington, KY 40508, USA
| | - Dana Napier
- Biospecimen Procurement & Translational Pathology Shared Resource Facility, University of Kentucky, Lexington, KY 40536, USA
| | - Daheng He
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Jinpeng Liu
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Yeqing Zhang
- Department of Biology, College of Arts & Sciences, University of Kentucky, Lexington, KY 40506, USA
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Yifan Kong
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Chaohao Li
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Guangbing Li
- Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Jinghui Liu
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Zhiguo Li
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Chi Wang
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
| | - Xiaoqi Liu
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA.
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9
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Hao S, Lee YJ, Benhamou Goldfajn N, Flores E, Liang J, Fuehrer H, Demmerle J, Lippincott-Schwartz J, Liu Z, Sukenik S, Cai D. YAP condensates are highly organized hubs. iScience 2024; 27:109927. [PMID: 38784009 PMCID: PMC11111833 DOI: 10.1016/j.isci.2024.109927] [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: 11/10/2022] [Revised: 10/24/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
YAP/TEAD signaling is essential for organismal development, cell proliferation, and cancer progression. As a transcriptional coactivator, how YAP activates its downstream target genes is incompletely understood. YAP forms biomolecular condensates in response to hyperosmotic stress, concentrating transcription-related factors to activate downstream target genes. However, whether YAP forms condensates under other signals, how YAP condensates organize and function, and how YAP condensates activate transcription in general are unknown. Here, we report that endogenous YAP forms sub-micron scale condensates in response to Hippo pathway regulation and actin cytoskeletal tension. YAP condensates are stabilized by the transcription factor TEAD1, and recruit BRD4, a coactivator that is enriched at active enhancers. Using single-particle tracking, we found that YAP condensates slowed YAP diffusion within condensate boundaries, a possible mechanism for promoting YAP target search. These results reveal that YAP condensate formation is a highly regulated process that is critical for YAP/TEAD target gene expression.
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Affiliation(s)
- Siyuan Hao
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Ye Jin Lee
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Nadav Benhamou Goldfajn
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Eduardo Flores
- Department of Chemistry and Chemical Biology, University of California, Merced, Merced, CA 95343, USA
| | - Jindayi Liang
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Hannah Fuehrer
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Justin Demmerle
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | | | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Shahar Sukenik
- Department of Chemistry and Chemical Biology, University of California, Merced, Merced, CA 95343, USA
| | - Danfeng Cai
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
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10
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Mondal A, Singh B, Felkner RH, De Falco A, Swapna G, Montelione GT, Roth MJ, Perez A. A Computational Pipeline for Accurate Prioritization of Protein-Protein Binding Candidates in High-Throughput Protein Libraries. Angew Chem Int Ed Engl 2024; 63:e202405767. [PMID: 38588243 DOI: 10.1002/anie.202405767] [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: 03/26/2024] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/10/2024]
Abstract
Identifying the interactome for a protein of interest is challenging due to the large number of possible binders. High-throughput experimental approaches narrow down possible binding partners but often include false positives. Furthermore, they provide no information about what the binding region is (e.g., the binding epitope). We introduce a novel computational pipeline based on an AlphaFold2 (AF) Competitive Binding Assay (AF-CBA) to identify proteins that bind a target of interest from a pull-down experiment and the binding epitope. Our focus is on proteins that bind the Extraterminal (ET) domain of Bromo and Extraterminal domain (BET) proteins, but we also introduce nine additional systems to show transferability to other peptide-protein systems. We describe a series of limitations to the methodology based on intrinsic deficiencies of AF and AF-CBA to help users identify scenarios where the approach will be most useful. Given the method's speed and accuracy, we anticipate its broad applicability to identify binding epitope regions among potential partners, setting the stage for experimental verification.
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Affiliation(s)
- Arup Mondal
- Department of Chemistry and Quantum Theory Project, University of Florida, Leigh Hall 240, Gainesville, FL, USA
| | - Bhumika Singh
- Department of Chemistry and Quantum Theory Project, University of Florida, Leigh Hall 240, Gainesville, FL, USA
| | - Roland H Felkner
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, 675 Hoes Lane Rm 636, Piscataway, NJ 08854, USA
| | - Anna De Falco
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Gvt Swapna
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Gaetano T Montelione
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Monica J Roth
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, 675 Hoes Lane Rm 636, Piscataway, NJ 08854, USA
| | - Alberto Perez
- Department of Chemistry and Quantum Theory Project, University of Florida, Leigh Hall 240, Gainesville, FL, USA
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11
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Bachus S, Akkerman N, Fulham L, Graves D, Helwer R, Rempel J, Pelka P. ARGLU1 enhances promoter-proximal pausing of RNA polymerase II and stimulates DNA damage repair. Nucleic Acids Res 2024; 52:5658-5675. [PMID: 38520408 PMCID: PMC11162773 DOI: 10.1093/nar/gkae208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024] Open
Abstract
Arginine and glutamate rich 1 (ARGLU1) is a poorly understood cellular protein with functions in RNA splicing and transcription. Computational prediction suggests that ARGLU1 contains intrinsically disordered regions and lacks any known structural or functional domains. We used adenovirus Early protein 1A (E1A) to probe for critical regulators of important cellular pathways and identified ARGLU1 as a significant player in transcription and the DNA damage response pathway. Transcriptional effects induced by ARGLU1 occur via enhancement of promoter-proximal RNA polymerase II pausing, likely by inhibiting the interaction between JMJD6 and BRD4. When overexpressed, ARGLU1 increases the growth rate of cancer cells, while its knockdown leads to growth arrest. Significantly, overexpression of ARGLU1 increased cancer cell resistance to genotoxic drugs and promoted DNA damage repair. These results identify new roles for ARGLU1 in cancer cell survival and the DNA damage repair pathway, with potential clinical implications for chemotherapy resistance.
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Affiliation(s)
- Scott Bachus
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Nikolas Akkerman
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Lauren Fulham
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Drayson Graves
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Rafe Helwer
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Jordan Rempel
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
| | - Peter Pelka
- Department of Microbiology, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 45 Chancellor's Circle, Buller Building Room 427, Winnipeg, MB R3T 2N2, Canada
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12
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Strom AR, Eeftens JM, Polyachenko Y, Weaver CJ, Watanabe HF, Bracha D, Orlovsky ND, Jumper CC, Jacobs WM, Brangwynne CP. Interplay of condensation and chromatin binding underlies BRD4 targeting. Mol Biol Cell 2024; 35:ar88. [PMID: 38656803 PMCID: PMC11238092 DOI: 10.1091/mbc.e24-01-0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/10/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024] Open
Abstract
Nuclear compartments form via biomolecular phase separation, mediated through multivalent properties of biomolecules concentrated within condensates. Certain compartments are associated with specific chromatin regions, including transcriptional initiation condensates, which are composed of transcription factors and transcriptional machinery, and form at acetylated regions including enhancer and promoter loci. While protein self-interactions, especially within low-complexity and intrinsically disordered regions, are known to mediate condensation, the role of substrate-binding interactions in regulating the formation and function of biomolecular condensates is underexplored. Here, utilizing live-cell experiments in parallel with coarse-grained simulations, we investigate how chromatin interaction of the transcriptional activator BRD4 modulates its condensate formation. We find that both kinetic and thermodynamic properties of BRD4 condensation are affected by chromatin binding: nucleation rate is sensitive to BRD4-chromatin interactions, providing an explanation for the selective formation of BRD4 condensates at acetylated chromatin regions, and thermodynamically, multivalent acetylated chromatin sites provide a platform for BRD4 clustering below the concentration required for off-chromatin condensation. This provides a molecular and physical explanation of the relationship between nuclear condensates and epigenetically modified chromatin that results in their mutual spatiotemporal regulation, suggesting that epigenetic modulation is an important mechanism by which the cell targets transcriptional condensates to specific chromatin loci.
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Affiliation(s)
- Amy R. Strom
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
| | - Jorine M. Eeftens
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
- Radboud Institute for Molecular Life Sciences, Radboud University, 6525 XZ Nijmegen, Netherlands
| | - Yury Polyachenko
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - Claire J. Weaver
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
- Department of Molecular and Cellular Biology, Princeton University, Princeton, NJ 08544
| | | | - Dan Bracha
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
- Department of Biotechnology and Food Engineering, Technion, Haifa 3200, Israel
| | - Natalia D. Orlovsky
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
- Biological and Biomedical Sciences Program, Harvard University, Boston, MA 02115
| | - Chanelle C. Jumper
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
- Nereid Therapeutics, Boston, MA
| | | | - Clifford P. Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
- Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ 08544
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
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13
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Tong D, Tang Y, Zhong P. The emerging roles of histone demethylases in cancers. Cancer Metastasis Rev 2024; 43:795-821. [PMID: 38227150 DOI: 10.1007/s10555-023-10160-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 12/05/2023] [Indexed: 01/17/2024]
Abstract
Modulation of histone methylation status is regarded as an important mechanism of epigenetic regulation and has substantial clinical potential for the therapy of diseases, including cancer and other disorders. The present study aimed to provide a comprehensive introduction to the enzymology of histone demethylases, as well as their cancerous roles, molecular mechanisms, therapeutic possibilities, and challenges for targeting them, in order to advance drug design for clinical therapy and highlight new insight into the mechanisms of these enzymes in cancer. A series of clinical trials have been performed to explore potential roles of histone demethylases in several cancer types. Numerous targeted inhibitors associated with immunotherapy, chemotherapy, radiotherapy, and targeted therapy have been used to exert anticancer functions. Future studies should evaluate the dynamic transformation of histone demethylases leading to carcinogenesis and explore individual therapy.
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Affiliation(s)
- Dali Tong
- Department of Urological Surgery, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, People's Republic of China.
| | - Ying Tang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China.
| | - Peng Zhong
- Department of Pathology, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, People's Republic of China.
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14
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Hashimoto M, Masuda T, Nakano Y, Tobo T, Saito H, Koike K, Takahashi J, Abe T, Ando Y, Ozato Y, Hosoda K, Higuchi S, Hisamatsu Y, Toshima T, Yonemura Y, Hata T, Uemura M, Eguchi H, Doki Y, Mori M, Mimori K. Tumor suppressive role of the epigenetic master regulator BRD3 in colorectal cancer. Cancer Sci 2024; 115:1866-1880. [PMID: 38494600 PMCID: PMC11145117 DOI: 10.1111/cas.16129] [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: 07/26/2023] [Revised: 02/13/2024] [Accepted: 02/16/2024] [Indexed: 03/19/2024] Open
Abstract
Bromodomain and extraterminal domain (BET) family proteins are epigenetic master regulators of gene expression via recognition of acetylated histones and recruitment of transcription factors and co-activators to chromatin. Hence, BET family proteins have emerged as promising therapeutic targets in cancer. In this study, we examined the functional role of bromodomain containing 3 (BRD3), a BET family protein, in colorectal cancer (CRC). In vitro and vivo analyses using BRD3-knockdown or BRD3-overexpressing CRC cells showed that BRD3 suppressed tumor growth and cell cycle G1/S transition and induced p21 expression. Clinical analysis of CRC datasets from our hospital or The Cancer Genome Atlas revealed that BET family genes, including BRD3, were overexpressed in tumor tissues. In immunohistochemical analyses, BRD3 was observed mainly in the nucleus of CRC cells. According to single-cell RNA sequencing in untreated CRC tissues, BRD3 was highly expressed in malignant epithelial cells, and cell cycle checkpoint-related pathways were enriched in the epithelial cells with high BRD3 expression. Spatial transcriptomic and single-cell RNA sequencing analyses of CRC tissues showed that BRD3 expression was positively associated with high p21 expression. Furthermore, overexpression of BRD3 combined with knockdown of, a driver gene in the BRD family, showed strong inhibition of CRC cells in vitro. In conclusion, we demonstrated a novel tumor suppressive role of BRD3 that inhibits tumor growth by cell cycle inhibition in part via induction of p21 expression. BRD3 activation might be a novel therapeutic approach for CRC.
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Affiliation(s)
- Masahiro Hashimoto
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
- Department of Gastroenterological SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | - Takaaki Masuda
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Yusuke Nakano
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
- Department of Gastroenterological SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | - Taro Tobo
- Department of PathologyKyushu University Beppu HospitalBeppuJapan
| | - Hideyuki Saito
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Kensuke Koike
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | | | - Tadashi Abe
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Yuki Ando
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Yuki Ozato
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
- Department of Gastroenterological SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | - Kiyotaka Hosoda
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Satoshi Higuchi
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
- Department of Gastroenterological SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | | | - Takeo Toshima
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Yusuke Yonemura
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
| | - Tsuyoshi Hata
- Department of Gastroenterological SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | - Mamoru Uemura
- Department of Gastroenterological SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | - Hidetoshi Eguchi
- Department of Gastroenterological SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | - Yuichiro Doki
- Department of Gastroenterological SurgeryOsaka University Graduate School of MedicineSuitaJapan
| | - Masaki Mori
- Tokai University School of MedicineIseharaJapan
| | - Koshi Mimori
- Department of SurgeryKyushu University Beppu HospitalBeppuJapan
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15
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Ji Y, Chen W, Wang X. Bromodomain and Extraterminal Domain Protein 2 in Multiple Human Diseases. J Pharmacol Exp Ther 2024; 389:277-288. [PMID: 38565308 DOI: 10.1124/jpet.123.002036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/04/2024] Open
Abstract
Bromodomain and extraterminal domain protein 2 (BRD2), a member of the bromodomain and extraterminal domain (BET) protein family, is a crucial epigenetic regulator with significant function in various diseases and cellular processes. The central function of BRD2 is modulating gene transcription by binding to acetylated lysine residues on histones and transcription factors. This review highlights key findings on BRD2 in recent years, emphasizing its roles in maintaining genomic stability, influencing chromatin spatial organization, and participating in transcriptional regulation. BRD2's diverse functions are underscored by its involvement in diseases such as malignant tumors, neurologic disorders, inflammatory conditions, metabolic diseases, and virus infection. Notably, the potential role of BRD2 as a diagnostic marker and therapeutic target is discussed in the context of various diseases. Although pan inhibitors targeting the BET family have shown promise in preclinical studies, a critical need exists for the development of highly selective BRD2 inhibitors. In conclusion, this review offers insights into the multifaceted nature of BRD2 and calls for continued research to unravel its intricate mechanisms and harness its therapeutic potential. SIGNIFICANCE STATEMENT: BRD2 is involved in the occurrence and development of diseases through maintaining genomic stability, influencing chromatin spatial organization, and participating in transcriptional regulation. Targeting BRD2 through protein degradation-targeting complexes technology is emerging as a promising therapeutic approach for malignant cancer and inflammatory diseases.
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Affiliation(s)
- Yikang Ji
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology
| | - Wantao Chen
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology
| | - Xu Wang
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology
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16
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Huang QX, Fan DM, Zheng ZZ, Ran T, Bai A, Xiao RQ, Hu GS, Liu W. Peptide Inhibitor Targeting the Extraterminal Domain in BRD4 Potently Suppresses Breast Cancer Both In Vitro and In Vivo. J Med Chem 2024; 67:6658-6672. [PMID: 38569135 PMCID: PMC11056977 DOI: 10.1021/acs.jmedchem.4c00141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/27/2024] [Accepted: 03/20/2024] [Indexed: 04/05/2024]
Abstract
BRD4 is associated with a variety of human diseases, including breast cancer. The crucial roles of amino-terminal bromodomains (BDs) of BRD4 in binding with acetylated histones to regulate oncogene expression make them promising drug targets. However, adverse events impede the development of the BD inhibitors. BRD4 adopts an extraterminal (ET) domain, which recruits proteins to drive oncogene expression. We discovered a peptide inhibitor PiET targeting the ET domain to disrupt BRD4/JMJD6 interaction, a protein complex critical in oncogene expression and breast cancer. The cell-permeable form of PiET, TAT-PiET, and PROTAC-modified TAT-PiET, TAT-PiET-PROTAC, potently inhibits the expression of BRD4/JMJD6 target genes and breast cancer cell growth. Combination therapy with TAT-PiET/TAT-PiET-PROTAC and JQ1, iJMJD6, or Fulvestrant exhibits synergistic effects. TAT-PiET or TAT-PiET-PROTAC treatment overcomes endocrine therapy resistance in ERα-positive breast cancer cells. Taken together, we demonstrated that targeting the ET domain is effective in suppressing breast cancer, providing a therapeutic avenue in the clinic.
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Affiliation(s)
- Qi-xuan Huang
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang
An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty
of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Da-meng Fan
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang
An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty
of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Zao-zao Zheng
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang
An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty
of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Ting Ran
- Bioland
Laboratory (Guangzhou Regenerative Medicine and Health—Guangdong
Laboratory), KaiYuan
Road, Guangzhou, Guangdong 510530, China
| | - Ao Bai
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang
An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty
of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Rong-quan Xiao
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang
An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty
of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Guo-sheng Hu
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang
An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty
of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
| | - Wen Liu
- State
Key Laboratory of Cellular Stress Biology, School of Pharmaceutical
Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Fujian
Provincial Key Laboratory of Innovative Drug Target Research, School
of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
- Xiang
An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty
of Medicine and Life Sciences, Xiamen University, Xiang’an South Road, Xiamen, Fujian 361102, China
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17
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Rosenthal ZC, Fass DM, Payne NC, She A, Patnaik D, Hennig KM, Tesla R, Werthmann GC, Guhl C, Reis SA, Wang X, Chen Y, Placzek M, Williams NS, Hooker J, Herz J, Mazitschek R, Haggarty SJ. Epigenetic modulation through BET bromodomain inhibitors as a novel therapeutic strategy for progranulin-deficient frontotemporal dementia. Sci Rep 2024; 14:9064. [PMID: 38643236 PMCID: PMC11032351 DOI: 10.1038/s41598-024-59110-7] [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: 12/06/2023] [Accepted: 04/08/2024] [Indexed: 04/22/2024] Open
Abstract
Frontotemporal dementia (FTD) is a debilitating neurodegenerative disorder with currently no disease-modifying treatment options available. Mutations in GRN are one of the most common genetic causes of FTD, near ubiquitously resulting in progranulin (PGRN) haploinsufficiency. Small molecules that can restore PGRN protein to healthy levels in individuals bearing a heterozygous GRN mutation may thus have therapeutic value. Here, we show that epigenetic modulation through bromodomain and extra-terminal domain (BET) inhibitors (BETi) potently enhance PGRN protein levels, both intracellularly and secreted forms, in human central nervous system (CNS)-relevant cell types, including in microglia-like cells. In terms of potential for disease modification, we show BETi treatment effectively restores PGRN levels in neural cells with a GRN mutation known to cause PGRN haploinsufficiency and FTD. We demonstrate that BETi can rapidly and durably enhance PGRN in neural progenitor cells (NPCs) in a manner dependent upon BET protein expression, suggesting a gain-of-function mechanism. We further describe a CNS-optimized BETi chemotype that potently engages endogenous BRD4 and enhances PGRN expression in neuronal cells. Our results reveal a new epigenetic target for treating PGRN-deficient forms of FTD and provide mechanistic insight to aid in translating this discovery into therapeutics.
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Affiliation(s)
- Zachary C Rosenthal
- Chemical Neurobiology Laboratory, Precision Therapeutics Unit, Center for Genomic Medicine, Departments of Neurology and Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Daniel M Fass
- Chemical Neurobiology Laboratory, Precision Therapeutics Unit, Center for Genomic Medicine, Departments of Neurology and Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - N Connor Payne
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Angela She
- Chemical Neurobiology Laboratory, Precision Therapeutics Unit, Center for Genomic Medicine, Departments of Neurology and Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Debasis Patnaik
- Chemical Neurobiology Laboratory, Precision Therapeutics Unit, Center for Genomic Medicine, Departments of Neurology and Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Krista M Hennig
- Chemical Neurobiology Laboratory, Precision Therapeutics Unit, Center for Genomic Medicine, Departments of Neurology and Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Rachel Tesla
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Translational Neurodegeneration Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gordon C Werthmann
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Translational Neurodegeneration Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Charlotte Guhl
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Surya A Reis
- Chemical Neurobiology Laboratory, Precision Therapeutics Unit, Center for Genomic Medicine, Departments of Neurology and Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Xiaoyu Wang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yueting Chen
- Department of Radiology, Harvard Medical School, Boston, MA, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA
| | - Michael Placzek
- Department of Radiology, Harvard Medical School, Boston, MA, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA
| | - Noelle S Williams
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jacob Hooker
- Department of Radiology, Harvard Medical School, Boston, MA, USA
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA
| | - Joachim Herz
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Translational Neurodegeneration Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Precision Therapeutics Unit, Center for Genomic Medicine, Departments of Neurology and Psychiatry, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA.
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18
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Qiang Y, Fan J, Xie C, Yan L, Song X, Zhang N, Lin Y, Xiong J, Zhang W, Liu Y, Wei L, Li Y, Chen S, Liang K, Li F. KDM5C-Mediated Recruitment of BRD4 to Chromatin Regulates Enhancer Activation and BET Inhibitor Sensitivity. Cancer Res 2024; 84:1252-1269. [PMID: 38285760 DOI: 10.1158/0008-5472.can-23-2888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/05/2023] [Accepted: 01/24/2024] [Indexed: 01/31/2024]
Abstract
The BET family member BRD4 is a bromodomain-containing protein that plays a vital role in driving oncogene expression. Given their pivotal role in regulating oncogenic networks in various cancer types, BET inhibitors (BETi) have been developed, but the clinical application has been impeded by dose-limiting toxicity and resistance. Understanding the mechanisms of BRD4 activity and identifying predictive biomarkers could facilitate the successful clinical use of BETis. Herein, we show that KDM5C and BRD4 cooperate to sustain tumor cell growth. Mechanistically, KDM5C interacted with BRD4 and stimulated BRD4 enhancer recruitment. Moreover, binding of the BRD4 C-terminus to KDM5C stimulated the H3K4 demethylase activity of KDM5C. The abundance of both KDM5C-associated BRD4 and H3K4me1/3 determined the transcriptional activation of many oncogenes. Notably, depletion or pharmacologic degradation of KDM5C dramatically reduced BRD4 chromatin enrichment and significantly increased BETi efficacy across multiple cancer types in both tumor cell lines and patient-derived organoid models. Furthermore, targeting KDM5C in combination with BETi suppressed tumor growth in vivo in a xenograft mouse model. Collectively, this work reveals a KDM5C-mediated mechanism by which BRD4 regulates transcription, providing a rationale for incorporating BETi into combination therapies with KDM5C inhibitors to enhance treatment efficacy. SIGNIFICANCE BRD4 is recruited to enhancers in a bromodomain-independent manner by binding KDM5C and stimulates KDM5C H3K4 demethylase activity, leading to synergistic effects of BET and KDM5C inhibitor combinations in cancer.
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Affiliation(s)
- Yulong Qiang
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, China
| | - Jiachen Fan
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, China
| | - Chuanshuai Xie
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Leilei Yan
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, China
| | - Xiaofei Song
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, China
| | - Nan Zhang
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, China
| | - Yan Lin
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, China
| | - Jie Xiong
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Wei Zhang
- Department of Gynaecology and Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yu Liu
- Department of Radiation and Medical Oncology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Lei Wei
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Yu Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Shizhen Chen
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Kaiwei Liang
- Department of Physiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Feng Li
- Department of Medical Genetics, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, China
- Hubei Provincial Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, China
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19
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Zhu X, Fu Z, Dutchak K, Arabzadeh A, Milette S, Steinberger J, Morin G, Monast A, Pilon V, Kong T, Adams BN, Prando Munhoz E, Hosein HJB, Fang T, Su J, Xue Y, Rayes R, Sangwan V, Walsh LA, Chen G, Quail DF, Spicer JD, Park M, Dankort D, Huang S. Cotargeting CDK4/6 and BRD4 Promotes Senescence and Ferroptosis Sensitivity in Cancer. Cancer Res 2024; 84:1333-1351. [PMID: 38277141 DOI: 10.1158/0008-5472.can-23-1749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/21/2023] [Accepted: 01/17/2024] [Indexed: 01/27/2024]
Abstract
Cyclin-dependent kinase 4/6 (CDK4/6) inhibitors are approved for breast cancer treatment and show activity against other malignancies, including KRAS-mutant non-small cell lung cancer (NSCLC). However, the clinical efficacy of CDK4/6 inhibitors is limited due to frequent drug resistance and their largely cytostatic effects. Through a genome-wide cDNA screen, we identified that bromodomain-containing protein 4 (BRD4) overexpression conferred resistance to the CDK4/6 inhibitor palbociclib in KRAS-mutant NSCLC cells. Inhibition of BRD4, either by RNA interference or small-molecule inhibitors, synergized with palbociclib to induce senescence in NSCLC cells and tumors, and the combination prolonged survival in a KRAS-mutant NSCLC mouse model. Mechanistically, BRD4-inhibition enhanced cell-cycle arrest and reactive oxygen species (ROS) accumulation, both of which are necessary for senescence induction; this in turn elevated GPX4, a peroxidase that suppresses ROS-triggered ferroptosis. Consequently, GPX4 inhibitor treatment selectively induced ferroptotic cell death in the senescent cancer cells, resulting in tumor regression. Cotargeting CDK4/6 and BRD4 also promoted senescence and ferroptosis vulnerability in pancreatic and breast cancer cells. Together, these findings reveal therapeutic vulnerabilities and effective combinations to enhance the clinical utility of CDK4/6 inhibitors. SIGNIFICANCE The combination of cytostatic CDK4/6 and BRD4 inhibitors induces senescent cancer cells that are primed for activation of ferroptotic cell death by targeting GPX4, providing an effective strategy for treating cancer.
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Affiliation(s)
- Xianbing Zhu
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Zheng Fu
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Kendall Dutchak
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Azadeh Arabzadeh
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Simon Milette
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
- Department of Physiology, McGill University, Montreal, Quebec, Canada
| | - Jutta Steinberger
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Geneviève Morin
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Anie Monast
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Virginie Pilon
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Tim Kong
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Bianca N Adams
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Erika Prando Munhoz
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Hannah J B Hosein
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Tianxu Fang
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
- Department of Biomedical Engineering, McGill University, Montreal, Quebec, Canada
| | - Jing Su
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Yibo Xue
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Roni Rayes
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
- Department of Surgery, McGill University Health Center, Montreal, Quebec, Canada
| | - Veena Sangwan
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Logan A Walsh
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Guojun Chen
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
- Department of Biomedical Engineering, McGill University, Montreal, Quebec, Canada
| | - Daniela F Quail
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Jonathan D Spicer
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
- Department of Surgery, McGill University Health Center, Montreal, Quebec, Canada
| | - Morag Park
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - David Dankort
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
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20
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He L, Cao Y, Sun L. NSD family proteins: Rising stars as therapeutic targets. CELL INSIGHT 2024; 3:100151. [PMID: 38371593 PMCID: PMC10869250 DOI: 10.1016/j.cellin.2024.100151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 02/20/2024]
Abstract
Epigenetic modifications, including DNA methylation and histone post-translational modifications, intricately regulate gene expression patterns by influencing DNA accessibility and chromatin structure in higher organisms. These modifications are heritable, are independent of primary DNA sequences, undergo dynamic changes during development and differentiation, and are frequently disrupted in human diseases. The reversibility of epigenetic modifications makes them promising targets for therapeutic intervention and drugs targeting epigenetic regulators (e.g., tazemetostat, targeting the H3K27 methyltransferase EZH2) have been applied in clinical therapy for multiple cancers. The NSD family of H3K36 methyltransferase enzymes-including NSD1 (KMT3B), NSD2 (MMSET/WHSC1), and NSD3 (WHSC1L1)-are now receiving drug development attention, with the exciting advent of an NSD2 inhibitor (KTX-1001) advancing to Phase I clinical trials for relapsed or refractory multiple myeloma. NSD proteins recognize and catalyze methylation of histone lysine marks, thereby regulating chromatin integrity and gene expression. Multiple studies have implicated NSD proteins in human disease, noting impacts from translocations, aberrant expression, and various dysfunctional somatic mutations. Here, we review the biological functions of NSD proteins, epigenetic cooperation related to NSD proteins, and the accumulating evidence linking these proteins to developmental disorders and tumorigenesis, while additionally considering prospects for the development of innovative epigenetic therapies.
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Affiliation(s)
- Lin He
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University Health Science Center, Beijing 100191, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University International Cancer Institute, Peking University Health Science Center, Beijing 100191, China
| | - Yiping Cao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University International Cancer Institute, Peking University Health Science Center, Beijing 100191, China
| | - Luyang Sun
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University Health Science Center, Beijing 100191, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University International Cancer Institute, Peking University Health Science Center, Beijing 100191, China
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21
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Piao L, Gao Y, Xu X, Su Y, Wang YD, Zhou J, Gao Y, Fang J, Li Q, Chang S, Kong R. Discovery of potent small molecule inhibitors of histone lysine methyltransferase NSDs. Eur J Med Chem 2024; 268:116264. [PMID: 38412693 DOI: 10.1016/j.ejmech.2024.116264] [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: 11/28/2023] [Revised: 01/31/2024] [Accepted: 02/18/2024] [Indexed: 02/29/2024]
Abstract
Nuclear receptor binding SET domain (NSD) proteins are a class of histone lysine methyltransferases and implicated in multiple cancer types with aberrant expression and involvement of cancer related signaling pathways. In this study, a series of small-molecule compounds including compound 2 and 3 are identified against the SET domain of NSDs through structure-based virtual screening. Our lead compound 3 exhibits potent inhibitory activities in vitro towards the NSD2-SET and NSD3-SET with an IC50 of 0.81 μM and 0.84 μM, respectively, and efficiently inhibits histone H3 lysine 36 dimethylation and decreases the expression of NSDs-targeted genes in non-small cell lung cancer cells at 100 nM. Compound 3 suppresses cell proliferation and reduces the clonogenicity in H460 and H1299 non-small cell lung cancer cells, and induces s-phase cell cycle arrest and apoptosis. These data establish our compounds as a valuable tool-kit for the study of the biological roles of NSDs in cancer.
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Affiliation(s)
- Lianhua Piao
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, Jiangsu, 213001, China
| | - Ying Gao
- Primary Biotechnology Co., Ltd., Changzhou, 213125, China
| | - Xiaoshuang Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, Jiangsu, 213001, China
| | - Yangyang Su
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, Jiangsu, 213001, China
| | | | - Jie Zhou
- Suzhou Medinoah Co., Ltd., Suzhou, 215125, China
| | - Yang Gao
- Suzhou Medinoah Co., Ltd., Suzhou, 215125, China
| | - Jin Fang
- Suzhou Medinoah Co., Ltd., Suzhou, 215125, China
| | - Qihui Li
- Primary Biotechnology Co., Ltd., Changzhou, 213125, China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, Jiangsu, 213001, China.
| | - Ren Kong
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, Jiangsu, 213001, China.
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22
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Cadesky A, Schulman-Rosenbaum R, Carter A, Paul E, Jaggi S. A Rare Case of NUT Carcinoma of the Thyroid. JCEM CASE REPORTS 2024; 2:luae037. [PMID: 38524390 PMCID: PMC10958768 DOI: 10.1210/jcemcr/luae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Indexed: 03/26/2024]
Abstract
NUT carcinoma is an aggressive, poorly differentiated squamous cell carcinoma, defined by rearrangement of the NUTM1 (Nuclear Protein in Testis) gene. Diagnosis is challenging due to histologic similarities with other poorly differentiated tumors requiring advanced diagnostic techniques. There is no established treatment, and prognosis remains extremely poor. A 27-year-old woman without known medical history presented with a rapidly enlarging neck mass and compressive symptoms. Chemotherapy for presumed squamous cell carcinoma with a component of anaplastic thyroid cancer based on pathology was initiated. Next-generation sequencing revealed thyroid NUT carcinoma with high PD-L1 expression, prompting PD-1 targeted therapy. The patient expired shortly afterwards from progressive disease. NUT carcinoma of thyroid origin is an extremely rare disease. This case brings awareness to the disease, highlights the importance of advanced diagnostic techniques and complexities in managing patients with NUT carcinoma.
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Affiliation(s)
- Adam Cadesky
- Department of Medicine, Division of Endocrinology, Metabolism & Diabetes, Northwell, New Hyde Park, NY 11042-1069, USA
| | - Rifka Schulman-Rosenbaum
- Department of Medicine, Division of Endocrinology, Metabolism & Diabetes, Northwell, New Hyde Park, NY 11042-1069, USA
| | - Amanda Carter
- Division of Endocrinology, Diabetes & Metabolism, NYU Langone Health, Manhasset, NY 11030, USA
| | - Elizabeth Paul
- Department of Medicine, Division of Endocrinology, Metabolism & Diabetes, Northwell, New Hyde Park, NY 11042-1069, USA
| | - Shuchie Jaggi
- Department of Medicine, Division of Endocrinology, Metabolism & Diabetes, Northwell, New Hyde Park, NY 11042-1069, USA
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23
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Li N, Zhang E, Li Z, Lv S, Zhao X, Ke Q, Zou Q, Li W, Wang Y, Guo H, Song T, Sun L. The P53-P21-RB1 pathway promotes BRD4 degradation in liver cancer through USP1. J Biol Chem 2024; 300:105707. [PMID: 38309505 PMCID: PMC10907170 DOI: 10.1016/j.jbc.2024.105707] [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: 10/02/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 02/05/2024] Open
Abstract
Liver cancer is notoriously refractory to conventional therapeutics. Tumor progression is governed by the interplay between tumor-promoting genes and tumor-suppressor genes. BRD4, an acetyl lysine-binding protein, is overexpressed in many cancer types, which promotes activation of a pro-tumor gene network. But the underlying mechanism for BRD4 overexpression remains incompletely understood. In addition, understanding the regulatory mechanism of BRD4 protein level will shed insight into BRD4-targeting therapeutics. In this study, we investigated the potential relation between BRD4 protein level and P53, the most frequently dysregulated tumor suppressor. By analyzing the TCGA datasets, we first identify a strong negative correlation between protein levels of P53 and BRD4 in liver cancer. Further investigation shows that P53 promotes BRD4 protein degradation. Mechanistically, P53 indirectly represses the transcription of USP1, a deubiquitinase, through the P21-RB1 axis. USP1 itself is also overexpressed in liver cancer and we show USP1 deubiquitinates BRD4 in vivo and in vitro, which increases BRD4 stability. With cell proliferation assays and xenograft model, we show the pro-tumor role of USP1 is partially mediated by BRD4. With functional transcriptomic analysis, we find the USP1-BRD4 axis upholds expression of a group of cancer-related genes. In summary, we identify a functional P53-P21-RB1-USP1-BRD4 axis in liver cancer.
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Affiliation(s)
- Neng Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Erlei Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology, Wuhan, Hubei, China; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, Hubei, China
| | - Zhenyong Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Suli Lv
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuefeng Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Ke
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qingli Zou
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wensheng Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yifei Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haocheng Guo
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tanjing Song
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Cell Architecture Research Institute, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Lidong Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Cell Architecture Research Institute, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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24
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Herbison H, Davis S, Nickless D, Haydon A, Ameratunga M. Sustained Clinical Response to Immunotherapy Followed by BET Inhibitor in a Patient with Unresectable Sinonasal NUT Carcinoma. JOURNAL OF IMMUNOTHERAPY AND PRECISION ONCOLOGY 2024; 7:67-72. [PMID: 38327754 PMCID: PMC10846633 DOI: 10.36401/jipo-23-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/24/2023] [Accepted: 09/13/2023] [Indexed: 02/09/2024]
Abstract
NUT carcinomas (NCs) are a group of rare tumors that can occur anywhere in the body and are defined by the fusion of the nuclear protein in testis (NUTM1) resulting in increased transcription of proto-oncogenes. NCs have a poor prognosis that varies according to the site of origin with an urgent need to develop new treatment strategies. Case reports on immunotherapy in pulmonary NC have been published, and bromodomain and extraterminal (BET) inhibitors have shown activity in NC in phase I/II trials. We present the case of a 27-year-old woman with an unresectable sinonasal NC who had a sustained clinical response to both immunotherapy and BET inhibitor therapy. This is the first reported case of immunotherapy in sinonasal NC, and it highlights the different responses to a range of treatments including BET inhibitor therapy. This case supports the theory that NCs arising from different primary sites have differing prognoses.
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Affiliation(s)
- Harriet Herbison
- Department of Medical Oncology, Monash Health, Clayton, Victoria, Australia
| | - Sidney Davis
- Department of Radiation Oncology, The Alfred Hospital, Melbourne, Victoria, Australia
| | - David Nickless
- Department of Anatomical Pathology, Cabrini Pathology, Melbourne, Victoria, Australia
| | - Andrew Haydon
- Department of Medical Oncology, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Malaka Ameratunga
- Department of Medical Oncology, The Alfred Hospital, Melbourne, Victoria, Australia
- Central Clinical School, Monash University, Melbourne, Victoria, Australia
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25
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Mondal A, Singh B, Felkner RH, De Falco A, Swapna GVT, Montelione GT, Roth MJ, Perez A. Sifting Through the Noise: A Computational Pipeline for Accurate Prioritization of Protein-Protein Binding Candidates in High-Throughput Protein Libraries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576374. [PMID: 38328039 PMCID: PMC10849530 DOI: 10.1101/2024.01.20.576374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Identifying the interactome for a protein of interest is challenging due to the large number of possible binders. High-throughput experimental approaches narrow down possible binding partners, but often include false positives. Furthermore, they provide no information about what the binding region is (e.g. the binding epitope). We introduce a novel computational pipeline based on an AlphaFold2 (AF) Competition Assay (AF-CBA) to identify proteins that bind a target of interest from a pull-down experiment, along with the binding epitope. Our focus is on proteins that bind the Extraterminal (ET) domain of Bromo and Extraterminal domain (BET) proteins, but we also introduce nine additional systems to show transferability to other peptide-protein systems. We describe a series of limitations to the methodology based on intrinsic deficiencies to AF and AF-CBA, to help users identify scenarios where the approach will be most useful. Given the speed and accuracy of the methodology, we expect it to be generally applicable to facilitate target selection for experimental verification starting from high-throughput protein libraries.
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Affiliation(s)
- Arup Mondal
- Department of Chemistry and Quantum Theory Project, University of Florida, Leigh Hall 240, Gainesville, FL
| | - Bhumika Singh
- Department of Chemistry and Quantum Theory Project, University of Florida, Leigh Hall 240, Gainesville, FL
| | - Roland H. Felkner
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, 675 Hoes Lane Rm 636, Piscataway, NJ 08854
| | - Anna De Falco
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - GVT Swapna
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Gaetano T. Montelione
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Monica J. Roth
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, 675 Hoes Lane Rm 636, Piscataway, NJ 08854
| | - Alberto Perez
- Department of Chemistry and Quantum Theory Project, University of Florida, Leigh Hall 240, Gainesville, FL
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26
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Musa RE, Lester KL, Quickstad G, Vardabasso S, Shumate TV, Salcido RT, Ge K, Shpargel KB. BRD4 binds to active cranial neural crest enhancers to regulate RUNX2 activity during osteoblast differentiation. Development 2024; 151:dev202110. [PMID: 38063851 PMCID: PMC10905746 DOI: 10.1242/dev.202110] [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: 06/22/2023] [Accepted: 11/16/2023] [Indexed: 01/25/2024]
Abstract
Cornelia de Lange syndrome (CdLS) is a congenital disorder featuring facial dysmorphism, postnatal growth deficits, cognitive disability and upper limb abnormalities. CdLS is genetically heterogeneous, with cases arising from mutation of BRD4, a bromodomain protein that binds and reads acetylated histones. In this study, we have modeled CdLS facial pathology through mouse neural crest cell (NCC)-specific mutation of BRD4 to characterize cellular and molecular function in craniofacial development. Mice with BRD4 NCC loss of function died at birth with severe facial hypoplasia, cleft palate, mid-facial clefting and exencephaly. Following migration, BRD4 mutant NCCs initiated RUNX2 expression for differentiation to osteoblast lineages but failed to induce downstream RUNX2 targets required for lineage commitment. BRD4 bound to active enhancers to regulate expression of osteogenic transcription factors and extracellular matrix components integral for bone formation. RUNX2 physically interacts with a C-terminal domain in the long isoform of BRD4 and can co-occupy osteogenic enhancers. This BRD4 association is required for RUNX2 recruitment and appropriate osteoblast differentiation. We conclude that BRD4 controls facial bone development through osteoblast enhancer regulation of the RUNX2 transcriptional program.
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Affiliation(s)
- Rachel E. Musa
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264, USA
| | - Kaitlyn L. Lester
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264, USA
| | - Gabrielle Quickstad
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264, USA
| | - Sara Vardabasso
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264, USA
| | - Trevor V. Shumate
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264, USA
| | - Ryan T. Salcido
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264, USA
| | - Kai Ge
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Karl B. Shpargel
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599-7264, USA
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27
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Nuñez Y, Vera S, Baeza V, Gonzalez-Pecchi V. NSD3 in Cancer: Unraveling Methyltransferase-Dependent and Isoform-Specific Functions. Int J Mol Sci 2024; 25:944. [PMID: 38256018 PMCID: PMC10815784 DOI: 10.3390/ijms25020944] [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: 12/19/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
NSD3 (nuclear receptor-binding SET domain protein 3) is a member of the NSD histone methyltransferase family of proteins. In recent years, it has been identified as a potential oncogene in certain types of cancer. The NSD3 gene encodes three isoforms, the long version (NSD3L), a short version (NSD3S) and the WHISTLE isoforms. Importantly, the NSD3S isoform corresponds to the N-terminal region of the full-length protein, lacking the methyltransferase domain. The chromosomal location of NSD3 is frequently amplified across cancer types, such as breast, lung, and colon, among others. Recently, this amplification has been correlated to a chromothripsis event, that could explain the different NSD3 alterations found in cancer. The fusion proteins containing NSD3 have also been reported in leukemia (NSD3-NUP98), and in NUT (nuclear protein of the testis) midline carcinoma (NSD3-NUT). Its role as an oncogene has been described by modulating different cancer pathways through its methyltransferase activity, or the short isoform of the protein, through protein interactions. Specifically, in this review we will focus on the functions that have been characterized as methyltransferase dependent, and those that have been correlated with the expression of the NSD3S isoform. There is evidence that both the NSD3L and NSD3S isoforms are relevant for cancer progression, establishing NSD3 as a therapeutic target. However, further functional studies are needed to differentiate NSD3 oncogenic activity as dependent or independent of the catalytic domain of the protein, as well as the contribution of each isoform and its clinical significance in cancer progression.
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Affiliation(s)
- Yanara Nuñez
- Biomedical Science Research Laboratory, Department of Basic Sciences, Faculty of Medicine, Universidad Católica de la Santísima Concepción, Concepción 4090541, Chile; (Y.N.); (S.V.); (V.B.)
- Biochemistry, Faculty of Pharmacy, Universidad de Concepción, Concepción 4070383, Chile
| | - Sebastian Vera
- Biomedical Science Research Laboratory, Department of Basic Sciences, Faculty of Medicine, Universidad Católica de la Santísima Concepción, Concepción 4090541, Chile; (Y.N.); (S.V.); (V.B.)
| | - Victor Baeza
- Biomedical Science Research Laboratory, Department of Basic Sciences, Faculty of Medicine, Universidad Católica de la Santísima Concepción, Concepción 4090541, Chile; (Y.N.); (S.V.); (V.B.)
| | - Valentina Gonzalez-Pecchi
- Biomedical Science Research Laboratory, Department of Basic Sciences, Faculty of Medicine, Universidad Católica de la Santísima Concepción, Concepción 4090541, Chile; (Y.N.); (S.V.); (V.B.)
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Zhang L, Chai R, Tai Z, Miao F, Shi X, Chen Z, Zhu Q. Noval advance of histone modification in inflammatory skin diseases and related treatment methods. Front Immunol 2024; 14:1286776. [PMID: 38235133 PMCID: PMC10792063 DOI: 10.3389/fimmu.2023.1286776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/08/2023] [Indexed: 01/19/2024] Open
Abstract
Inflammatory skin diseases are a group of diseases caused by the disruption of skin tissue due to immune system disorders. Histone modification plays a pivotal role in the pathogenesis and treatment of chronic inflammatory skin diseases, encompassing a wide range of conditions, including psoriasis, atopic dermatitis, lupus, systemic sclerosis, contact dermatitis, lichen planus, and alopecia areata. Analyzing histone modification as a significant epigenetic regulatory approach holds great promise for advancing our understanding and managing these complex disorders. Additionally, therapeutic interventions targeting histone modifications have emerged as promising strategies for effectively managing inflammatory skin disorders. This comprehensive review provides an overview of the diverse types of histone modification. We discuss the intricate association between histone modification and prevalent chronic inflammatory skin diseases. We also review current and potential therapeutic approaches that revolve around modulating histone modifications. Finally, we investigated the prospects of research on histone modifications in the context of chronic inflammatory skin diseases, paving the way for innovative therapeutic interventions and improved patient outcomes.
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Affiliation(s)
- Lichen Zhang
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of External Chinese Medicine, Shanghai, China
| | - Rongrong Chai
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of External Chinese Medicine, Shanghai, China
| | - Zongguang Tai
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of External Chinese Medicine, Shanghai, China
| | - Fengze Miao
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of External Chinese Medicine, Shanghai, China
| | - Xinwei Shi
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of External Chinese Medicine, Shanghai, China
| | - Zhongjian Chen
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of External Chinese Medicine, Shanghai, China
| | - Quangang Zhu
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of External Chinese Medicine, Shanghai, China
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Tracy KM, Prior S, Trowbridge WT, Boyd JR, Ghule PN, Frietze S, Stein JL, Stein GS, Lian JB. Bromodomain Proteins Epigenetically Regulate the Mitotically Associated lncRNA MANCR in Triple Negative Breast Cancer Cells. Crit Rev Eukaryot Gene Expr 2024; 34:61-71. [PMID: 38073442 PMCID: PMC11023627 DOI: 10.1615/critreveukaryotgeneexpr.2023050109] [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] [Indexed: 12/18/2023]
Abstract
Long non-coding RNA (lncRNA)-mediated control of gene expression contributes to regulation of biological processes that include proliferation and phenotype, as well as compromised expression of genes that are functionally linked to cancer initiation and tumor progression. lncRNAs have emerged as novel targets and biomarkers in breast cancer. We have shown that mitotically associated lncRNA MANCR is expressed in triple-negative breast cancer (TNBC) cells and that it serves a critical role in promoting genome stability and survival in aggressive breast cancer cells. Using an siRNA strategy, we selectively depleted BRD2, BRD3, and BRD4, singly and in combination, to establish which bromodomain proteins regulate MANCR expression in TNBC cells. Our findings were confirmed by using in situ hybridization combined with immunofluorescence analysis that revealed BRD4, either alone or with BRD2 and BRD3, can support MANCR regulation of TNBC cells. Here we provide evidence for MANCR-responsive epigenetic control of super enhancers by histone modifications that are required for gene transcription to support cell survival and expression of the epithelial tumor phenotype in triple negative breast cancer cells.
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Affiliation(s)
- Kirsten M. Tracy
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Shannon Prior
- Department of Biomedical and Health Sciences, University of Vermont College of Nursing and Health Sciences, Burlington, VT 05405
| | - Willem T. Trowbridge
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Joseph R. Boyd
- Department of Biomedical and Health Sciences, University of Vermont College of Nursing and Health Sciences, Burlington, VT 05405
| | - Prachi N. Ghule
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405
- Department of Biomedical and Health Sciences, University of Vermont College of Nursing and Health Sciences, Burlington, VT 05405
| | - Seth Frietze
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405
- Department of Biomedical and Health Sciences, University of Vermont College of Nursing and Health Sciences, Burlington, VT 05405
- University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Janet L. Stein
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405
- University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Gary S. Stein
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405
- University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT 05405
| | - Jane B. Lian
- Department of Biochemistry, University of Vermont Larner College of Medicine, Burlington, VT 05405
- University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT 05405
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30
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Rani AQ, Bonam SR, Zhou J, Li J, Hu H, Liu X. BRD4 as a potential target for human papillomaviruses associated cancer. J Med Virol 2023; 95:e29294. [PMID: 38100650 PMCID: PMC11315413 DOI: 10.1002/jmv.29294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
Around 99% of cervical cancer and 5%-10% of human cancer are associated with human papillomaviruses (HPV). Notably, the life-cycle of HPV begins by low-level infection of the basal cells of the stratified epithelium, where the viral genomes are replicated and passed on to the daughter proliferating basal cells. The production of new viral particles remains restricted to eventually differentiated cells. HPVs support their persistent infectious cycle by hijacking pivotal pathways and cellular processes. Bromodomain-containing protein 4 (BRD4) is one of the essential cellular factors involved in multiple stages of viral transcription and replication. In this review, we demonstrate the role of BRD4 in the multiple stages of HPV infectious cycle. Also, we provide an overview of the intense research about the cellular functions of BRD4, the mechanism of action of bromodomain and extra terminal inhibitors, and how it could lead to the development of antiviral/anticancer therapies.
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Affiliation(s)
- Abdul Qawee Rani
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
| | - Srinivasa Reddy Bonam
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), 301 University Blvd, Galveston, TX 77555, USA
| | - Jia Zhou
- Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), 301 University Blvd, Galveston, TX 77555, USA
| | - Jenny Li
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
| | - Haitao Hu
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), 301 University Blvd, Galveston, TX 77555, USA
| | - Xuefeng Liu
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA
- Departments of Pathology, Urology and Radiation Oncology, Wexner Medical Center, Ohio State University, Columbus, OH 43210, USA
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31
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Lee J, Lee BK, Gross JM. Brd activity regulates Müller glia-dependent retinal regeneration in zebrafish. Glia 2023; 71:2866-2883. [PMID: 37584502 DOI: 10.1002/glia.24457] [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: 07/24/2020] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
The zebrafish retina possesses tremendous regenerative potential. Müller glia underlie retinal regeneration through their ability to reprogram and generate multipotent neuronal progenitors that re-differentiate into lost neurons. Many factors required for Müller glia reprogramming and proliferation have been identified; however, we know little about the epigenetic and transcriptional regulation of these genes during regeneration. Here, we determined whether transcriptional regulation by members of the Bromodomain (Brd) family is required for Müller glia-dependent retinal regeneration. Our data demonstrate that three brd genes were expressed in Müller glia upon injury. brd2a and brd2b were expressed in all Müller glia and brd4 was expressed only in reprogramming Müller glia. Utilizing (+)-JQ1, a pharmacological inhibitor of Brd function, we demonstrate that transcriptional regulation by Brds plays a critical role in Müller glia reprogramming and regeneration. (+)-JQ1 treatment prevented cell cycle re-entry of Müller glia and the generation of neurogenic progenitors. Modulating the (+)-JQ1 exposure window, we identified the first 48 h post-injury as the time-period during which Müller glia reprogramming occurs. (+)-JQ1 treatments after 48 h post-injury had no effect on the re-differentiation of UV cones, indicating that Brd function is required only for Müller glia reprogramming and not subsequent specification/differentiation events. Brd inhibition also prevented the expression of reprogramming genes like ascl1a and lepb in Müller glia, but not effector genes like mmp9, nor did it affect microglial recruitment after injury. These results demonstrate that transcriptional regulation by Brds plays a critical role during Müller glia-dependent retinal regeneration in zebrafish.
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Affiliation(s)
- Jiwoon Lee
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, New York, USA
| | - Jeffrey M Gross
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
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Palumbo GA, Duminuco A. Myelofibrosis: In Search for BETter Targeted Therapies. J Clin Oncol 2023; 41:5044-5048. [PMID: 37751563 DOI: 10.1200/jco.23.00833] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 07/22/2023] [Accepted: 07/31/2023] [Indexed: 09/28/2023] Open
Affiliation(s)
- Giuseppe A Palumbo
- Department of Scienze Mediche, Chirurgiche e Tecnologie Avanzate "G.F. Ingrassia," University of Catania, Catania, Italy
| | - Andrea Duminuco
- Postgraduate School of Hematology, University of Catania, Catania, Italy
- Department of Haematology, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
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33
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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: 22] [Impact Index Per Article: 22.0] [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.
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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.
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34
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Tu Y, Fang C, Xu J, Zhou Y, Liang M, Yang Z. A de novo variant of BICRA results in Coffin-Siris syndrome 12. Mol Genet Genomic Med 2023; 11:e2250. [PMID: 37485815 PMCID: PMC10655513 DOI: 10.1002/mgg3.2250] [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: 01/10/2023] [Revised: 03/22/2023] [Accepted: 07/13/2023] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND BICRA, a transcript regulator, was identified as the genetic factor of Coffin-Siris syndrome 12 (CSS12) recently, which was characterized by diverse neurodevelopmental delays. Up to now, limited studies of BICRA in neurodevelopmental delay have been reported. METHODS Clinical data such as EEGs, MRIs, routine blood, and physical examination were collected. Trio whole exome sequencing (WES) of the family was performed, and all variants with a minor allele frequency (<0.01) in exon and canonical splicing sites were selected for further pathogenic evaluation. Candidate variants were validated by Sanger sequencing. The BICRA-related literature was reviewed and the clinical characteristics were summarized. RESULTS We reported a CSS12 proband with a narrow and slightly clinical phenotype who only exhibited language developmental delay, hypotonia, and slight gastrointestinal features. WES revealed a de novo variant in exon 6 of BICRA [NM_015711.3: c.1666C>T, p.Gln556*]. This variant resulted in an early translation termination at 556th of BICRA, not collected in the public population database (gnomAD), and classified as pathogenic according to the ACMG guideline. CONCLUSION Our results expanded the pathogenic genetic and clinical spectrum of BICRA-related diseases.
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Affiliation(s)
- Youquan Tu
- Department of Pediatric NeurologyNingbo Women and Children's HospitalNingboChina
| | - Chunyan Fang
- Department of Pediatric NeurologyNingbo Women and Children's HospitalNingboChina
| | - Jian Xu
- Department of RadiologyNingbo Women and Children's HospitalNingboChina
| | - Yun Zhou
- Department of Pediatric NeurologyNingbo Women and Children's HospitalNingboChina
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35
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Zhao C, Zhang Y, Zhang J, Li S, Liu M, Geng Y, Liu F, Chai Q, Meng H, Li M, Li J, Zheng Y, Zhang Y. Discovery of Novel Fedratinib-Based HDAC/JAK/BRD4 Triple Inhibitors with Remarkable Antitumor Activity against Triple Negative Breast Cancer. J Med Chem 2023; 66:14150-14174. [PMID: 37796543 DOI: 10.1021/acs.jmedchem.3c01242] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
Multitarget HDAC inhibitors capable of simultaneously blocking the BRD4-LIFR-JAK1-STAT3 signaling pathway hold great potential for the treatment of TNBC and other solid tumors. Herein, novel Fedratinib-based multitarget HDAC inhibitors were rationally designed, synthesized, and biologically evaluated, among which compound 25ap stood out as a potent HDAC/JAK/BRD4 triple inhibitor. Satisfyingly, compound 25ap led to concurrent inhibition of HDACs and the BRD4-LIFR-JAK1-STAT3 signaling pathway, which was validated by hyper-acetylation of histone and α-tubulin, hypo-phosphorylation of STAT3, downregulation of LIFR, MCL-1, and c-Myc in MDA-MB-231 cells. The multitarget effects of 25ap contributed to its robust antitumor response, including potent antiproliferative activity, remarkable apoptosis-inducing activity, and inhibition of colony formation. Notably, 25ap possessed an acceptable therapeutic window between normal and cancerous cells, desirable in vitro metabolic stability in mouse microsome, and sufficient in vivo exposure via intraperitoneal administration. Additionally, the in vivo antitumor potency of 25ap was demonstrated in an MDA-MB-231 xenograft model.
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Affiliation(s)
- Chunlong Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Yu Zhang
- Key Lab of Advanced Drug Preparation Technologies (Ministry of Education), State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Jin'ge Zhang
- Key Lab of Advanced Drug Preparation Technologies (Ministry of Education), State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Shunda Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Mengyang Liu
- Key Lab of Advanced Drug Preparation Technologies (Ministry of Education), State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Yinping Geng
- Key Lab of Advanced Drug Preparation Technologies (Ministry of Education), State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Fengling Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Qipeng Chai
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Hongwei Meng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Mengzhe Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Jintao Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong 250012, P.R. China
| | - Yichao Zheng
- Key Lab of Advanced Drug Preparation Technologies (Ministry of Education), State Key Laboratory of Esophageal Cancer Prevention & Treatment, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
| | - Yingjie Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Ji'nan, Shandong 250012, P.R. China
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36
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Kotekar A, Singh AK, Devaiah BN. BRD4 and MYC: power couple in transcription and disease. FEBS J 2023; 290:4820-4842. [PMID: 35866356 PMCID: PMC9867786 DOI: 10.1111/febs.16580] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/16/2022] [Accepted: 07/20/2022] [Indexed: 01/26/2023]
Abstract
The MYC proto-oncogene and BRD4, a BET family protein, are two cardinal proteins that have a broad influence in cell biology and disease. Both proteins are expressed ubiquitously in mammalian cells and play central roles in controlling growth, development, stress responses and metabolic function. As chromatin and transcriptional regulators, they play a critical role in regulating the expression of a burgeoning array of genes, maintaining chromatin architecture and genome stability. Consequently, impairment of their function or regulation leads to many diseases, with cancer being the most predominant. Interestingly, accumulating evidence indicates that regulation of the expression and functions of MYC are tightly intertwined with BRD4 at both transcriptional and post-transcriptional levels. Here, we review the mechanisms by which MYC and BRD4 are regulated, their functions in governing various molecular mechanisms and the consequences of their dysregulation that lead to disease. We present a perspective of how the regulatory mechanisms for the two proteins could be entwined at multiple points in a BRD4-MYC nexus that leads to the modulation of their functions and disease upon dysregulation.
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Affiliation(s)
- Aparna Kotekar
- Experimental Immunology Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Amit Kumar Singh
- Experimental Immunology Branch, NCI, NIH, Bethesda, MD 20892, USA
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37
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Li Z, Deeks SG, Ott M, Greene WC. Comprehensive synergy mapping links a BAF- and NSL-containing "supercomplex" to the transcriptional silencing of HIV-1. Cell Rep 2023; 42:113055. [PMID: 37682714 PMCID: PMC10591912 DOI: 10.1016/j.celrep.2023.113055] [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: 12/09/2022] [Revised: 05/26/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023] Open
Abstract
Host repressors mediate HIV latency, but how they interactively silence the virus remains unclear. Here, we develop "reiterative enrichment and authentication of CRISPRi targets for synergies (REACTS)" to probe the genome for synergies between HIV transcription repressors. Using eight known host repressors as queries, we identify 32 synergies involving eleven repressors, including BCL7C, KANSL2, and SIRT2. Overexpression of these three proteins reduces HIV reactivation in Jurkat T cells and in CD4 T cells from people living with HIV on antiretroviral therapy (ART). We show that the BCL7C-containing BAF complex and the KANSL2-containing NSL complex form a "supercomplex" that increases inhibitory histone acetylation of the HIV long-terminal repeat (LTR) and its occupancy by the short variant of the acetyl-lysine reader Brd4. Collectively, we provide a validated platform for defining gene synergies genome wide, and the BAF-NSL "supercomplex" represents a potential target for overcoming HIV rebound after ART cessation.
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Affiliation(s)
- Zichong Li
- Gladstone Institute of Virology, San Francisco, CA 94158, USA.
| | - Steven G Deeks
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Melanie Ott
- Gladstone Institute of Virology, San Francisco, CA 94158, USA; University of California, San Francisco, San Francisco, CA 94143, USA
| | - Warner C Greene
- Gladstone Institute of Virology, San Francisco, CA 94158, USA; University of California, San Francisco, San Francisco, CA 94143, USA.
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38
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Liu Y, Liu H, Ye M, Jiang M, Chen X, Song G, Ji H, Wang ZW, Zhu X. Methylation of BRD4 by PRMT1 regulates BRD4 phosphorylation and promotes ovarian cancer invasion. Cell Death Dis 2023; 14:624. [PMID: 37737256 PMCID: PMC10517134 DOI: 10.1038/s41419-023-06149-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023]
Abstract
Bromodomain-containing protein 4 (BRD4), the major component of bromodomain and extra-terminal domain (BET) protein family, has important functions in early embryonic development and cancer development. However, the posttranslational modification of BRD4 is not well understood. Multiple approaches were used to explore the mechanism of PRMT1-mediated BRD4 methylation and to determine the biological functions of BRD4 and PRMT1 in ovarian cancer. Here we report that BRD4 is asymmetrically methylated at R179/181/183 by PRMT1, which is antagonized by the Jumonji-family demethylase, JMJD6. PRMT1 is overexpressed in ovarian cancer tissue and is a potential marker for poor prognosis in ovarian cancer patients. Silencing of PRMT1 inhibited ovarian cancer proliferation, migration, and invasion in vivo and in vitro. PRMT1-mediated BRD4 methylation was found to promote BRD4 phosphorylation. Compared to BRD4 wild-type (WT) cells, BRD4 R179/181/183K mutant-expressing cells showed reduced ovarian cancer metastasis. BRD4 arginine methylation is also associated with TGF-β signaling. Our results indicate that arginine methylation of BRD4 by PRMT1 is involved in ovarian cancer tumorigenesis. Targeting PRMT1-mediated arginine methylation may provide a novel diagnostic target and an effective therapeutic strategy for ovarian cancer treatment.
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Affiliation(s)
- Yi Liu
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, 325027, Wenzhou, China
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Hejing Liu
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, 325027, Wenzhou, China
| | - Miaomiao Ye
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, 325027, Wenzhou, China
| | - Mengying Jiang
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, 325027, Wenzhou, China
| | - Xin Chen
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, 325027, Wenzhou, China
| | - Gendi Song
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, 325027, Wenzhou, China
| | - Huihui Ji
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, 325027, Wenzhou, China
| | - Zhi-Wei Wang
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, 325027, Wenzhou, China.
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| | - Xueqiong Zhu
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Wenzhou Medical University, 325027, Wenzhou, China.
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Guo X, Olajuyin A, Tucker TA, Idell S, Qian G. BRD4 as a Therapeutic Target in Pulmonary Diseases. Int J Mol Sci 2023; 24:13231. [PMID: 37686037 PMCID: PMC10487829 DOI: 10.3390/ijms241713231] [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: 07/25/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Bromodomain and extra-terminal domain (BET) proteins are epigenetic modulators that regulate gene transcription through interacting with acetylated lysine residues of histone proteins. BET proteins have multiple roles in regulating key cellular functions such as cell proliferation, differentiation, inflammation, oxidative and redox balance, and immune responses. As a result, BET proteins have been found to be actively involved in a broad range of human lung diseases including acute lung inflammation, asthma, pulmonary arterial hypertension, pulmonary fibrosis, and chronic obstructive pulmonary disease (COPD). Due to the identification of specific small molecular inhibitors of BET proteins, targeting BET in these lung diseases has become an area of increasing interest. Emerging evidence has demonstrated the beneficial effects of BET inhibitors in preclinical models of various human lung diseases. This is, in general, largely related to the ability of BET proteins to bind to promoters of genes that are critical for inflammation, differentiation, and beyond. By modulating these critical genes, BET proteins are integrated into the pathogenesis of disease progression. The intrinsic histone acetyltransferase activity of bromodomain-containing protein 4 (BRD4) is of particular interest, seems to act independently of its bromodomain binding activity, and has implication in some contexts. In this review, we provide a brief overview of the research on BET proteins with a focus on BRD4 in several major human lung diseases, the underlying molecular mechanisms, as well as findings of targeting BET proteins using pharmaceutical inhibitors in different lung diseases preclinically.
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Affiliation(s)
| | | | | | | | - Guoqing Qian
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX 75708, USA; (X.G.); (A.O.); (T.A.T.); (S.I.)
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40
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Yang JF, Liu W, You J. Characterization of molecular mechanisms driving Merkel cell polyomavirus oncogene transcription and tumorigenic potential. PLoS Pathog 2023; 19:e1011598. [PMID: 37647312 PMCID: PMC10468096 DOI: 10.1371/journal.ppat.1011598] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/03/2023] [Indexed: 09/01/2023] Open
Abstract
Merkel cell polyomavirus (MCPyV) is associated with approximately 80% of cases of Merkel cell carcinoma (MCC), an aggressive type of skin cancer. The incidence of MCC has tripled over the past twenty years, but there are currently very few effective targeted treatments. A better understanding of the MCPyV life cycle and its oncogenic mechanisms is needed to unveil novel strategies for the prevention and treatment of MCC. MCPyV infection and oncogenesis are reliant on the expression of the early viral oncoproteins, which drive the viral life cycle and MCPyV+ MCC tumor cell growth. To date, the molecular mechanisms regulating the transcription of the MCPyV oncogenes remain largely uncharacterized. In this study, we investigated how MCPyV early transcription is regulated to support viral infection and MCC tumorigenesis. Our studies established the roles of multiple cellular factors in the control of MCPyV gene expression. Inhibitor screening experiments revealed that the histone acetyltransferases p300 and CBP positively regulate MCPyV transcription. Their regulation of viral gene expression occurs through coactivation of the transcription factor NF-κB, which binds to the viral genome to drive MCPyV oncogene expression in a manner that is tightly controlled through a negative feedback loop. Furthermore, we discovered that small molecule inhibitors specifically targeting p300/CBP histone acetyltransferase activity are effective at blocking MCPyV tumor antigen expression and MCPyV+ MCC cell proliferation. Together, our work establishes key cellular factors regulating MCPyV transcription, providing the basis for understanding the largely unknown mechanisms governing MCPyV transcription that defines its infectious host cell tropism, viral life cycle, and oncogenic potential. Our studies also identify a novel therapeutic strategy against MCPyV+ MCC through specific blockage of MCPyV oncogene expression and MCC tumor growth.
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Affiliation(s)
- June F. Yang
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Wei Liu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jianxin You
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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41
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Li D, Tian T, Ko CN, Yang C. Prospect of targeting lysine methyltransferase NSD3 for tumor therapy. Pharmacol Res 2023; 194:106839. [PMID: 37400043 DOI: 10.1016/j.phrs.2023.106839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 07/05/2023]
Abstract
Nuclear receptor binding SET domain protein 3 (NSD3) has recently been recognized as a new epigenetic target in the fight against cancer. NSD3, which is amplified, overexpressed or mutated in a variety of tumors, promotes tumor development by regulating the cell cycle, apoptosis, DNA repair and EMT. Therefore, the inhibition, silencing or knockdown of NSD3 are highly promising antitumor strategies. This paper summarizes the structure and biological functions of NSD3 with an emphasis on its carcinogenic or cancer-promoting activity. The development of NSD3-specific inhibitors or degraders is also discussed and reviewed in this paper.
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Affiliation(s)
- Dan Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Tiantian Tian
- Center for Biological Science and Technology, Beijing Normal University, Zhuhai, Guangdong Province, 519087, China
| | - Chung-Nga Ko
- C-MER Dennis Lam and Partners Eye Center, Hong Kong International Eye Care Group, Hong Kong, China.
| | - Chao Yang
- National Engineering Research Center For Marine Aquaculture, Institute of Innovation & Application, Zhejiang Ocean University, Zhoushan, Zhejiang Province 316022, China.
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42
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Han H, Lv F, Liu Z, Chen T, Xue T, Liang W, Liu M. BcTaf14 regulates growth and development, virulence, and stress responses in the phytopathogenic fungus Botrytis cinerea. MOLECULAR PLANT PATHOLOGY 2023; 24:849-865. [PMID: 37026690 PMCID: PMC10346378 DOI: 10.1111/mpp.13331] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 03/15/2023] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
TATA box-binding protein (TBP)-associated factor 14 (Taf14), a transcription-associated factor containing a conserved YEATS domain and an extra-terminal (ET) domain, is a multifunctional protein in Saccharomyces cerevisiae. However, the role of Taf14 in filamentous phytopathogenic fungi is not well understood. In this study, the homologue of ScTaf14 in Botrytis cinerea (named BcTaf14), a destructive phytopathogen causing grey mould, was investigated. The BcTaf14 deletion strain (ΔBcTaf14) showed pleiotropic defects, including slow growth, abnormal colony morphology, reduced conidiation, abnormal conidial morphology, reduced virulence, and altered responses to various stresses. The ΔBcTaf14 strain also exhibited differential expression of numerous genes compared to the wild-type strain. BcTaf14 could interact with the crotonylated H3K9 peptide, and mutation of two key sites (G80 and W81) in the YEATS domain disrupted this interaction. The mutation of G80 and W81 affected the regulatory effect of BcTaf14 on mycelial growth and virulence but did not affect the production and morphology of conidia. The absence of the ET domain at the C-terminus rendered BcTaf14 unable to localize to the nucleus, and the defects of ΔBcTaf14 were not recovered to wild-type levels when BcTaf14 without the ET domain was expressed. Our results provide insight into the regulatory roles of BcTaf14 and its two conserved domains in B. cinerea and will be helpful for understanding the function of the Taf14 protein in plant-pathogenic fungi.
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Affiliation(s)
- Hongjia Han
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
| | - Fangjiao Lv
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
| | - Zhishan Liu
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
| | - Tongge Chen
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
| | - Tianzi Xue
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
| | - Wenxing Liang
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
| | - Mengjie Liu
- College of Plant Health and MedicineQingdao Agricultural UniversityQingdao266109China
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43
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Kosno M, Currie SL, Kumar A, Xing C, Rosen MK. Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct. Sci Rep 2023; 13:11907. [PMID: 37488172 PMCID: PMC10366142 DOI: 10.1038/s41598-023-39102-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/20/2023] [Indexed: 07/26/2023] Open
Abstract
Aberrant formation of biomolecular condensates has been proposed to play a role in several cancers. The oncogenic fusion protein BRD4-NUT forms condensates and drives changes in gene expression in Nut Carcinoma. Here we sought to understand the molecular elements of BRD4-NUT and its associated histone acetyltransferase (HAT), p300, that promote these activities. We determined that a minimal fragment of NUT (MIN) in fusion with BRD4 is necessary and sufficient to bind p300 and form condensates. Furthermore, a BRD4-p300 fusion protein also forms condensates and drives gene expression similarly to BRD4-NUT(MIN), suggesting the p300 fusion may mimic certain features of BRD4-NUT. The intrinsically disordered regions, transcription factor-binding domains, and HAT activity of p300 all collectively contribute to condensate formation by BRD4-p300, suggesting that these elements might contribute to condensate formation by BRD4-NUT. Conversely, only the HAT activity of BRD4-p300 appears necessary to mimic the transcriptional profile of cells expressing BRD4-NUT. Our results suggest a model for condensate formation by the BRD4-NUT:p300 complex involving a combination of positive feedback and phase separation, and show that multiple overlapping, yet distinct, regions of p300 contribute to condensate formation and transcriptional regulation.
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Affiliation(s)
- Martyna Kosno
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Simon L Currie
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ashwani Kumar
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Michael K Rosen
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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Zheng X, Diktonaite K, Qiu H. Epigenetic Reader Bromodomain-Containing Protein 4 in Aging-Related Vascular Pathologies and Diseases: Molecular Basis, Functional Relevance, and Clinical Potential. Biomolecules 2023; 13:1135. [PMID: 37509171 PMCID: PMC10376956 DOI: 10.3390/biom13071135] [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: 06/29/2023] [Revised: 07/10/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Aging is a key independent risk factor of various vascular diseases, for which the regulatory mechanisms remain largely unknown. Bromodomain-containing protein 4 (BRD4) is a member of the Bromodomain and Extra-Terminal domain (BET) family and is an epigenetic reader playing diverse roles in regulating transcriptional elongation, chromatin remodeling, DNA damage response, and alternative splicing in various cells and tissues. While BRD4 was initially recognized for its involvement in cancer progression, recent studies have revealed that the aberrant expression and impaired function of BRD4 were highly associated with aging-related vascular pathology, affecting multiple key biological processes in the vascular cells and tissues, providing new insights into the understanding of vascular pathophysiology and pathogenesis of vascular diseases. This review summarizes the recent advances in BRD4 biological function, and the progression of the studies related to BRD4 in aging-associated vascular pathologies and diseases, including atherosclerosis, aortic aneurism vascular neointima formation, pulmonary hypertension, and essential hypertension, providing updated information to advance our understanding of the epigenetic mechanisms in vascular diseases during aging and paving the way for future research and therapeutic approaches.
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Affiliation(s)
- Xiaoxu Zheng
- Center for Molecular and Translational Medicine, Institute of Biomedical Science, Georgia State University, Atlanta, GA 30303, USA; (X.Z.); (K.D.)
| | - Kotryna Diktonaite
- Center for Molecular and Translational Medicine, Institute of Biomedical Science, Georgia State University, Atlanta, GA 30303, USA; (X.Z.); (K.D.)
| | - Hongyu Qiu
- Center for Molecular and Translational Medicine, Institute of Biomedical Science, Georgia State University, Atlanta, GA 30303, USA; (X.Z.); (K.D.)
- Department of Internal Medicine, Translational Cardiovascular Research Center, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA
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45
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Abstract
Proteolysis-targeting chimeras (PROTACs) are heterobifunctional small molecules that induce the ternary complex formation between a protein-of-interest (POI) and an E3 ligase, leading to targeted polyubiquitination and degradation of the POI. Particularly, PROTACs have the distinct advantage of targeting both canonical and noncanonical functions of epigenetic targets over traditional inhibitors, which typically target canonical functions only, resulting in greater therapeutic efficacy. In this review, we methodically analyze published PROTAC degraders of epigenetic writer, reader, and eraser proteins and their in vitro and in vivo effects. We highlight the mechanism of action of these degraders and their advantages in targeting both canonical and noncanonical functions of epigenetic targets in the context of cancer treatment. Furthermore, we present a future outlook for this exciting field. Overall, pharmacological degradation of epigenetic targets has emerged as an effective and attractive strategy to thwart cancer progression and growth.
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Affiliation(s)
- Md Kabir
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
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46
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Chen Z, Tian D, Chen X, Cheng M, Xie H, Zhao J, Liu J, Fang Z, Zhao B, Bian E. Super-enhancer-driven lncRNA LIMD1-AS1 activated by CDK7 promotes glioma progression. Cell Death Dis 2023; 14:383. [PMID: 37385987 PMCID: PMC10310775 DOI: 10.1038/s41419-023-05892-z] [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: 11/27/2022] [Revised: 05/07/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023]
Abstract
Long non-coding RNAs (lncRNAs) are tissue-specific expression patterns and dysregulated in cancer. How they are regulated still needs to be determined. We aimed to investigate the functions of glioma-specific lncRNA LIMD1-AS1 activated by super-enhancer (SE) and identify the potential mechanisms. In this paper, we identified a SE-driven lncRNA, LIMD1-AS1, which is expressed at significantly higher levels in glioma than in normal brain tissue. High LIMD1-AS1 levels were significantly associated with a shorter survival time of glioma patients. LIMD1-AS1 overexpression significantly enhanced glioma cells proliferation, colony formation, migration, and invasion, whereas LIMD1-AS1 knockdown inhibited their proliferation, colony formation, migration, and invasion, and the xenograft tumor growth of glioma cells in vivo. Mechanically, inhibition of CDK7 significantly attenuates MED1 recruitment to the super-enhancer of LIMD1-AS1 and then decreases the expression of LIMD1-AS1. Most importantly, LIMD1-AS1 could directly bind to HSPA5, leading to the activation of interferon signaling. Our findings support the idea that CDK7 mediated-epigenetically activation of LIMD1-AS1 plays a crucial role in glioma progression and provides a promising therapeutic approach for patients with glioma.
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Affiliation(s)
- Zhigang Chen
- Department of Neurosurgery, the Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui, 230601, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui, 230601, China
| | - Dasheng Tian
- Department of Orthopaedics, the Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui, 230601, China
| | - Xueran Chen
- Department of Laboratory Medicine, Hefei Cancer Hospital, Chinese Academy of Sciences, No. 350, Shushan Hu Road, Hefei, Anhui, 230601, China
- Anhui Province Key Laboratory of Medical Physics and Technology; Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, No. 350, Shushan Hu Road, Hefei, Anhui, 230601, China
| | - Meng Cheng
- Department of Neurosurgery, the Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui, 230601, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui, 230601, China
| | - Han Xie
- Department of Neurosurgery, the Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui, 230601, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui, 230601, China
| | - JiaJia Zhao
- Department of Neurosurgery, the Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui, 230601, China
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui, 230601, China
| | - Jun Liu
- Department of Orthopaedics, the Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui, 230601, China
| | - Zhiyou Fang
- Department of Laboratory Medicine, Hefei Cancer Hospital, Chinese Academy of Sciences, No. 350, Shushan Hu Road, Hefei, Anhui, 230601, China.
- Anhui Province Key Laboratory of Medical Physics and Technology; Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, No. 350, Shushan Hu Road, Hefei, Anhui, 230601, China.
| | - Bing Zhao
- Department of Neurosurgery, the Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui, 230601, China.
- Cerebral Vascular Disease Research Center, Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui, 230601, China.
| | - Erbao Bian
- Department of Neurosurgery, the Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui, 230601, China.
- Department of Orthopaedics, the Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui, 230601, China.
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47
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Takemon Y, LeBlanc VG, Song J, Chan SY, Lee SD, Trinh DL, Ahmad ST, Brothers WR, Corbett RD, Gagliardi A, Moradian A, Cairncross JG, Yip S, Aparicio SAJR, Chan JA, Hughes CS, Morin GB, Gorski SM, Chittaranjan S, Marra MA. Multi-Omic Analysis of CIC's Functional Networks Reveals Novel Interaction Partners and a Potential Role in Mitotic Fidelity. Cancers (Basel) 2023; 15:2805. [PMID: 37345142 PMCID: PMC10216487 DOI: 10.3390/cancers15102805] [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: 04/07/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023] Open
Abstract
CIC encodes a transcriptional repressor and MAPK signalling effector that is inactivated by loss-of-function mutations in several cancer types, consistent with a role as a tumour suppressor. Here, we used bioinformatic, genomic, and proteomic approaches to investigate CIC's interaction networks. We observed both previously identified and novel candidate interactions between CIC and SWI/SNF complex members, as well as novel interactions between CIC and cell cycle regulators and RNA processing factors. We found that CIC loss is associated with an increased frequency of mitotic defects in human cell lines and an in vivo mouse model and with dysregulated expression of mitotic regulators. We also observed aberrant splicing in CIC-deficient cell lines, predominantly at 3' and 5' untranslated regions of genes, including genes involved in MAPK signalling, DNA repair, and cell cycle regulation. Our study thus characterises the complexity of CIC's functional network and describes the effect of its loss on cell cycle regulation, mitotic integrity, and transcriptional splicing, thereby expanding our understanding of CIC's potential roles in cancer. In addition, our work exemplifies how multi-omic, network-based analyses can be used to uncover novel insights into the interconnected functions of pleiotropic genes/proteins across cellular contexts.
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Affiliation(s)
- Yuka Takemon
- Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, BC V5Z 4S6, Canada;
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Véronique G. LeBlanc
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Jungeun Song
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Susanna Y. Chan
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Stephen Dongsoo Lee
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Diane L. Trinh
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Shiekh Tanveer Ahmad
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4Z6, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - William R. Brothers
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Richard D. Corbett
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Alessia Gagliardi
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Annie Moradian
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - J. Gregory Cairncross
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4Z6, Canada
- Department of Clinical Neurosciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Stephen Yip
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (S.Y.); (S.A.J.R.A.); (C.S.H.)
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada
| | - Samuel A. J. R. Aparicio
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (S.Y.); (S.A.J.R.A.); (C.S.H.)
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada
| | - Jennifer A. Chan
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4Z6, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Christopher S. Hughes
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (S.Y.); (S.A.J.R.A.); (C.S.H.)
| | - Gregg B. Morin
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Sharon M. Gorski
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Suganthi Chittaranjan
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
| | - Marco A. Marra
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.L.); (A.M.); (S.M.G.)
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
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48
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Kosno M, Currie SL, Kumar A, Xing C, Rosen MK. Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540414. [PMID: 37214845 PMCID: PMC10197624 DOI: 10.1101/2023.05.11.540414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Aberrant formation of biomolecular condensates has been proposed to play a role in several cancers. The oncogenic fusion protein BRD4-NUT forms condensates and drives changes in gene expression in Nut Carcinoma (NC). Here we sought to understand the molecular elements of BRD4-NUT and its associated histone acetyltransferase (HAT), p300, that promote these activities. We determined that a minimal fragment of NUT (MIN) in fusion with BRD4 is necessary and sufficient to bind p300 and form condensates. Furthermore, a BRD4-p300 fusion protein also forms condensates and drives gene expression similarly to BRD4-NUT(MIN), suggesting the p300 fusion may mimic certain features of BRD4-NUT. The intrinsically disordered regions, transcription factor-binding domains, and HAT activity of p300 all collectively contribute to condensate formation by BRD4-p300, suggesting that these elements might contribute to condensate formation by BRD4-NUT. Conversely, only the HAT activity of BRD4-p300 appears necessary to mimic the transcriptional profile of cells expressing BRD4-NUT. Our results suggest a model for condensate formation by the BRD4-NUT:p300 complex involving a combination of positive feedback and phase separation, and show that multiple overlapping, yet distinct, regions of p300 contribute to condensate formation and transcriptional regulation.
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Xiu S, Chi X, Jia Z, Shi C, Zhang X, Li Q, Gao T, Zhang L, Liu Z. NSD3: Advances in cancer therapeutic potential and inhibitors research. Eur J Med Chem 2023; 256:115440. [PMID: 37182335 DOI: 10.1016/j.ejmech.2023.115440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/16/2023]
Abstract
Nuclear receptor-binding SET domain 3, otherwise known as NSD3, is a member of the group of lysine methyltransferases and is involved in a variety of cellular processes, including transcriptional regulation, DNA damage repair, non-histone related functions and several others. NSD3 gene is mutated or loss of function in a variety of cancers, including breast, lung, pancreatic, and osteosarcoma. These mutations produce dysfunction of the corresponding tumor tissue proteins, leading to tumorigenesis, progression, chemoresistance, and unfavorable prognosis, which suggests that the development of NSD3 probe molecules is important for understanding the specific role of NSD3 in disease and drug discovery. In recent years, NSD3 has been increasingly reported, demonstrating that this target is a very hot epigenetic target. However, the number of NSD3 inhibitors available for cancer therapy is limited and none of the drugs that target NSD3 are currently available on the market. In addition, there are very few reviews describing NSD3. Within this review, we highlight the role of NSD3 in tumorigenesis and the development of NSD3 targeted small-molecule inhibitors over the last decade. We hope that this publication can serve as a guide for the development of potential drug candidates for various diseases in the field of epigenetics, especially for the NSD3 target.
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Affiliation(s)
- Siyu Xiu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China
| | - Xiaowei Chi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China
| | - Zhenyu Jia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China
| | - Cheng Shi
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China
| | - Xiangyu Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China
| | - Qi Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China
| | - Tongfei Gao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China.
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, PR China.
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Kurata K, Samur MK, Liow P, Wen K, Yamamoto L, Liu J, Morelli E, Gulla A, Tai YT, Qi J, Hideshima T, Anderson KC. BRD9 Degradation Disrupts Ribosome Biogenesis in Multiple Myeloma. Clin Cancer Res 2023; 29:1807-1821. [PMID: 36780189 PMCID: PMC10150249 DOI: 10.1158/1078-0432.ccr-22-3668] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/12/2023] [Accepted: 02/09/2023] [Indexed: 02/14/2023]
Abstract
PURPOSE BRD9 is a defining component of the noncanonical SWI/SNF complex, which regulates gene expression by controlling chromatin dynamics. Although recent studies have found an oncogenic role for BRD9 in multiple cancer types including multiple myeloma, its clinical significance and oncogenic mechanism have not yet been elucidated. Here, we sought to identify the clinical and biological impact of BRD9 in multiple myeloma, which may contribute to the development of novel therapeutic strategies. EXPERIMENTAL DESIGN We performed integrated analyses of BRD9 in vitro and in vivo using multiple myeloma cell lines and primary multiple myeloma cells in established preclinical models, which identified the molecular functions of BRD9 contributing to multiple myeloma cell survival. RESULTS We found that high BRD9 expression was a poor prognostic factor in multiple myeloma. Depleting BRD9 by genetic (shRNA) and pharmacologic (dBRD9-A; proteolysis-targeting chimera; BRD9 degrader) approaches downregulated ribosome biogenesis genes, decreased the expression of the master regulator MYC, and disrupted the protein-synthesis maintenance machinery, thereby inhibiting multiple myeloma cell growth in vitro and in vivo in preclinical models. Importantly, we identified that the expression of ribosome biogenesis genes was associated with the disease progression and prognosis of patients with multiple myeloma. Our results suggest that BRD9 promotes gene expression by predominantly occupying the promoter regions of ribosome biogenesis genes and cooperating with BRD4 to enhance the transcriptional function of MYC. CONCLUSIONS Our study identifies and validates BRD9 as a novel therapeutic target in preclinical models of multiple myeloma, which provides the framework for the clinical evaluation of BRD9 degraders to improve patient outcome.
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Affiliation(s)
- Keiji Kurata
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Mehmet K. Samur
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts
| | - Priscilla Liow
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kenneth Wen
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Leona Yamamoto
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Jiye Liu
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Eugenio Morelli
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Annamaria Gulla
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Yu-Tzu Tai
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Teru Hideshima
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Kenneth C. Anderson
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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