1
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Mayse L, Wang Y, Ahmad M, Movileanu L. Real-Time Measurement of a Weak Interaction of a Transcription Factor Motif with a Protein Hub at Single-Molecule Precision. ACS NANO 2024; 18:20468-20481. [PMID: 39049818 PMCID: PMC11308778 DOI: 10.1021/acsnano.4c04857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024]
Abstract
Transcription factors often interact with other protein cofactors, regulating gene expression. Direct detection of these brief events using existing technologies remains challenging due to their transient nature. In addition, intrinsically disordered domains, intranuclear location, and lack of cofactor-dependent active sites of transcription factors further complicate the quantitative analysis of these critical processes. Here, we create a genetically encoded label-free sensor to identify the interaction between a motif of the MYC transcription factor, a primary cancer driver, and WDR5, a chromatin-associated protein hub. Using an engineered nanopore equipped with this motif, WDR5 is probed through reversible captures and releases in a one-by-one and time-resolved fashion. Our single-molecule kinetic measurements indicate a weak-affinity interaction arising from a relatively slow complex association and a fast dissociation of WDR5 from the tethered motif. Further, we validate this subtle interaction by determinations in an ensemble using single nanodisc-wrapped nanopores immobilized on a biolayer interferometry sensor. This study also provides the proof-of-concept for a sensor that reveals unique recognition signatures of different protein binding sites. Our foundational work may be further developed to produce sensing elements for analytical proteomics and cancer nanomedicine.
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Affiliation(s)
- Lauren
A. Mayse
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244, United States
- Department
of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
| | - Yazheng Wang
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244, United States
- Department
of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
| | - Mohammad Ahmad
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244, United States
| | - Liviu Movileanu
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244, United States
- Department
of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
- Department
of Biology, Syracuse University, 114 Life Sciences Complex, Syracuse, New York 13244, United States
- The
BioInspired Institute, Syracuse University, Syracuse, New York 13244, United States
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2
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Mayfield JM, Hitefield NL, Czajewski I, Vanhye L, Holden L, Morava E, van Aalten DMF, Wells L. O-GlcNAc Transferase Congenital Disorder of Glycosylation (OGT-CDG): Potential mechanistic targets revealed by evaluating the OGT interactome. J Biol Chem 2024:107599. [PMID: 39059494 DOI: 10.1016/j.jbc.2024.107599] [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: 10/25/2023] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
O-GlcNAc transferase (OGT) is the sole enzyme responsible for the post-translational modification O-GlcNAc on thousands of target nucleocytoplasmic proteins. To date, nine variants of OGT that segregate with OGT Congenital Disorder of Glycosylation (OGT-CDG) have been reported and characterized. Numerous additional variants have been associated with OGT-CDG, some of which are currently undergoing investigation. This disorder primarily presents with global developmental delay and intellectual disability (ID), alongside other variable neurological features and subtle facial dysmorphisms in patients. Several hypotheses aim to explain the etiology of OGT-CDG, with a prominent hypothesis attributing the pathophysiology of OGT-CDG to mutations segregating with this disorder disrupting the OGT interactome. The OGT interactome consists of thousands of proteins, including substrates as well as interactors that require noncatalytic functions of OGT. A key aim in the field is to identify which interactors and substrates contribute to the primarily neural-specific phenotype of OGT-CDG. In this review, we will discuss the heterogenous phenotypic features of OGT-CDG seen clinically, the variable biochemical effects of mutations associated with OGT-CDG, and the use of animal models to understand this disorder. Furthermore, we will discuss how previously identified OGT interactors causal for ID provide mechanistic targets for investigation that could explain the dysregulated gene expression seen in OGT-CDG models. Identifying shared or unique altered pathways impacted in OGT-CDG patients will provide a better understanding of the disorder as well as potential therapeutic targets.
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Affiliation(s)
- Johnathan M Mayfield
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, 30605, United States of America
| | - Naomi L Hitefield
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, 30605, United States of America
| | - Ignacy Czajewski
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Lotte Vanhye
- Department of Clinical Genomics and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Laura Holden
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, 30605, United States of America
| | - Eva Morava
- Department of Clinical Genomics and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Daan M F van Aalten
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, DK.
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, 30605, United States of America.
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3
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Yang Y, Xu L, Zhang S, Yao L, Ding Y, Li W, Chen X. Structural studies of WDR5 in complex with MBD3C WIN motif reveal a unique binding mode. J Biol Chem 2024; 300:107468. [PMID: 38876301 PMCID: PMC11261779 DOI: 10.1016/j.jbc.2024.107468] [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: 05/20/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024] Open
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex plays a pivotal role in chromatin regulation and transcriptional repression. In mice, methyl-CpG binding domain 3 isoform C (MBD3C) interacts specifically with the histone H3 binding protein WD repeat-containing protein 5 (WDR5) and forms the WDR5-MBD3C/Norde complex. Despite the functional significance of this interaction on embryonic stem cell gene regulation, the molecular mechanism underlying MBD3C recognition by WDR5 remains elusive. Here, we determined the crystal structure of WDR5 in complex with the peptide (residues 40-51) derived from the MBD3C protein at a resolution of 1.9 Å. Structural analysis revealed that MBD3C utilizes a unique binding mode to interact with WDR5, wherein MBD3C Arg43 and Phe47 are involved in recognizing the WDR5-interacting (WIN) site and Tyr191-related B site on the small surface of WDR5, respectively. Notably, the binding induces a ∼91° rotation of WDR5 Tyr191, generating the hydrophobic B site. Furthermore, mutation experiments combined with isothermal titration calorimetry (ITC) assays confirmed the importance of both Arg43 and Phe47 in mediating WDR5 binding affinity. By determining structures of various peptides bound to WDR5, we demonstrated that the WDR5 WIN site and B site can be concurrently recognized by WIN motif peptides containing ''Arg-Cies/Ser-Arg-Val-Phe'' consensus sequence. Overall, this study reveals the structural basis for the formation of the WDR5-MBD3C subcomplex and provides new insights into the recognition mode of WDR5 for the WIN motif. Moreover, these findings shed light on structural-based designs of WDR5-targeted anti-cancer small molecule inhibitors or peptide-mimic drugs.
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Affiliation(s)
- Yang Yang
- School of Life Sciences, Anhui University, Hefei, Anhui, China.
| | - Li Xu
- Institute of Biotechnology and Health, Beijing Academy of Science and Technology, Beijing, China.
| | - Shuting Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Liangrui Yao
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Yuqing Ding
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Wenwen Li
- School of Life Sciences, Anhui University, Hefei, Anhui, China
| | - Xuemin Chen
- School of Life Sciences, Anhui University, Hefei, Anhui, China.
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4
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Huang X, Zhang C, Shang X, Chen Y, Xiao Q, Wei Z, Wang G, Zhen X, Xu G, Min J, Shen S, Liu Y. The NTE domain of PTENα/β promotes cancer progression by interacting with WDR5 via its SSSRRSS motif. Cell Death Dis 2024; 15:335. [PMID: 38744853 PMCID: PMC11094138 DOI: 10.1038/s41419-024-06714-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/16/2024]
Abstract
PTENα/β, two variants of PTEN, play a key role in promoting tumor growth by interacting with WDR5 through their N-terminal extensions (NTEs). This interaction facilitates the recruitment of the SET1/MLL methyltransferase complex, resulting in histone H3K4 trimethylation and upregulation of oncogenes such as NOTCH3, which in turn promotes tumor growth. However, the molecular mechanism underlying this interaction has remained elusive. In this study, we determined the first crystal structure of PTENα-NTE in complex with WDR5, which reveals that PTENα utilizes a unique binding motif of a sequence SSSRRSS found in the NTE domain of PTENα/β to specifically bind to the WIN site of WDR5. Disruption of this interaction significantly impedes cell proliferation and tumor growth, highlighting the potential of the WIN site inhibitors of WDR5 as a way of therapeutic intervention of the PTENα/β associated cancers. These findings not only shed light on the important role of the PTENα/β-WDR5 interaction in carcinogenesis, but also present a promising avenue for developing cancer treatments that target this pathway.
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Affiliation(s)
- Xiaolei Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Cheng Zhang
- Institute of Aging & Tissue Regeneration, Ren-Ji Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), 200127, Shanghai, China
| | - Xinci Shang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Yichang Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Qin Xiao
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Zhengguo Wei
- School of Biology and Basic Medical Science, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Guanghui Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Xuechu Zhen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, 430079, Wuhan, Hubei, China
| | - Shaoming Shen
- Institute of Aging & Tissue Regeneration, Ren-Ji Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), 200127, Shanghai, China.
| | - Yanli Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, 215123, Suzhou, Jiangsu, China.
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5
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Ding Y, Zhang C, Zuo Q, Jin K, Li B. lncCPSET1 acts as a scaffold for MLL2/COMPASS to regulate Bmp4 and promote the formation of chicken primordial germ cells. Mol Genet Genomics 2024; 299:41. [PMID: 38551742 DOI: 10.1007/s00438-024-02127-4] [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: 09/05/2023] [Accepted: 02/15/2024] [Indexed: 04/02/2024]
Abstract
Primordial germ cells (PGCs) are the ancestors of female and male germ cells. Recent studies have shown that long non-coding RNA (lncRNA) and histone methylation are key epigenetic factors affecting PGC formation; however, their joint regulatory mechanisms have rarely been studied. Here, we explored the mechanism by which lncCPSET1 and H3K4me2 synergistically regulate the formation of chicken PGCs for the first time. Combined with chromatin immunoprecipitation (CHIP) sequencing and RNA-seq of PGCs transfected with the lncCPSET1 overexpression vector, GO annotation and KEGG enrichment analysis revealed that Wnt and TGF-β signaling pathways were significantly enriched, and Fzd2, Id1, Id4, and Bmp4 were identified as candidate genes. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed that ASH2L, DPY30, WDR5, and RBBP5 overexpression significantly increased the expression of Bmp4, which was up-regulated after lncCPSET1 overexpression as well. It indicated that Bmp4 is a target gene co-regulated by lncCPSET1 and MLL2/COMPASS. Interestingly, co-immunoprecipitation results showed that ASH2L, DPY30 and WDR5 combined and RBBP5 weakly combined with DPY30 and WDR5. lncCPSET1 overexpression significantly increased Dpy30 expression and co-immunoprecipitation showed that interference/overexpression of lncCPSET1 did not affect the binding between the proteins in the complexes, but interference with lncCPSET1 inhibited DPY30 expression, which was confirmed by RNA immunoprecipitation that lncCPSET1 binds to DPY30. Additionally, CHIP-qPCR results showed that DPY30 enriched in the Bmp4 promoter region promoted its transcription, thus promoting the formation of PGCs. This study demonstrated that lncCPSET1 and H3K4me2 synergistically promote PGC formation, providing a reference for the study of the regulatory mechanisms between lncRNA and histone methylation, as well as a molecular basis for elucidating the formation mechanism of PGCs in chickens.
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Affiliation(s)
- Ying Ding
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Chen Zhang
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
- RNA Medicine Center, International Institutes of Medicine, Zhejiang University, Hangzhou, China
| | - Qisheng Zuo
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Kai Jin
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
- Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou University, Yangzhou, 225009, China
| | - Bichun Li
- Key Laboratory of Animal Genetics, Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, 88 South University Ave, Yangzhou, Jiangsu, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China.
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6
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Ahmad M, Imran A, Movileanu L. Overlapping characteristics of weak interactions of two transcriptional regulators with WDR5. Int J Biol Macromol 2024; 258:128969. [PMID: 38158065 PMCID: PMC10922662 DOI: 10.1016/j.ijbiomac.2023.128969] [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: 08/04/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
The WD40 repeat protein 5 (WDR5) is a nuclear hub that critically influences gene expression by interacting with transcriptional regulators. Utilizing the WDR5 binding motif (WBM) site, WDR5 interacts with the myelocytomatosis (MYC), an oncoprotein transcription factor, and the retinoblastoma-binding protein 5 (RbBP5), a scaffolding element of an epigenetic complex. Given the clinical significance of these protein-protein interactions (PPIs), there is a pressing necessity for a quantitative assessment of these processes. Here, we use biolayer interferometry (BLI) to examine interactions of WDR5 with consensus peptide ligands of MYC and RbBP5. We found that both interactions exhibit relatively weak affinities arising from a fast dissociation process. Remarkably, live-cell imaging identified distinctive WDR5 localizations in the absence and presence of full-length binding partners. Although WDR5 tends to accumulate within nucleoli, WBM-mediated interactions with MYC and RbBP5 require their localization outside nucleoli. We utilize fluorescence resonance energy transfer (FRET) microscopy to confirm these weak interactions through a low FRET efficiency of the MYC-WDR5 and RbBP5-WDR5 complexes in living cells. In addition, we evaluate the impact of peptide and small-molecule inhibitors on these interactions. These outcomes form a fundamental basis for further developments to clarify the multitasking role of the WBM binding site of WDR5.
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Affiliation(s)
- Mohammad Ahmad
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA
| | - Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA; Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, NY 13244, USA; The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA.
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7
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Teuscher KB, Mills JJ, Tian J, Han C, Meyers KM, Sai J, South TM, Crow MM, Van Meveren M, Sensintaffar JL, Zhao B, Amporndanai K, Moore WJ, Stott GM, Tansey WP, Lee T, Fesik SW. Structure-Based Discovery of Potent, Orally Bioavailable Benzoxazepinone-Based WD Repeat Domain 5 Inhibitors. J Med Chem 2023; 66:16783-16806. [PMID: 38085679 DOI: 10.1021/acs.jmedchem.3c01529] [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] [Indexed: 12/29/2023]
Abstract
The chromatin-associated protein WDR5 (WD repeat domain 5) is an essential cofactor for MYC and a conserved regulator of ribosome protein gene transcription. It is also a high-profile target for anti-cancer drug discovery, with proposed utility against both solid and hematological malignancies. We have previously discovered potent dihydroisoquinolinone-based WDR5 WIN-site inhibitors with demonstrated efficacy and safety in animal models. In this study, we sought to optimize the bicyclic core to discover a novel series of WDR5 WIN-site inhibitors with improved potency and physicochemical properties. We identified the 3,4-dihydrobenzo[f][1,4]oxazepin-5(2H)-one core as an alternative scaffold for potent WDR5 inhibitors. Additionally, we used X-ray structural analysis to design partially saturated bicyclic P7 units. These benzoxazepinone-based inhibitors exhibited increased cellular potency and selectivity and favorable physicochemical properties compared to our best-in-class dihydroisoquinolinone-based counterparts. This study opens avenues to discover more advanced WDR5 WIN-site inhibitors and supports their development as novel anti-cancer therapeutics.
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Affiliation(s)
| | | | - Jianhua Tian
- Molecular Design and Synthesis Center, Vanderbilt Institute of Chemical Biology, Nashville, Tennessee 37232-0142, United States
| | | | | | | | | | | | | | | | | | | | - William J Moore
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702-1201, United States
| | - Gordon M Stott
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701-4907, United States
| | | | | | - Stephen W Fesik
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232-0142, United States
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8
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Yu X, Li D, Kottur J, Kim HS, Herring LE, Yu Y, Xie L, Hu X, Chen X, Cai L, Liu J, Aggarwal AK, Wang GG, Jin J. Discovery of Potent and Selective WDR5 Proteolysis Targeting Chimeras as Potential Therapeutics for Pancreatic Cancer. J Med Chem 2023; 66:16168-16186. [PMID: 38019706 PMCID: PMC10872723 DOI: 10.1021/acs.jmedchem.3c01521] [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] [Indexed: 12/01/2023]
Abstract
As a core chromatin-regulatory scaffolding protein, WDR5 mediates numerous protein-protein interactions (PPIs) with other partner oncoproteins. However, small-molecule inhibitors that block these PPIs exert limited cell-killing effects. Here, we report structure-activity relationship studies in pancreatic ductal adenocarcinoma (PDAC) cells that led to the discovery of several WDR5 proteolysis-targeting chimer (PROTAC) degraders, including 11 (MS132), a highly potent and selective von Hippel-Lindau (VHL)-recruiting WDR5 degrader, which displayed positive binding cooperativity between WDR5 and VHL, effectively inhibited proliferation in PDAC cells, and was bioavailable in mice and 25, a cereblon (CRBN)-recruiting WDR5 degrader, which selectively degraded WDR5 over the CRBN neo-substrate IKZF1. Furthermore, by conducting site-directed mutagenesis studies, we determined that WDR5 K296, but not K32, was involved in the PROTAC-induced WDR5 degradation. Collectively, these studies resulted in a highly effective WDR5 degrader, which could be a potential therapeutic for pancreatic cancer and several potentially useful tool compounds.
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Affiliation(s)
- Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Dongxu Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jithesh Kottur
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Huen Suk Kim
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Laura E Herring
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Yao Yu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina 27710, United States
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina 27710, United States
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Ling Xie
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Xiaoping Hu
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina 27710, United States
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Jing Liu
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Aneel K Aggarwal
- Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina 27710, United States
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina 27710, United States
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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9
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Gurung R, Om D, Pun R, Hyun S, Shin D. Recent Progress in Modulation of WD40-Repeat Domain 5 Protein (WDR5): Inhibitors and Degraders. Cancers (Basel) 2023; 15:3910. [PMID: 37568727 PMCID: PMC10417795 DOI: 10.3390/cancers15153910] [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: 07/01/2023] [Revised: 07/29/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
WD40-repeat (WDR) domain proteins play a crucial role in mediating protein-protein interactions that sustain oncogenesis in human cancers. One prominent example is the interaction between the transcription factor MYC and its chromatin co-factor, WD40-repeat domain protein 5 (WDR5), which is essential for oncogenic processes. The MYC family of proteins is frequently overexpressed in various cancers and has been validated as a promising target for anticancer therapies. The recruitment of MYC to chromatin is facilitated by WDR5, highlighting the significance of their interaction. Consequently, inhibiting the MYC-WDR5 interaction has been shown to induce the regression of malignant tumors, offering an alternative approach to targeting MYC in the development of anticancer drugs. WDR5 has two protein interaction sites, the "WDR5-binding motif" (WBM) site for MYC interaction and the histone methyltransferases SET1 recognition motif "WDR5-interacting" (WIN) site forming MLL complex. Significant efforts have been dedicated to the discovery of inhibitors that target the WDR5 protein. More recently, the successful application of targeted protein degradation technology has enabled the removal of WDR5. This breakthrough has opened up new avenues for inhibiting the interaction between WDR5 and the binding partners. In this review, we address the recent progress made in targeting WDR5 to inhibit MDR5-MYC and MDR5-MLL1 interactions, including its targeted protein degradation and their potential impact on anticancer drug discovery.
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Affiliation(s)
- Raju Gurung
- College of Pharmacy, Gachon University, 191 Hambakmoe-ro, Yeonsu-gu, Incheon 21936, Republic of Korea; (R.G.); (D.O.); (R.P.)
| | - Darlami Om
- College of Pharmacy, Gachon University, 191 Hambakmoe-ro, Yeonsu-gu, Incheon 21936, Republic of Korea; (R.G.); (D.O.); (R.P.)
| | - Rabin Pun
- College of Pharmacy, Gachon University, 191 Hambakmoe-ro, Yeonsu-gu, Incheon 21936, Republic of Korea; (R.G.); (D.O.); (R.P.)
| | - Soonsil Hyun
- College of Pharmacy, Chungbuk National University, 194-31 Osongsaengmyeong 1-ro, Heungdeok-gu, Cheongju-si 28160, Republic of Korea
| | - Dongyun Shin
- College of Pharmacy, Gachon University, 191 Hambakmoe-ro, Yeonsu-gu, Incheon 21936, Republic of Korea; (R.G.); (D.O.); (R.P.)
- Gachon Institute of Pharmaceutical Science, Gachon University, 191 Hambakmoe-ro, Yeonsu-gu, Incheon 21936, Republic of Korea
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10
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Zhang Z, Yang C, Wang Z, Guo L, Xu Y, Gao C, Sun Y, Zhang Z, Peng J, Hu M, Jan Lo L, Ma Z, Chen J. Wdr5-mediated H3K4me3 coordinately regulates cell differentiation, proliferation termination, and survival in digestive organogenesis. Cell Death Discov 2023; 9:227. [PMID: 37407577 DOI: 10.1038/s41420-023-01529-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/05/2023] [Accepted: 06/22/2023] [Indexed: 07/07/2023] Open
Abstract
Food digestion requires the cooperation of different digestive organs. The differentiation of digestive organs is crucial for larvae to start feeding. Therefore, during digestive organogenesis, cell identity and the tissue morphogenesis must be tightly coordinated but how this is accomplished is poorly understood. Here, we demonstrate that WD repeat domain 5 (Wdr5)-mediated H3K4 tri-methylation (H3K4me3) coordinately regulates cell differentiation, proliferation and apoptosis in zebrafish organogenesis of three major digestive organs including intestine, liver, and exocrine pancreas. During zebrafish digestive organogenesis, some of cells in these organ primordia usually undergo differentiation without apoptotic activity and gradually reduce their proliferation capacity. In contrast, cells in the three digestive organs of wdr5-/- mutant embryos retain progenitor-like status with high proliferation rates, and undergo apoptosis. Wdr5 is a core member of COMPASS complex to implement H3K4me3 and its expression is enriched in digestive organs from 2 days post-fertilization (dpf). Further analysis reveals that lack of differentiation gene expression is due to significant decreases of H3K4me3 around the transcriptional start sites of these genes; this histone modification also reduces the proliferation capacity in differentiated cells by increasing the expression of apc to promote the degradation of β-Catenin; in addition, H3K4me3 promotes the expression of anti-apoptotic genes such as xiap-like, which modulates p53 activity to guarantee differentiated cell survival. Thus, our findings have discovered a common molecular mechanism for cell fate determination in different digestive organs during organogenesis, and also provided insights to understand mechanistic basis of human diseases in these digestive organs.
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Affiliation(s)
- Zhe Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chun Yang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zixu Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Liwei Guo
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yongpan Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ce Gao
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yonghua Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zhenhai Zhang
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Jinrong Peng
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Minjie Hu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Li Jan Lo
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Zhipeng Ma
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Jun Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
- Cancer Center, Zhejiang University, Hangzhou, 310058, China.
- Department of Plastic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Hangzhou, 310016, China.
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11
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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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12
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Structural insights on the KMT2-NCP interaction. Biochem Soc Trans 2023; 51:427-434. [PMID: 36695549 DOI: 10.1042/bst20221155] [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: 11/28/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/26/2023]
Abstract
The MLL/KMT2 family enzymes are frequently mutated in human cancers and congenital diseases. They deposit the majority of histone 3 lysine 4 (H3K4) mono-, di-, or tri-methylation in mammals and are tightly associated with gene activation. Structural and biochemical studies in recent years provide in-depth understanding of how the MLL1 and homologous yeast SET1 complexes interact with the nucleosome core particle (NCP) and how their activities for H3K4 methylation are regulated by the conserved core components. Here, we will discuss the recent single molecule cryo-EM studies on the MLL1 and ySET1 complexes bound on the NCP. These studies highlight the dynamic regulation of the MLL/SET1 family lysine methyltransferases with unique features as compared with other histone lysine methyltransferases. These studies provide insights for loci-specific regulation of H3K4 methylation states in cells. The mechanistic studies on the MLL1 complex have already led to the development of the MLL1 inhibitors that show efficacy in acute leukemia and metastatic breast cancers. Future studies on the MLL/SET1 family enzymes will continue to bring to light potential therapeutic opportunities.
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13
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Teuscher KB, Chowdhury S, Meyers KM, Tian J, Sai J, Van Meveren M, South TM, Sensintaffar JL, Rietz TA, Goswami S, Wang J, Grieb BC, Lorey SL, Howard GC, Liu Q, Moore WJ, Stott GM, Tansey WP, Lee T, Fesik SW. Structure-based discovery of potent WD repeat domain 5 inhibitors that demonstrate efficacy and safety in preclinical animal models. Proc Natl Acad Sci U S A 2023; 120:e2211297120. [PMID: 36574664 PMCID: PMC9910433 DOI: 10.1073/pnas.2211297120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/30/2022] [Indexed: 12/28/2022] Open
Abstract
WD repeat domain 5 (WDR5) is a core scaffolding component of many multiprotein complexes that perform a variety of critical chromatin-centric processes in the nucleus. WDR5 is a component of the mixed lineage leukemia MLL/SET complex and localizes MYC to chromatin at tumor-critical target genes. As a part of these complexes, WDR5 plays a role in sustaining oncogenesis in a variety of human cancers that are often associated with poor prognoses. Thus, WDR5 has been recognized as an attractive therapeutic target for treating both solid and hematological tumors. Previously, small-molecule inhibitors of the WDR5-interaction (WIN) site and WDR5 degraders have demonstrated robust in vitro cellular efficacy in cancer cell lines and established the therapeutic potential of WDR5. However, these agents have not demonstrated significant in vivo efficacy at pharmacologically relevant doses by oral administration in animal disease models. We have discovered WDR5 WIN-site inhibitors that feature bicyclic heteroaryl P7 units through structure-based design and address the limitations of our previous series of small-molecule inhibitors. Importantly, our lead compounds exhibit enhanced on-target potency, excellent oral pharmacokinetic (PK) profiles, and potent dose-dependent in vivo efficacy in a mouse MV4:11 subcutaneous xenograft model by oral dosing. Furthermore, these in vivo probes show excellent tolerability under a repeated high-dose regimen in rodents to demonstrate the safety of the WDR5 WIN-site inhibition mechanism. Collectively, our results provide strong support for WDR5 WIN-site inhibitors to be utilized as potential anticancer therapeutics.
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Affiliation(s)
- Kevin B. Teuscher
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37232-0146
| | - Somenath Chowdhury
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37232-0146
| | - Kenneth M. Meyers
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37232-0146
| | - Jianhua Tian
- Molecular Design and Synthesis Center, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN37232-0142
| | - Jiqing Sai
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37232-0146
| | - Mayme Van Meveren
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37232-0146
| | - Taylor M. South
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37232-0146
| | - John L. Sensintaffar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37232-0146
| | - Tyson A. Rietz
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37232-0146
| | - Soumita Goswami
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN37232-0146
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN37232-0004
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN37232-0004
| | - Brian C. Grieb
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN37232-0146
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN37232-0011
| | - Shelly L. Lorey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN37232-0146
| | - Gregory C. Howard
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN37232-0146
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN37232-0004
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN37232-0004
| | - William J. Moore
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD21702-1201
| | - Gordon M. Stott
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD21701-4907
| | - William P. Tansey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37232-0146
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN37232-0146
| | - Taekyu Lee
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37232-0146
| | - Stephen W. Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37232-0146
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN37232-0146
- Department of Chemistry, Vanderbilt University, Nashville, TN37232-0146
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14
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Roth C, Kilpinen H, Kurian MA, Barral S. Histone lysine methyltransferase-related neurodevelopmental disorders: current knowledge and saRNA future therapies. Front Cell Dev Biol 2023; 11:1090046. [PMID: 36923252 PMCID: PMC10009263 DOI: 10.3389/fcell.2023.1090046] [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: 12/07/2022] [Accepted: 02/06/2023] [Indexed: 03/02/2023] Open
Abstract
Neurodevelopmental disorders encompass a group of debilitating diseases presenting with motor and cognitive dysfunction, with variable age of onset and disease severity. Advances in genetic diagnostic tools have facilitated the identification of several monogenic chromatin remodeling diseases that cause Neurodevelopmental disorders. Chromatin remodelers play a key role in the neuro-epigenetic landscape and regulation of brain development; it is therefore not surprising that mutations, leading to loss of protein function, result in aberrant neurodevelopment. Heterozygous, usually de novo mutations in histone lysine methyltransferases have been described in patients leading to haploinsufficiency, dysregulated protein levels and impaired protein function. Studies in animal models and patient-derived cell lines, have highlighted the role of histone lysine methyltransferases in the regulation of cell self-renewal, cell fate specification and apoptosis. To date, in depth studies of histone lysine methyltransferases in oncology have provided strong evidence of histone lysine methyltransferase dysregulation as a determinant of cancer progression and drug resistance. As a result, histone lysine methyltransferases have become an important therapeutic target for the treatment of different cancer forms. Despite recent advances, we still lack knowledge about the role of histone lysine methyltransferases in neuronal development. This has hampered both the study and development of precision therapies for histone lysine methyltransferases-related Neurodevelopmental disorders. In this review, we will discuss the current knowledge of the role of histone lysine methyltransferases in neuronal development and disease progression. We will also discuss how RNA-based technologies using small-activating RNAs could potentially provide a novel therapeutic approach for the future treatment of histone lysine methyltransferase haploinsufficiency in these Neurodevelopmental disorders, and how they could be first tested in state-of-the-art patient-derived neuronal models.
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Affiliation(s)
- Charlotte Roth
- Molecular Neurosciences, Developmental Neurosciences Programme, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Helena Kilpinen
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Manju A Kurian
- Molecular Neurosciences, Developmental Neurosciences Programme, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom.,Department of Neurology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Serena Barral
- Molecular Neurosciences, Developmental Neurosciences Programme, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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15
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Rahman S, Hoffmann NA, Worden EJ, Smith ML, Namitz KEW, Knutson BA, Cosgrove MS, Wolberger C. Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome. Proc Natl Acad Sci U S A 2022; 119:e2205691119. [PMID: 36095189 PMCID: PMC9499523 DOI: 10.1073/pnas.2205691119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/09/2022] [Indexed: 11/18/2022] Open
Abstract
The human Mixed Lineage Leukemia-1 (MLL1) complex methylates histone H3K4 to promote transcription and is stimulated by monoubiquitination of histone H2B. Recent structures of the MLL1-WRAD core complex, which comprises the MLL1 methyltransferase, WDR5, RbBp5, Ash2L, and DPY-30, have revealed variability in the docking of MLL1-WRAD on nucleosomes. In addition, portions of the Ash2L structure and the position of DPY30 remain ambiguous. We used an integrated approach combining cryoelectron microscopy (cryo-EM) and mass spectrometry cross-linking to determine a structure of the MLL1-WRAD complex bound to ubiquitinated nucleosomes. The resulting model contains the Ash2L intrinsically disordered region (IDR), SPRY insertion region, Sdc1-DPY30 interacting region (SDI-motif), and the DPY30 dimer. We also resolved three additional states of MLL1-WRAD lacking one or more subunits, which may reflect different steps in the assembly of MLL1-WRAD. The docking of subunits in all four states differs from structures of MLL1-WRAD bound to unmodified nucleosomes, suggesting that H2B-ubiquitin favors assembly of the active complex. Our results provide a more complete picture of MLL1-WRAD and the role of ubiquitin in promoting formation of the active methyltransferase complex.
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Affiliation(s)
- Sanim Rahman
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Niklas A. Hoffmann
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Evan J. Worden
- Department of Structural Biology, Van Andel Research Institute, Grand Rapids, MI 49503
| | - Marissa L. Smith
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Kevin E. W. Namitz
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Bruce A. Knutson
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
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16
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Sehrawat P, Shobhawat R, Kumar A. Catching Nucleosome by Its Decorated Tails Determines Its Functional States. Front Genet 2022; 13:903923. [PMID: 35910215 PMCID: PMC9329655 DOI: 10.3389/fgene.2022.903923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
The fundamental packaging unit of chromatin, i.e., nucleosome, consists of ∼147 bp of DNA wrapped around a histone octamer composed of the core histones, H2A, H2B, H3, and H4, in two copies each. DNA packaged in nucleosomes must be accessible to various machineries, including replication, transcription, and DNA damage repair, implicating the dynamic nature of chromatin even in its compact state. As the tails protrude out of the nucleosome, they are easily accessible to various chromatin-modifying machineries and undergo post-translational modifications (PTMs), thus playing a critical role in epigenetic regulation. PTMs can regulate chromatin states via charge modulation on histones, affecting interaction with various chromatin-associated proteins (CAPs) and DNA. With technological advancement, the list of PTMs is ever-growing along with their writers, readers, and erasers, expanding the complexity of an already intricate epigenetic field. In this review, we discuss how some of the specific PTMs on flexible histone tails affect the nucleosomal structure and regulate the accessibility of chromatin from a mechanistic standpoint and provide structural insights into some newly identified PTM–reader interaction.
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17
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Imran A, Moyer BS, Kalina D, Duncan TM, Moody KJ, Wolfe AJ, Cosgrove MS, Movileanu L. Convergent Alterations of a Protein Hub Produce Divergent Effects within a Binding Site. ACS Chem Biol 2022; 17:1586-1597. [PMID: 35613319 PMCID: PMC9207812 DOI: 10.1021/acschembio.2c00273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Progress in tumor
sequencing and cancer databases has created an
enormous amount of information that scientists struggle to sift through.
While several research groups have created computational methods to
analyze these databases, much work still remains in distinguishing
key implications of pathogenic mutations. Here, we describe an approach
to identify and evaluate somatic cancer mutations of WD40 repeat protein
5 (WDR5), a chromatin-associated protein hub. This multitasking protein
maintains the functional integrity of large multi-subunit enzymatic
complexes of the six human SET1 methyltransferases. Remarkably, the
somatic cancer mutations of WDR5 preferentially distribute within
and around an essential cavity, which hosts the WDR5 interaction (Win)
binding site. Hence, we assessed the real-time binding kinetics of
the interactions of key clustered WDR5 mutants with the Win motif
peptide ligands of the SET1 family members (SET1Win). Our
measurements highlight that this subset of mutants exhibits divergent
perturbations in the kinetics and strength of interactions not only
relative to those of the native WDR5 but also among various SET1Win ligands. These outcomes could form a fundamental basis
for future drug discovery and other developments in medical biotechnology.
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Affiliation(s)
- Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
| | - Brandon S. Moyer
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
| | - Dan Kalina
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
| | - Thomas M. Duncan
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, United States
| | - Kelsey J. Moody
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - Aaron J. Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, United States
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
- The BioInspired Institute, Syracuse University, Syracuse, New York 13244, United States
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18
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Imran A, Moyer BS, Wolfe AJ, Cosgrove MS, Makarov DE, Movileanu L. Interplay of Affinity and Surface Tethering in Protein Recognition. J Phys Chem Lett 2022; 13:4021-4028. [PMID: 35485934 PMCID: PMC9106920 DOI: 10.1021/acs.jpclett.2c00621] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/27/2022] [Indexed: 05/10/2023]
Abstract
Surface-tethered ligand-receptor complexes are key components in biological signaling and adhesion. They also find increasing utility in single-molecule assays and biotechnological applications. Here, we study the real-time binding kinetics between various surface-immobilized peptide ligands and their unrestrained receptors. A long peptide tether increases the association of ligand-receptor complexes, experimentally proving the fly casting mechanism where the disorder accelerates protein recognition. On the other hand, a short peptide tether enhances the complex dissociation. Notably, the rate constants measured for the same receptor, but under different spatial constraints, are strongly correlated to one another. Furthermore, this correlation can be used to predict how surface tethering on a ligand-receptor complex alters its binding kinetics. Our results have immediate implications in the broad areas of biomolecular recognition, intrinsically disordered proteins, and biosensor technology.
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Affiliation(s)
- Ali Imran
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
| | - Brandon S. Moyer
- Ichor
Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United
States
- Lewis
School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - Aaron J. Wolfe
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Ichor
Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United
States
- Lewis
School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
- Department
of Chemistry, State University of New York
College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
| | - Michael S. Cosgrove
- Department
of Biochemistry and Molecular Biology, State
University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving
Avenue, Syracuse, New York 13210, United States
| | - Dmitrii E. Makarov
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
- Oden
Institute
for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Liviu Movileanu
- Department
of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Department
of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United
States
- The BioInspired
Institute, Syracuse University, Syracuse, New York 13244, United States
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19
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Li D, Yu X, Kottur J, Gong W, Zhang Z, Storey AJ, Tsai YH, Uryu H, Shen Y, Byrum SD, Edmondson RD, Mackintosh SG, Cai L, Liu Z, Aggarwal AK, Tackett AJ, Liu J, Jin J, Wang GG. Discovery of a dual WDR5 and Ikaros PROTAC degrader as an anti-cancer therapeutic. Oncogene 2022; 41:3328-3340. [PMID: 35525905 PMCID: PMC9189076 DOI: 10.1038/s41388-022-02340-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/21/2022]
Abstract
WD repeat domain 5 (WDR5), an integral component of the MLL/KMT2A lysine methyltransferase complex, is critically involved in oncogenesis and represents an attractive onco-target. Inhibitors targeting protein-protein interactions (PPIs) between WDR5 and its binding partners, however, do not inhibit all of WDR5-mediated oncogenic functions and exert rather limited antitumor effects. Here, we report a cereblon (CRBN)-recruiting proteolysis targeting chimera (PROTAC) of WDR5, MS40, which selectively degrades WDR5 and the well-established neo-substrates of immunomodulatory drugs (IMiDs):CRBN, the Ikaros zinc finger (IKZF) transcription factors IKZF1 and IKZF3. MS40-induced WDR5 degradation caused disassociation of the MLL/KMT2A complex off chromatin, resulting in decreased H3K4me2. Transcriptomic profiling revealed that targets of both WDR5 and IMiDs:CRBN were significantly repressed by treatment of MS40. In MLL-rearranged leukemias, which exhibit IKZF1 high expression and dependency, co-suppression of WDR5 and Ikaros by MS40 is superior in suppressing oncogenesis to the WDR5 PPI inhibitor, to MS40's non-PROTAC analog controls (MS40N1 and MS40N2, which do not bind CRBN and WDR5, respectively), and to a matched VHL-based WDR5 PROTAC (MS169, which degrades WDR5 but not Ikaros). MS40 suppressed the growth of primary leukemia patient cells in vitro and patient-derived xenografts in vivo. Thus, dual degradation of WDR5 and Ikaros is a promising anti-cancer strategy.
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Affiliation(s)
- Dongxu Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jithesh Kottur
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Weida Gong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhao Zhang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hidetaka Uryu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yudao Shen
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Rick D Edmondson
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhijie Liu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Aneel K Aggarwal
- Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jing Liu
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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20
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Teuscher KB, Meyers KM, Wei Q, Mills JJ, Tian J, Alvarado J, Sai J, Van Meveren M, South TM, Rietz TA, Zhao B, Moore WJ, Stott GM, Tansey WP, Lee T, Fesik SW. Discovery of Potent Orally Bioavailable WD Repeat Domain 5 (WDR5) Inhibitors Using a Pharmacophore-Based Optimization. J Med Chem 2022; 65:6287-6312. [PMID: 35436124 PMCID: PMC10081510 DOI: 10.1021/acs.jmedchem.2c00195] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
WD repeat domain 5 (WDR5) is a nuclear scaffolding protein that forms many biologically important multiprotein complexes. The WIN site of WDR5 represents a promising pharmacological target in a variety of human cancers. Here, we describe the optimization of our initial WDR5 WIN-site inhibitor using a structure-guided pharmacophore-based convergent strategy to improve its druglike properties and pharmacokinetic profile. The core of the previous lead remained constant while a focused SAR effort on the three pharmacophore units was combined to generate a new in vivo lead series. Importantly, this new series of compounds has picomolar binding affinity, improved cellular antiproliferative activity and selectivity, and increased kinetic aqueous solubility. They also exhibit a desirable oral pharmacokinetic profile with manageable intravenous clearance and high oral bioavailability. Thus, these new leads are useful probes toward studying the effects of WDR5 inhibition.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - William J Moore
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701-4907, United States
| | - Gordon M Stott
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701-4907, United States
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21
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Mayse LA, Imran A, Larimi MG, Cosgrove MS, Wolfe AJ, Movileanu L. Disentangling the recognition complexity of a protein hub using a nanopore. Nat Commun 2022; 13:978. [PMID: 35190547 PMCID: PMC8861093 DOI: 10.1038/s41467-022-28465-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/25/2022] [Indexed: 11/12/2022] Open
Abstract
WD40 repeat proteins are frequently involved in processing cell signaling and scaffolding large multi-subunit machineries. Despite their significance in physiological and disease-like conditions, their reversible interactions with other proteins remain modestly examined. Here, we show the development and validation of a protein nanopore for the detection and quantification of WD40 repeat protein 5 (WDR5), a chromatin-associated hub involved in epigenetic regulation of histone methylation. Our nanopore sensor is equipped with a 14-residue Win motif of mixed lineage leukemia 4 methyltransferase (MLL4Win), a WDR5 ligand. Our approach reveals a broad dynamic range of MLL4Win-WDR5 interactions and three distant subpopulations of binding events, representing three modes of protein recognition. The three binding events are confirmed as specific interactions using a weakly binding WDR5 derivative and various environmental contexts. These outcomes demonstrate the substantial sensitivity of our nanopore sensor, which can be utilized in protein analytics. Nanopores are powerful tools for sampling protein-peptide interactions. Here, the authors convert a protein-based nanopore into a sensitive biosensor to characterize the complex binding of WDR5 protein to a 14-residue ligand.
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22
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Tan M, Li S, Juillard F, Chitas R, Custódio TF, Xue H, Szymula A, Sun Q, Liu B, Álvarez ÁL, Chen S, Huang J, Simas JP, McVey CE, Kaye KM. MLL1 is regulated by KSHV LANA and is important for virus latency. Nucleic Acids Res 2021; 49:12895-12911. [PMID: 34850113 PMCID: PMC8682764 DOI: 10.1093/nar/gkab1094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/29/2021] [Accepted: 10/20/2021] [Indexed: 01/19/2023] Open
Abstract
Mixed lineage leukemia 1 (MLL1) is a histone methyltransferase. Kaposi's sarcoma-associated herpesvirus (KSHV) is a leading cause of malignancy in AIDS. KSHV latently infects tumor cells and its genome is decorated with epigenetic marks. Here, we show that KSHV latency-associated nuclear antigen (LANA) recruits MLL1 to viral DNA where it establishes H3K4me3 modifications at the extensive KSHV terminal repeat elements during primary infection. LANA interacts with MLL1 complex members, including WDR5, integrates into the MLL1 complex, and regulates MLL1 activity. We describe the 1.5-Å crystal structure of N-terminal LANA peptide complexed with MLL1 complex member WDR5, which reveals a potential regulatory mechanism. Disruption of MLL1 expression rendered KSHV latency establishment highly deficient. This deficiency was rescued by MLL1 but not by catalytically inactive MLL1. Therefore, MLL1 is LANA regulable and exerts a central role in virus infection. These results suggest broad potential for MLL1 regulation, including by non-host factors.
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Affiliation(s)
- Min Tan
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Shijun Li
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Franceline Juillard
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Rute Chitas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - Tânia F Custódio
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - Han Xue
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Agnieszka Szymula
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Qiming Sun
- Departments of Biochemistry and Cardiology, Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Bing Liu
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ángel L Álvarez
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - She Chen
- Proteomics Center, National Institute of Biological Sciences, Beijing 102206, China
| | - Jing Huang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine 200125 Shanghai, China
| | - J Pedro Simas
- Instituto de Medicina Molecular, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal.,Católica Biomedical Research, Católica Medical School, Universidade Católica Portuguesa, Palma de Cima, 1649-023 Lisboa, Portugal
| | - Colin E McVey
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - Kenneth M Kaye
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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23
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Gu Y, Chen Y, Wei L, Wu S, Shen K, Liu C, Dong Y, Zhao Y, Zhang Y, Zhang C, Zheng W, He J, Wang Y, Li Y, Zhao X, Wang H, Tan J, Wang L, Zhou Q, Xie G, Liang H, Ou J. ABHD5 inhibits YAP-induced c-Met overexpression and colon cancer cell stemness via suppressing YAP methylation. Nat Commun 2021; 12:6711. [PMID: 34795238 PMCID: PMC8602706 DOI: 10.1038/s41467-021-26967-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/26/2021] [Indexed: 01/05/2023] Open
Abstract
Cancer stemness represents a major source of development and progression of colorectal cancer (CRC). c-Met critically contributes to CRC stemness, but how c-Met is activated in CRC remains elusive. We previously identified the lipolytic factor ABHD5 as an important tumour suppressor gene in CRC. Here, we show that loss of ABHD5 promotes c-Met activation to sustain CRC stemness in a non-canonical manner. Mechanistically, we demonstrate that ABHD5 interacts in the cytoplasm with the core subunit of the SET1A methyltransferase complex, DPY30, thereby inhibiting the nuclear translocation of DPY30 and activity of SET1A. In the absence of ABHD5, DPY30 translocates to the nucleus and supports SET1A-mediated methylation of YAP and histone H3, which sequesters YAP in the nucleus and increases chromatin accessibility to synergistically promote YAP-induced transcription of c-Met, thus promoting the stemness of CRC cells. This study reveals a novel role of ABHD5 in regulating histone/non-histone methylation and CRC stemness.
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Affiliation(s)
- Yan Gu
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Yanrong Chen
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Lai Wei
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Shuang Wu
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Kaicheng Shen
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Chengxiang Liu
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Yan Dong
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Yang Zhao
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Yue Zhang
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Chi Zhang
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Wenling Zheng
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Jiangyi He
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Yunlong Wang
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Yifei Li
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Xiaoxin Zhao
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Hongwei Wang
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Jun Tan
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Liting Wang
- Biomedical Analysis Center, Third Military Medical University (Army Medical University), 400038, Chongqing, China
| | - Qi Zhou
- Department of Oncology, Fuling Central Hospital of Chongqing City, 408000, Chongqing, China.
| | - Ganfeng Xie
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China.
| | - Houjie Liang
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China.
| | - Juanjuan Ou
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), 400038, Chongqing, China.
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24
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Yu X, Li D, Kottur J, Shen Y, Kim HS, Park KS, Tsai YH, Gong W, Wang J, Suzuki K, Parker J, Herring L, Kaniskan HÜ, Cai L, Jain R, Liu J, Aggarwal AK, Wang GG, Jin J. A selective WDR5 degrader inhibits acute myeloid leukemia in patient-derived mouse models. Sci Transl Med 2021; 13:eabj1578. [PMID: 34586829 PMCID: PMC8500670 DOI: 10.1126/scitranslmed.abj1578] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Interactions between WD40 repeat domain protein 5 (WDR5) and its various partners such as mixed lineage leukemia (MLL) and c-MYC are essential for sustaining oncogenesis in human cancers. However, inhibitors that block protein-protein interactions (PPIs) between WDR5 and its binding partners exhibit modest cancer cell killing effects and lack in vivo efficacy. Here, we present pharmacological degradation of WDR5 as a promising therapeutic strategy for treating WDR5-dependent tumors and report two high-resolution crystal structures of WDR5-degrader-E3 ligase ternary complexes. We identified an effective WDR5 degrader via structure-based design and demonstrated its in vitro and in vivo antitumor activities. On the basis of the crystal structure of an initial WDR5 degrader in complex with WDR5 and the E3 ligase von Hippel–Lindau (VHL), we designed a WDR5 degrader, MS67, and demonstrated the high cooperativity of MS67 binding to WDR5 and VHL by another ternary complex structure and biophysical characterization. MS67 potently and selectively depleted WDR5 and was more effective than WDR5 PPI inhibitors in suppressing transcription of WDR5-regulated genes, decreasing the chromatin-bound fraction of MLL complex components and c-MYC, and inhibiting the proliferation of cancer cells. In addition, MS67 suppressed malignant growth of MLL-rearranged acute myeloid leukemia patient cells in vitro and in vivo and was well tolerated in vivo. Collectively, our results demonstrate that structure-based design can be an effective strategy to identify highly active degraders and suggest that pharmacological degradation of WDR5 might be a promising treatment for WDR5-dependent cancers.
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Affiliation(s)
- Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dongxu Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jithesh Kottur
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yudao Shen
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Huen Suk Kim
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kwang-Su Park
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Weida Gong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jun Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kyogo Suzuki
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joel Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laura Herring
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - H. Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rinku Jain
- Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jing Liu
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aneel K Aggarwal
- Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Corresponding author. (J.J.); (G.G.W.)
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Corresponding author. (J.J.); (G.G.W.)
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25
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Yang Y, Yang Y, Chan K, Couture JF. Analyzing the impact of CFP1 mutational landscape on epigenetic signaling. FASEB J 2021; 35:e21790. [PMID: 34320252 DOI: 10.1096/fj.202100427r] [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: 03/11/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 11/11/2022]
Abstract
CXXC Zinc finger protein 1 (CFP1) is a multitasking protein playing essential roles during various developmental processes. Its ability to interact with several proteins contribute to several epigenetic events. Here, we review CFP1's functions and its impact on DNA methylation and the post-translational modification of histone proteins such as lysine acetylation and methylation. We will also discuss the potential role of CFP1 in carcinogenesis and the impact of the mutations identified in patients suffering from various cancers.
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Affiliation(s)
- Yidai Yang
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Yaqing Yang
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Kin Chan
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Jean-Francois Couture
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada.,Shanghai Institute of Materia Medica-University of Ottawa Research Center in Systems and Personalized Pharmacology, University of Ottawa, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
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26
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Chen W, Chen X, Li D, Wang X, Long G, Jiang Z, You Q, Guo X. Discovery of a potent MLL1 and WDR5 protein-protein interaction inhibitor with in vivo antitumor activity. Eur J Med Chem 2021; 223:113677. [PMID: 34225179 DOI: 10.1016/j.ejmech.2021.113677] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/18/2021] [Accepted: 06/25/2021] [Indexed: 10/21/2022]
Abstract
MLL1-WDR5 interaction is essential for the formation of MLL core complex and its H3K4 methyltransferase activity. Disrupting MLL1-WDR5 interaction has been proposed as a potential therapeutic approach in the treatment of leukemia. A "toolkit" of well-characterized chemical probe will allow exploring animal studies. Based on a specific MLL1-WDR5 PPI inhibitor (DDO-2117), which was previously reported by our group, we conducted a bioisosterism approach by click chemistry to discover novel phenyltriazole scaffold MLL1-WDR5 interaction blockers. Here, our efforts resulted in the best inhibitor 24 (DDO-2093) with high binding affinity (Kd = 11.6 nM) and with improved drug-like properties. Both in vitro and in vivo assays revealed 24 could efficiently block the MLL1-WDR5 interaction. Furthermore, 24 significantly suppressed tumor growth in the MV4-11 xenograft mouse model and showed a favorable safety profile. We propose 24 as a chemical probe that is suitable for in vivo pharmacodynamic and biological studies of MLL1-WDR5 interaction.
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Affiliation(s)
- Weilin Chen
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Xin Chen
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Dongdong Li
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Xianghan Wang
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Guanlu Long
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhengyu Jiang
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Qidong You
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Xiaoke Guo
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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Imran A, Moyer BS, Canning AJ, Kalina D, Duncan TM, Moody KJ, Wolfe AJ, Cosgrove MS, Movileanu L. Kinetics of the multitasking high-affinity Win binding site of WDR5 in restricted and unrestricted conditions. Biochem J 2021; 478:2145-2161. [PMID: 34032265 PMCID: PMC8214142 DOI: 10.1042/bcj20210253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 02/05/2023]
Abstract
Recent advances in quantitative proteomics show that WD40 proteins play a pivotal role in numerous cellular networks. Yet, they have been fairly unexplored and their physical associations with other proteins are ambiguous. A quantitative understanding of these interactions has wide-ranging significance. WD40 repeat protein 5 (WDR5) interacts with all members of human SET1/MLL methyltransferases, which regulate methylation of the histone 3 lysine 4 (H3K4). Here, using real-time binding measurements in a high-throughput setting, we identified the kinetic fingerprint of transient associations between WDR5 and 14-residue WDR5 interaction (Win) motif peptides of each SET1 protein (SET1Win). Our results reveal that the high-affinity WDR5-SET1Win interactions feature slow association kinetics. This finding is likely due to the requirement of SET1Win to insert into the narrow WDR5 cavity, also named the Win binding site. Furthermore, our explorations indicate fairly slow dissociation kinetics. This conclusion is in accordance with the primary role of WDR5 in maintaining the functional integrity of a large multisubunit complex, which regulates the histone methylation. Because the Win binding site is considered a key therapeutic target, the immediate outcomes of this study could form the basis for accelerated developments in medical biotechnology.
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Affiliation(s)
- Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Brandon S. Moyer
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
| | - Ashley J. Canning
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Dan Kalina
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Thomas M. Duncan
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Kelsey J. Moody
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Aaron J. Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Ichor Therapeutics, Inc., 2521 US Route 11, LaFayette, New York 13084, USA
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, USA
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York - Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- The BioInspired Institute, Syracuse University, Syracuse, New York, 13244, USA
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, USA
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Li X, Song Y. Structure, function and inhibition of critical protein-protein interactions involving mixed lineage leukemia 1 and its fusion oncoproteins. J Hematol Oncol 2021; 14:56. [PMID: 33823889 PMCID: PMC8022399 DOI: 10.1186/s13045-021-01057-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/05/2021] [Indexed: 12/13/2022] Open
Abstract
Mixed lineage leukemia 1 (MLL1, also known as MLL or KMT2A) is an important transcription factor and histone-H3 lysine-4 (H3K4) methyltransferase. It is a master regulator for transcription of important genes (e.g., Hox genes) for embryonic development and hematopoiesis. However, it is largely dispensable in matured cells. Dysregulation of MLL1 leads to overexpression of certain Hox genes and eventually leukemia initiation. Chromosome translocations involving MLL1 cause ~ 75% of acute leukemia in infants and 5–10% in children and adults with a poor prognosis. Targeted therapeutics against oncogenic fusion MLL1 (onco-MLL1) are therefore needed. Onco-MLL1 consists of the N-terminal DNA-interacting domains of MLL1 fused with one of > 70 fusion partners, among which transcription cofactors AF4, AF9 and its paralog ENL, and ELL are the most frequent. Wild-type (WT)- and onco-MLL1 involve numerous protein–protein interactions (PPI), which play critical roles in regulating gene expression in normal physiology and leukemia. Moreover, WT-MLL1 has been found to be essential for MLL1-rearranged (MLL1-r) leukemia. Rigorous studies of such PPIs have been performed and much progress has been achieved in understanding their structures, structure–function relationships and the mechanisms for activating gene transcription as well as leukemic transformation. Inhibition of several critical PPIs by peptides, peptidomimetic or small-molecule compounds has been explored as a therapeutic approach for MLL1-r leukemia. This review summarizes the biological functions, biochemistry, structure and inhibition of the critical PPIs involving MLL1 and its fusion partner proteins. In addition, challenges and perspectives of drug discovery targeting these PPIs for the treatment of MLL1-r leukemia are discussed.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. .,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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29
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Localization of the WD repeat-containing protein 5 to the Virion Assembly Compartment Facilitates Human Cytomegalovirus Assembly. J Virol 2021; 95:JVI.02101-20. [PMID: 33504601 PMCID: PMC8103678 DOI: 10.1128/jvi.02101-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We previously reported that human cytomegalovirus (HCMV) utilizes the cellular protein WD repeat-containing protein 5 (WDR5) to facilitate capsid nuclear egress. Here, we further show that HCMV infection results in WDR5 localization in a juxtanuclear region, and that its localization to this cellular site is associated with viral replication and late viral gene expression. Furthermore, WDR5 accumulated in the virion assembly compartment (vAC) and co-localized with vAC markers of gamma-tubulin (γ-tubulin), early endosomes, and viral vAC marker proteins pp65, pp28, and glycoprotein B (gB). WDR5 co-immunoprecipitated with multiple virion proteins, including MCP, pp150, pp65, pIRS1, and pTRS1, which may explain WDR5 accumulation in the vAC during infection. WDR5 fractionated with virions either in the presence or absence of Triton X-100 and was present in purified viral particles, suggesting that WDR5 was incorporated into HCMV virions. Thus, WDR5 localized to the vAC and was incorporated into virions, raising the possibility that in addition to capsid nuclear egress, WDR5 could also participate in cytoplasmic HCMV virion morphogenesis.Importance Human cytomegalovirus (HCMV) has a large (∼235-kb) genome that contains over 170 ORFs and exploits numerous cellular factors to facilitate its replication. In the late phase of HCMV infection cytoplasmic membranes are reorganized to establish the virion assembly compartment (vAC), which has been shown to necessary for efficient assembly of progeny virions. We previously reported that WDR5 facilitates HCMV nuclear egress. Here, we show that WDR5 is localized to the vAC and incorporated into virions, perhaps contributing to efficient virion maturation. Thus, findings in this study identified a potential role for WDR5 in HCMV assembly in the cytoplasmic phase of virion morphogenesis.
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Rao VG, Kulkarni SS. Xenopus to the rescue: A model to validate and characterize candidate ciliopathy genes. Genesis 2021; 59:e23414. [PMID: 33576572 DOI: 10.1002/dvg.23414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 12/14/2022]
Abstract
Cilia are present on most vertebrate cells and play a central role in development, growth, and homeostasis. Thus, cilia dysfunction can manifest into an array of diseases, collectively termed ciliopathies, affecting millions of lives worldwide. Yet, our understanding of the gene regulatory networks that control cilia assembly and functions remain incomplete. With the advances in next-generation sequencing technologies, we can now rapidly predict pathogenic variants from hundreds of ciliopathy patients. While the pace of candidate gene discovery is exciting, most of these genes have never been previously implicated in cilia assembly or function. This makes assigning the disease causality difficult. This review discusses how Xenopus, a genetically tractable and high-throughput vertebrate model, has played a central role in identifying, validating, and characterizing candidate ciliopathy genes. The review is focused on multiciliated cells (MCCs) and diseases associated with MCC dysfunction. MCCs harbor multiple motile cilia on their apical surface to generate extracellular fluid flow inside the airway, the brain ventricles, and the oviduct. In Xenopus, these cells are external and present on the embryonic epidermal epithelia, facilitating candidate genes analysis in MCC development in vivo. The ability to introduce patient variants to study their effects on disease progression makes Xenopus a powerful model to improve our understanding of the underlying disease mechanisms and explain the patient phenotype.
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Affiliation(s)
- Venkatramanan G Rao
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Saurabh S Kulkarni
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia, USA.,Department of Biology, University of Virginia, Charlottesville, Virginia, USA
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Aberrant Activity of Histone-Lysine N-Methyltransferase 2 (KMT2) Complexes in Oncogenesis. Int J Mol Sci 2020; 21:ijms21249340. [PMID: 33302406 PMCID: PMC7762615 DOI: 10.3390/ijms21249340] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/04/2020] [Accepted: 12/06/2020] [Indexed: 02/06/2023] Open
Abstract
KMT2 (histone-lysine N-methyltransferase subclass 2) complexes methylate lysine 4 on the histone H3 tail at gene promoters and gene enhancers and, thus, control the process of gene transcription. These complexes not only play an essential role in normal development but have also been described as involved in the aberrant growth of tissues. KMT2 mutations resulting from the rearrangements of the KMT2A (MLL1) gene at 11q23 are associated with pediatric mixed-lineage leukemias, and recent studies demonstrate that KMT2 genes are frequently mutated in many types of human cancers. Moreover, other components of the KMT2 complexes have been reported to contribute to oncogenesis. This review summarizes the recent advances in our knowledge of the role of KMT2 complexes in cell transformation. In addition, it discusses the therapeutic targeting of different components of the KMT2 complexes.
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32
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Ye X, Chen G, Jin J, Zhang B, Wang Y, Cai Z, Ye F. The Development of Inhibitors Targeting the Mixed Lineage Leukemia 1 (MLL1)-WD Repeat Domain 5 Protein (WDR5) Protein- Protein Interaction. Curr Med Chem 2020; 27:5530-5542. [PMID: 31132972 DOI: 10.2174/0929867326666190528080514] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/17/2019] [Accepted: 05/06/2019] [Indexed: 12/22/2022]
Abstract
Mixed Lineage Leukemia 1 (MLL1), an important member of Histone Methyltransferases (HMT) family, is capable of catalyzing mono-, di-, and trimethylation of Histone 3 lysine 4 (H3K4). The optimal catalytic activity of MLL1 requires the formation of a core complex consisting of MLL1, WDR5, RbBP5, and ASH2L. The Protein-Protein Interaction (PPI) between WDR5 and MLL1 plays an important role in abnormal gene expression during tumorigenesis, and disturbing this interaction may have a potential for the treatment of leukemia harboring MLL1 fusion proteins. In this review, we will summarize recent progress in the development of inhibitors targeting MLL1- WDR5 interaction.
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Affiliation(s)
- Xiaoqing Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Gang Chen
- The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Jia Jin
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Binzhong Zhang
- The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Yinda Wang
- The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Zhenhai Cai
- The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Fei Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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33
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Fan Z, He L, Li M, Cao R, Deng M, Ping F, Liang X, He Y, Wu T, Tao X, Xu J, Cheng B, Xia J. Targeting methyltransferase PRMT5 retards the carcinogenesis and metastasis of HNSCC via epigenetically inhibiting Twist1 transcription. Neoplasia 2020; 22:617-629. [PMID: 33045527 PMCID: PMC7557877 DOI: 10.1016/j.neo.2020.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/25/2020] [Accepted: 09/11/2020] [Indexed: 12/22/2022]
Abstract
Protein arginine methyltransferase 5 (PRMT5) is an important type II arginine methyltransferase that can play roles in cancers in a highly tissue-specific manner, but its role in the carcinogenesis and metastasis of head and neck squamous cell carcinoma (HNSCC) remains unclear. Here, we detected PRMT5 expression in HNSCC tissues and performed series of in vivo and in vitro assays to investigate the function and mechanism of PRMT5 in HNSCC. We found that PRMT5 was overexpressed in dysplastic and cancer tissues, and associated with lymph node metastasis and worse patient survival. PRMT5 knockdown repressed the malignant phenotype of HNSCC cells in vitro and in vivo. PRMT5 specific inhibitor blocked the formation of precancerous lesion and HNSCC in 4NQO-induced tongue carcinogenesis model, prevented lymph node metastasis in tongue orthotopic xenograft model and inhibited cancer development in subcutaneous xenograft model and Patient-Derived tumor Xenograft (PDX) model. Mechanistically, PRMT5-catalyzed H3R2me2s promotes the enrichment of H3K4me3 in the Twist1 promoter region by recruiting WDR5, and subsequently activates the transcription of Twist1. The rescue experiments indicated that overexpressed Twist1 abrogated the inhibition of cell invasion induced by PRMT5 inhibitor. In summary, this study elucidates that PRMT5 inhibition could reduce H3K4me3-mediated Twist1 transcription and retard the carcinogenesis and metastasis of HNSCC.
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Affiliation(s)
- Zhaona Fan
- Hostpital of Stomatology, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, PR China
| | - Lihong He
- Hostpital of Stomatology, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, PR China
| | - Mianxiang Li
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, PR China
| | - Ruoyan Cao
- Hostpital of Stomatology, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, PR China
| | - Miao Deng
- Hostpital of Stomatology, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, PR China
| | - Fan Ping
- Hostpital of Stomatology, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, PR China
| | - Xueyi Liang
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, PR China
| | - Yuan He
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, PR China
| | - Tong Wu
- Hostpital of Stomatology, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, PR China
| | - Xiaoan Tao
- Hostpital of Stomatology, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, PR China
| | - Jian Xu
- Center for Craniofacial Molecular Biology, School of Dentistry, University of Southern California, Los Angeles, CA, USA
| | - Bin Cheng
- Hostpital of Stomatology, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, PR China.
| | - Juan Xia
- Hostpital of Stomatology, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, PR China.
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Campbell SA, McDonald CL, Krentz NAJ, Lynn FC, Hoffman BG. TrxG Complex Catalytic and Non-catalytic Activity Play Distinct Roles in Pancreas Progenitor Specification and Differentiation. Cell Rep 2020; 28:1830-1844.e6. [PMID: 31412250 DOI: 10.1016/j.celrep.2019.07.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 06/04/2019] [Accepted: 07/12/2019] [Indexed: 02/06/2023] Open
Abstract
Appropriate regulation of genes that coordinate pancreas progenitor proliferation and differentiation is required for pancreas development. Here, we explore the role of H3K4 methylation and the Trithorax group (TrxG) complexes in mediating gene expression during pancreas development. Disruption of TrxG complex assembly, but not catalytic activity, prevented endocrine cell differentiation in pancreas progenitor spheroids. In vivo loss of TrxG catalytic activity in PDX1+ cells increased apoptosis and the fraction of progenitors in the G1 phase of the cell cycle. Pancreas progenitors were reallocated to the acinar lineage, primarily at the expense of NEUROG3+ endocrine progenitors. Later in development, acinar and endocrine cell numbers were decreased, and increased gene expression variance and reduced terminal marker activation in acinar cells led to their incomplete differentiation. These findings demonstrate that TrxG co-activator activity is required for gene induction, whereas TrxG catalytic activity and H3K4 methylation help maintain transcriptional stability.
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Affiliation(s)
- Stephanie A Campbell
- Department of Surgery, University of British Columbia, Vancouver, BC V5Z 4E3, Canada; Diabetes Research Group, British Columbia Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada
| | - Cassandra L McDonald
- Department of Surgery, University of British Columbia, Vancouver, BC V5Z 4E3, Canada
| | - Nicole A J Krentz
- Department of Surgery, University of British Columbia, Vancouver, BC V5Z 4E3, Canada; Diabetes Research Group, British Columbia Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada
| | - Francis C Lynn
- Department of Surgery, University of British Columbia, Vancouver, BC V5Z 4E3, Canada; Diabetes Research Group, British Columbia Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada
| | - Brad G Hoffman
- Department of Surgery, University of British Columbia, Vancouver, BC V5Z 4E3, Canada; Diabetes Research Group, British Columbia Children's Hospital Research Institute, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada.
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Sugeedha J, Gautam J, Tyagi S. SET1/MLL family of proteins: functions beyond histone methylation. Epigenetics 2020; 16:469-487. [PMID: 32795105 PMCID: PMC8078731 DOI: 10.1080/15592294.2020.1809873] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The SET1 family of enzymes are well known for their involvement in the histone 3 lysine 4 (H3K4) methylation, a conserved trait of euchromatin associated with transcriptional activation. These methyltransferases are distinct, and involved in various biological functions in the cell. Impairment in the function of SET1 family members leads to a number of abnormalities such as skeletal and neurological defects, leukaemogenesis and even lethality. Tremendous progress has been made in understanding the unique biological roles and the mechanism of SET1 enzymes in context with H3K4 methylation/canonical functions. However, in recent years, several studies have indicated the novel role of SET1 family proteins, other than H3K4 methylation, which are equally important for cellular functions. In this review, we focus on these non-canonical function of SET1 family members.
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Affiliation(s)
- Jeyapal Sugeedha
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
| | - Jyoti Gautam
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
| | - Shweta Tyagi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
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36
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Janna A, Davarinejad H, Joshi M, Couture JF. Structural Paradigms in the Recognition of the Nucleosome Core Particle by Histone Lysine Methyltransferases. Front Cell Dev Biol 2020; 8:600. [PMID: 32850785 PMCID: PMC7412744 DOI: 10.3389/fcell.2020.00600] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/19/2020] [Indexed: 12/18/2022] Open
Abstract
Post-translational modifications (PTMs) of histone proteins play essential functions in shaping chromatin environment. Alone or in combination, these PTMs create templates recognized by dedicated proteins or change the chemistry of chromatin, enabling a myriad of nuclear processes to occur. Referred to as cross-talk, the positive or negative impact of a PTM on another PTM has rapidly emerged as a mechanism controlling nuclear transactions. One of those includes the stimulatory functions of histone H2B ubiquitylation on the methylation of histone H3 on K79 and K4 by Dot1L and COMPASS, respectively. While these findings were established early on, the structural determinants underlying the positive impact of H2B ubiquitylation on H3K79 and H3K4 methylation were resolved only recently. We will also review the molecular features controlling these cross-talks and the impact of H3K27 tri-methylation on EZH2 activity when embedded in the PRC2 complex.
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Affiliation(s)
- Ashley Janna
- Ottawa Institute of Systems Biology, Shanghai Institute of Materia Medica-University of Ottawa Research Center in Systems and Personalized Pharmacology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Hossein Davarinejad
- Ottawa Institute of Systems Biology, Shanghai Institute of Materia Medica-University of Ottawa Research Center in Systems and Personalized Pharmacology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Monika Joshi
- Ottawa Institute of Systems Biology, Shanghai Institute of Materia Medica-University of Ottawa Research Center in Systems and Personalized Pharmacology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Jean-Francois Couture
- Ottawa Institute of Systems Biology, Shanghai Institute of Materia Medica-University of Ottawa Research Center in Systems and Personalized Pharmacology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
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37
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Roston A, Evans D, Gill H, McKinnon M, Isidor B, Cogné B, Mwenifumbo J, van Karnebeek C, An J, Jones SJM, Farrer M, Demos M, Connolly M, Gibson WT. SETD1B-associated neurodevelopmental disorder. J Med Genet 2020; 58:196-204. [PMID: 32546566 DOI: 10.1136/jmedgenet-2019-106756] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/11/2020] [Accepted: 04/14/2020] [Indexed: 01/04/2023]
Abstract
BACKGROUND Dysfunction of histone methyltransferases and chromatin modifiers has been implicated in complex neurodevelopmental syndromes and cancers. SETD1B encodes a lysine-specific methyltransferase that assists in transcriptional activation of genes by depositing H3K4 methyl marks. Previous reports of patients with rare variants in SETD1B describe a distinctive phenotype that includes seizures, global developmental delay and intellectual disability. METHODS Two of the patients described herein were identified via genome-wide and exome-wide testing, with microarray and research-based exome, through the CAUSES (Clinical Assessment of the Utility of Sequencing and Evaluation as a Service) Research Clinic at the University of British Columbia. The third Vancouver patient had clinical trio exome sequencing through Blueprint Genetics. The fourth patient underwent singleton exome sequencing in Nantes, with subsequent recruitment to this cohort through GeneMatcher. RESULTS Here we present clinical reports of four patients with rare coding variants in SETD1B that demonstrate a shared phenotype, including intellectual disability, language delay, conserved musculoskeletal findings and seizures that may be treatment-refractory. We include supporting evidence from next-generation sequencing among a cohort of paediatric patients with epilepsy. CONCLUSION Rare coding variants in SETD1B can cause a diagnosable syndrome and could contribute as a risk factor for epilepsy, autism and other neurodevelopmental phenotypes. In the long term, some patients may also be at increased risk for cancers and other complex diseases. Thus, longitudinal studies are required to further elucidate the precise role of SETD1B in neurodevelopmental disorders and other systemic disease.
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Affiliation(s)
- Alexandra Roston
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Dan Evans
- Centre for Applied Neurogenetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Harinder Gill
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada.,Provincial Medical Genetics Program, BC Women's Hospital and Health Centre, Vancouver, British Columbia, Canada
| | - Margaret McKinnon
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Bertrand Isidor
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, Pays de la Loire, France
| | - Benjamin Cogné
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Nantes, Nantes, Pays de la Loire, France.,INSERM, CNRS, UNIV Nantes, l'institut du thorax, Nantes, Frances
| | - Jill Mwenifumbo
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Clara van Karnebeek
- Department of Pediatrics, Emma Children's Hospital, Amsterdam Gastroenterology and Metabolism, Amsterdam University Medical Centres, University of Amsterdam, Amsterdam, Netherlands.,Department of Pediatrics, Radboud Centre for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Jianghong An
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Matthew Farrer
- Centre for Applied Neurogenetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Michelle Demos
- Division of Neurology, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mary Connolly
- Division of Neurology, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - William T Gibson
- Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
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38
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Tian J, Teuscher KB, Aho ER, Alvarado JR, Mills JJ, Meyers KM, Gogliotti RD, Han C, Macdonald JD, Sai J, Shaw JG, Sensintaffar JL, Zhao B, Rietz TA, Thomas LR, Payne WG, Moore WJ, Stott GM, Kondo J, Inoue M, Coffey RJ, Tansey WP, Stauffer SR, Lee T, Fesik SW. Discovery and Structure-Based Optimization of Potent and Selective WD Repeat Domain 5 (WDR5) Inhibitors Containing a Dihydroisoquinolinone Bicyclic Core. J Med Chem 2020; 63:656-675. [PMID: 31858797 PMCID: PMC6986559 DOI: 10.1021/acs.jmedchem.9b01608] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
WD repeat domain 5 (WDR5) is a member of the WD40-repeat protein family that plays a critical role in multiple chromatin-centric processes. Overexpression of WDR5 correlates with a poor clinical outcome in many human cancers, and WDR5 itself has emerged as an attractive target for therapy. Most drug-discovery efforts center on the WIN site of WDR5 that is responsible for the recruitment of WDR5 to chromatin. Here, we describe discovery of a novel WDR5 WIN site antagonists containing a dihydroisoquinolinone bicyclic core using a structure-based design. These compounds exhibit picomolar binding affinity and selective concentration-dependent antiproliferative activities in sensitive MLL-fusion cell lines. Furthermore, these WDR5 WIN site binders inhibit proliferation in MYC-driven cancer cells and reduce MYC recruitment to chromatin at MYC/WDR5 co-bound genes. Thus, these molecules are useful probes to study the implication of WDR5 inhibition in cancers and serve as a potential starting point toward the discovery of anti-WDR5 therapeutics.
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Affiliation(s)
- Jianhua Tian
- Chemical Synthesis Core, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Kevin B. Teuscher
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Erin R. Aho
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Joseph R. Alvarado
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Jonathan J. Mills
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Kenneth M. Meyers
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Rocco D. Gogliotti
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Changho Han
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Jonathan D. Macdonald
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Jiqing Sai
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - J. Grace Shaw
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - John L. Sensintaffar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Bin Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Tyson A. Rietz
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Lance R. Thomas
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - William G. Payne
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - William J. Moore
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Gordon M. Stott
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Jumpei Kondo
- Department of Clinical Bio-resource Research and Development, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
- Department of Biochemistry, Osaka International Cancer Institute, Osaka, 541-8567, Japan
| | - Masahiro Inoue
- Department of Clinical Bio-resource Research and Development, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
- Department of Biochemistry, Osaka International Cancer Institute, Osaka, 541-8567, Japan
| | - Robert J. Coffey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - William P. Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Shaun R. Stauffer
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Taekyu Lee
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Stephen W. Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, USA
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39
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Lavery WJ, Barski A, Wiley S, Schorry EK, Lindsley AW. KMT2C/D COMPASS complex-associated diseases [K CDCOM-ADs]: an emerging class of congenital regulopathies. Clin Epigenetics 2020; 12:10. [PMID: 31924266 PMCID: PMC6954584 DOI: 10.1186/s13148-019-0802-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/23/2019] [Indexed: 12/15/2022] Open
Abstract
The type 2 lysine methyltransferases KMT2C and KMT2D are large, enzymatically active scaffold proteins that form the core of nuclear regulatory structures known as KMT2C/D COMPASS complexes (complex of proteins associating with Set1). These evolutionarily conserved proteins regulate DNA promoter and enhancer elements, modulating the activity of diverse cell types critical for embryonic morphogenesis, central nervous system development, and post-natal survival. KMT2C/D COMPASS complexes and their binding partners enhance active gene expression of specific loci via the targeted modification of histone-3 tail residues, in general promoting active euchromatic conformations. Over the last 20 years, mutations in five key COMPASS complex genes have been linked to three human congenital syndromes: Kabuki syndrome (type 1 [KMT2D] and 2 [KDM6A]), Rubinstein-Taybi syndrome (type 1 [CBP] and 2 [EP300]), and Kleefstra syndrome type 2 (KMT2C). Here, we review the composition and biochemical function of the KMT2 complexes. The specific cellular and embryonic roles of the KMT2C/D COMPASS complex are highlight with a focus on clinically relevant mechanisms sensitive to haploinsufficiency. The phenotypic similarities and differences between the members of this new family of disorders are outlined and emerging therapeutic strategies are detailed.
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Affiliation(s)
- William J Lavery
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center (CCHMC), 3333 Burnet Avenue, Cincinnati, OH, 45229-3026, USA
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center (CCHMC), 3333 Burnet Avenue, Cincinnati, OH, 45229-3026, USA
- Division of Human Genetics, CCHMC, Cincinnati, OH, USA
| | - Susan Wiley
- Division of Developmental and Behavioral Pediatrics, CCHMC, Cincinnati, OH, USA
| | | | - Andrew W Lindsley
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center (CCHMC), 3333 Burnet Avenue, Cincinnati, OH, 45229-3026, USA.
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Kaustov L, Lemak A, Wu H, Faini M, Fan L, Fang X, Zeng H, Duan S, Allali-Hassani A, Li F, Wei Y, Vedadi M, Aebersold R, Wang Y, Houliston S, Arrowsmith CH. The MLL1 trimeric catalytic complex is a dynamic conformational ensemble stabilized by multiple weak interactions. Nucleic Acids Res 2019; 47:9433-9447. [PMID: 31400120 PMCID: PMC6755125 DOI: 10.1093/nar/gkz697] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/22/2019] [Accepted: 07/31/2019] [Indexed: 11/14/2022] Open
Abstract
Histone H3K4 methylation is an epigenetic mark associated with actively transcribed genes. This modification is catalyzed by the mixed lineage leukaemia (MLL) family of histone methyltransferases including MLL1, MLL2, MLL3, MLL4, SET1A and SET1B. The catalytic activity of this family is dependent on interactions with additional conserved proteins, but the structural basis for subunit assembly and the mechanism of regulation is not well understood. We used a hybrid methods approach to study the assembly and biochemical function of the minimally active MLL1 complex (MLL1, WDR5 and RbBP5). A combination of small angle X-ray scattering, cross-linking mass spectrometry, nuclear magnetic resonance spectroscopy and computational modeling were used to generate a dynamic ensemble model in which subunits are assembled via multiple weak interaction sites. We identified a new interaction site between the MLL1 SET domain and the WD40 β-propeller domain of RbBP5, and demonstrate the susceptibility of the catalytic function of the complex to disruption of individual interaction sites.
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Affiliation(s)
- Lilia Kaustov
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, ON M5G 2M9, Canada
- Department of Anesthesia, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
| | - Alexander Lemak
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, ON M5G 2M9, Canada
| | - Hong Wu
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
| | - Marco Faini
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Lixin Fan
- The Small-Angel X-ray Scattering Core Facility, Center for Cancer Research of National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702, USA
| | - Xianyang Fang
- The Small-Angel X-ray Scattering Core Facility, Center for Cancer Research of National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702, USA
| | - Hong Zeng
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
| | - Shili Duan
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, ON M5G 2M9, Canada
| | - Abdellah Allali-Hassani
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
| | - Yong Wei
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
- Faculty of Science, University of Zürich, 8057 Zürich, Switzerland
| | - Yunxing Wang
- The Small-Angel X-ray Scattering Core Facility, Center for Cancer Research of National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702, USA
| | - Scott Houliston
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, ON M5G 2M9, Canada
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, ON M5G 2M9, Canada
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
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41
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Ye F, Huang J, Wang H, Luo C, Zhao K. Targeting epigenetic machinery: Emerging novel allosteric inhibitors. Pharmacol Ther 2019; 204:107406. [PMID: 31521697 DOI: 10.1016/j.pharmthera.2019.107406] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2019] [Indexed: 12/13/2022]
Abstract
Epigenetics has emerged as an extremely exciting fast-growing area of biomedical research in post genome era. Epigenetic dysfunction is tightly related with various diseases such as cancer and aging related degeneration, potentiating epigenetics modulators as important therapeutics targets. Indeed, inhibitors of histone deacetylase and DNA methyltransferase have been approved for treating blood tumor malignancies, whereas inhibitors of histone methyltransferase and histone acetyl-lysine recognizer bromodomain are in clinical stage. However, it remains a great challenge to discover potent and selective inhibitors by targeting catalytic site, as the same subfamily of epigenetic enzymes often share high sequence identity and very conserved catalytic core pocket. It is well known that epigenetic modifications are usually carried out by multi-protein complexes, and activation of catalytic subunit is often tightly regulated by other interactive protein component, especially in disease conditions. Therefore, it is not unusual that epigenetic complex machinery may exhibit allosteric regulation site induced by protein-protein interactions. Targeting allosteric site emerges as a compelling alternative strategy to develop epigenetic drugs with enhanced druggability and pharmacological profiles. In this review, we highlight recent progress in the development of allosteric inhibitors for epigenetic complexes through targeting protein-protein interactions. We also summarized the status of clinical applications of those inhibitors. Finally, we provide perspectives of future novel allosteric epigenetic machinery modulators emerging from otherwise undruggable single protein target.
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Affiliation(s)
- Fei Ye
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, China; College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018; Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China
| | - Jing Huang
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hongbo Wang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, China; Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China.
| | - Cheng Luo
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, South Dong Qing Road, Guizhou 550025, China.
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, China; Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China.
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42
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Wingelhofer B, Somervaille TCP. Emerging Epigenetic Therapeutic Targets in Acute Myeloid Leukemia. Front Oncol 2019; 9:850. [PMID: 31552175 PMCID: PMC6743337 DOI: 10.3389/fonc.2019.00850] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/19/2019] [Indexed: 01/23/2023] Open
Abstract
Acute myeloid leukemia (AML) is a genetically heterogeneous malignancy for which treatment options have been largely limited to cytotoxic chemotherapy for the past four decades. Next-generation sequencing and other approaches have identified a spectrum of genomic and epigenomic alterations that contribute to AML initiation and maintenance. The key role of epigenetic modifiers and the reversibility of epigenetic changes have paved the way for evaluation of a new set of drug targets, and facilitated the design of novel candidate treatment strategies. More recently, seven new targeted therapies have been FDA-approved demonstrating successful implementation of the past decades' research. In this review, we will summarize the most recent advances in targeted therapeutics designed for a focused group of key epigenetic regulators in AML, outline their mechanism of action and their current status in clinical development. Furthermore, we will discuss promising new approaches for epigenetic targeted treatment in AML which are currently being tested in pre-clinical trials.
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Affiliation(s)
| | - Tim C. P. Somervaille
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
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43
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Hillier C, Pardo M, Yu L, Bushell E, Sanderson T, Metcalf T, Herd C, Anar B, Rayner JC, Billker O, Choudhary JS. Landscape of the Plasmodium Interactome Reveals Both Conserved and Species-Specific Functionality. Cell Rep 2019; 28:1635-1647.e5. [PMID: 31390575 PMCID: PMC6693557 DOI: 10.1016/j.celrep.2019.07.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/28/2019] [Accepted: 07/08/2019] [Indexed: 11/16/2022] Open
Abstract
Malaria represents a major global health issue, and the identification of new intervention targets remains an urgent priority. This search is hampered by more than one-third of the genes of malaria-causing Plasmodium parasites being uncharacterized. We report a large-scale protein interaction network in Plasmodium schizonts, generated by combining blue native-polyacrylamide electrophoresis with quantitative mass spectrometry and machine learning. This integrative approach, spanning 3 species, identifies >20,000 putative protein interactions, organized into 600 protein clusters. We validate selected interactions, assigning functions in chromatin regulation to previously unannotated proteins and suggesting a role for an EELM2 domain-containing protein and a putative microrchidia protein as mechanistic links between AP2-domain transcription factors and epigenetic regulation. Our interactome represents a high-confidence map of the native organization of core cellular processes in Plasmodium parasites. The network reveals putative functions for uncharacterized proteins, provides mechanistic and structural insight, and uncovers potential alternative therapeutic targets.
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Affiliation(s)
- Charles Hillier
- Developmental Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Mercedes Pardo
- Functional Proteomics, The Institute of Cancer Research, London SW7 3RP, UK.
| | - Lu Yu
- Functional Proteomics, The Institute of Cancer Research, London SW7 3RP, UK
| | - Ellen Bushell
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden, Umeå University, 901 87 Umeå, Sweden
| | - Theo Sanderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Tom Metcalf
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Colin Herd
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Burcu Anar
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Julian C Rayner
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Oliver Billker
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden, Umeå University, 901 87 Umeå, Sweden.
| | - Jyoti S Choudhary
- Functional Proteomics, The Institute of Cancer Research, London SW7 3RP, UK.
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44
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Worden EJ, Wolberger C. Activation and regulation of H2B-Ubiquitin-dependent histone methyltransferases. Curr Opin Struct Biol 2019; 59:98-106. [PMID: 31229920 DOI: 10.1016/j.sbi.2019.05.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/06/2019] [Accepted: 05/09/2019] [Indexed: 12/22/2022]
Abstract
Covalent modifications of histone proteins regulate a wide variety of cellular processes. Methylation of histone H3K79 and H3K4 is associated with active transcription and is catalyzed by Dot1L and Set1, respectively. Both Dot1L and Set1 are activated by prior ubiquitination of histone H2B on K120 in a process termed 'histone crosstalk'. Recent structures of Dot1L bound to a ubiquitinated nucleosome revealed how Dot1L is activated by ubiquitin and how Dot1L distorts the nucleosome to access its substrate. Structures of Dot1L-interacting proteins have provided insight into how Dot1L is recruited to sites of active transcription. Cryo-EM and crystallographic studies of the complex of proteins associated with Set1 (COMPASS), uncovered the architecture of COMPASS and how Set1 is activated upon complex assembly.
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Affiliation(s)
- Evan J Worden
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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45
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Lu K, Tao H, Si X, Chen Q. The Histone H3 Lysine 4 Presenter WDR5 as an Oncogenic Protein and Novel Epigenetic Target in Cancer. Front Oncol 2018; 8:502. [PMID: 30488017 PMCID: PMC6246693 DOI: 10.3389/fonc.2018.00502] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/15/2018] [Indexed: 11/13/2022] Open
Abstract
The histone H3 lysine 4 (H3K4) presenter WDR5 forms protein complexes with H3K4 methyltransferases MLL1-MLL4 and binding partner proteins including RBBP5, ASH2L, and DPY30, and plays a key role in histone H3K4 trimethylation, chromatin remodeling, transcriptional activation of target genes, normal biology, and diseases such as MLL-rearranged leukemia. By forming protein complexes with other proteins such as Myc, WDR5 induces transcriptional activation of key oncogenes, tumor cell cycle progression, DNA replication, cell proliferation, survival, tumor initiation, progression, invasion, and metastasis of cancer of a variety of organ origins. Several small molecule MLL/WDR5 protein-protein interaction inhibitors, such as MM-401, MM-589, WDR5-0103, Piribedil, and OICR-9429, have been confirmed to reduce H3K4 trimethylation, oncogenic gene expression, cell cycle progression, cancer cell proliferation, survival and resistance to chemotherapy without general toxicity to normal cells. Derivatives of the MLL/WDR5 interaction inhibitors with improved pharmacokinetic properties and in vivo bioavailability are expected to have the potential to be trialed in cancer patients.
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Affiliation(s)
- Kebin Lu
- Department of Paediatrics, Shan Xian Central Hospital, Heze, China
| | - He Tao
- Department of Medical Oncology, Shan Xian Haijiya Hospital, Heze, China
| | - Xiaomin Si
- Department of Medical Oncology, Xian Yang Central Hospital, Xianyang, China
| | - Qingjuan Chen
- Department of Medical Oncology, Xian Yang Central Hospital, Xianyang, China
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46
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Kulkarni SS, Griffin JN, Date PP, Liem KF, Khokha MK. WDR5 Stabilizes Actin Architecture to Promote Multiciliated Cell Formation. Dev Cell 2018; 46:595-610.e3. [PMID: 30205038 PMCID: PMC6177229 DOI: 10.1016/j.devcel.2018.08.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 06/18/2018] [Accepted: 08/11/2018] [Indexed: 12/16/2022]
Abstract
The actin cytoskeleton is critical to shape cells and pattern intracellular organelles, which collectively drives tissue morphogenesis. In multiciliated cells (MCCs), apical actin drives expansion of the cell surface necessary to host hundreds of cilia. The apical actin also forms a lattice to uniformly distribute basal bodies. This apical actin network is dynamically remodeled, but the molecules that regulate its architecture remain poorly understood. We identify the chromatin modifier, WDR5, as a regulator of apical F-actin in MCCs. Unexpectedly in MCCs, WDR5 has a function independent of chromatin modification. We discover a scaffolding role for WDR5 between the basal body and F-actin. Specifically, WDR5 binds to basal bodies and migrates apically, where F-actin organizes around WDR5. Using a monomer trap for G-actin, we show that WDR5 stabilizes F-actin to maintain lattice architecture. In summary, we identify a non-chromatin role for WDR5 in stabilizing F-actin in MCCs.
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Affiliation(s)
- Saurabh S Kulkarni
- Pediatric Genomics Discovery Program, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Department of Pediatrics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - John N Griffin
- Pediatric Genomics Discovery Program, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Department of Pediatrics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Priya P Date
- Pediatric Genomics Discovery Program, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Department of Pediatrics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Karel F Liem
- Department of Pediatrics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Department of Pediatrics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
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47
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Crystal Structure of the COMPASS H3K4 Methyltransferase Catalytic Module. Cell 2018; 174:1106-1116.e9. [PMID: 30100181 PMCID: PMC6108940 DOI: 10.1016/j.cell.2018.06.038] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/08/2018] [Accepted: 06/20/2018] [Indexed: 01/07/2023]
Abstract
The SET1/MLL family of histone methyltransferases is conserved in eukaryotes and regulates transcription by catalyzing histone H3K4 mono-, di-, and tri-methylation. These enzymes form a common five-subunit catalytic core whose assembly is critical for their basal and regulated enzymatic activities through unknown mechanisms. Here, we present the crystal structure of the intact yeast COMPASS histone methyltransferase catalytic module consisting of Swd1, Swd3, Bre2, Sdc1, and Set1. The complex is organized by Swd1, whose conserved C-terminal tail not only nucleates Swd3 and a Bre2-Sdc1 subcomplex, but also joins Set1 to construct a regulatory pocket next to the catalytic site. This inter-subunit pocket is targeted by a previously unrecognized enzyme-modulating motif in Swd3 and features a doorstop-style mechanism dictating substrate selectivity among SET1/MLL family members. By spatially mapping the functional components of COMPASS, our results provide a structural framework for understanding the multifaceted functions and regulation of the H3K4 methyltransferase family.
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48
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Gupta A, Xu J, Lee S, Tsai ST, Zhou B, Kurosawa K, Werner MS, Koide A, Ruthenburg AJ, Dou Y, Koide S. Facile target validation in an animal model with intracellularly expressed monobodies. Nat Chem Biol 2018; 14:895-900. [PMID: 30013062 PMCID: PMC6103845 DOI: 10.1038/s41589-018-0099-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 06/07/2018] [Indexed: 11/16/2022]
Abstract
Rapidly determining the biological effect of perturbing a site within a potential drug target could guide drug discovery efforts but it remains challenging. Here, we describe a facile target validation approach that exploits monobodies, small synthetic binding proteins that can be fully functionally expressed in cells. We developed a potent and selective monobody to WDR5, a core component of the Mixed Lineage Leukemia (MLL) methyltransferase complex. The monobody bound to the MLL-interaction site of WDR5, the same site for small molecule inhibitors whose efficacy has been demonstrated in cells but not in animals. As a genetically encoded reagent, the monobody inhibited proliferation of an MLL-AF9 cell line in vitro, suppressed its leukemogenesis and conferred survival benefit in an in vivo mouse leukemia model. The capacity of this approach to readily bridge biochemical, structural, cellular characterization and tests in animal models may accelerate discovery and validation of druggable sites.
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Affiliation(s)
- Ankit Gupta
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Jing Xu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Shirley Lee
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Steven T Tsai
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Bo Zhou
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Kohei Kurosawa
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Michael S Werner
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | - Akiko Koide
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.,Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Alexander J Ruthenburg
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA. .,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA. .,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
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49
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Fang L, Teng H, Wang Y, Liao G, Weng L, Li Y, Wang X, Jin J, Jiao C, Chen L, Peng X, Chen J, Yang Y, Fang H, Han D, Li C, Jin X, Zhang S, Liu Z, Liu M, Wei Q, Liao L, Ge X, Zhao B, Zhou D, Qin HL, Zhou J, Wang P. SET1A-Mediated Mono-Methylation at K342 Regulates YAP Activation by Blocking Its Nuclear Export and Promotes Tumorigenesis. Cancer Cell 2018; 34:103-118.e9. [PMID: 30008322 DOI: 10.1016/j.ccell.2018.06.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 04/11/2018] [Accepted: 05/30/2018] [Indexed: 02/08/2023]
Abstract
YAP, a key effector of Hippo pathway, is activated by its translocation from cytoplasm to nucleus to regulate gene expression and promote tumorigenesis. Although the mechanism by which YAP is suppressed in cytoplasm has been well-studied, how the activated YAP is sequestered in the nucleus remains unknown. Here, we demonstrate that YAP is a nucleocytoplasmic shuttling protein and its nuclear export is controlled by SET1A-mediated mono-methylation of YAP at K342, which disrupts the binding of YAP to CRM1. YAP mimetic methylation knockin mice are more susceptible to colorectal tumorigenesis. Clinically, YAP K342 methylation is reversely correlated with cancer survival. Collectively, our study identifies SET1A-mediated mono-methylation at K342 as an essential regulatory mechanism for regulating YAP activity and tumorigenesis.
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Affiliation(s)
- Lan Fang
- Shanghai Tenth People's Hospital of Tongji University, School of Medicine and School of Life Science and Technology, Tongji University, Shanghai 200072, China
| | - Hongqi Teng
- Shanghai Tenth People's Hospital of Tongji University, School of Medicine and School of Life Science and Technology, Tongji University, Shanghai 200072, China
| | - Yilin Wang
- Department of Hepatic Surgery, Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Guanghong Liao
- Shanghai Key Laboratory of Regulatory Biology, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Linjun Weng
- Shanghai Tenth People's Hospital of Tongji University, School of Medicine and School of Life Science and Technology, Tongji University, Shanghai 200072, China
| | - Yaxu Li
- Shanghai Tenth People's Hospital of Tongji University, School of Medicine and School of Life Science and Technology, Tongji University, Shanghai 200072, China
| | - Xinbo Wang
- Shanghai Tenth People's Hospital of Tongji University, School of Medicine and School of Life Science and Technology, Tongji University, Shanghai 200072, China
| | - Jiali Jin
- Shanghai Tenth People's Hospital of Tongji University, School of Medicine and School of Life Science and Technology, Tongji University, Shanghai 200072, China
| | - Chenchen Jiao
- Shanghai Tenth People's Hospital of Tongji University, School of Medicine and School of Life Science and Technology, Tongji University, Shanghai 200072, China
| | - Lei Chen
- Shanghai Tenth People's Hospital of Tongji University, School of Medicine and School of Life Science and Technology, Tongji University, Shanghai 200072, China
| | - Xiaoping Peng
- Shanghai Tenth People's Hospital of Tongji University, School of Medicine and School of Life Science and Technology, Tongji University, Shanghai 200072, China
| | - Jiayu Chen
- School of Life Science and Technology, Tongji University, Shanghai 200072, China
| | - Yongzhi Yang
- Shanghai Tenth People's Hospital of Tongji University, School of Medicine and School of Life Science and Technology, Tongji University, Shanghai 200072, China
| | - Houqin Fang
- Shanghai Key Laboratory of Regulatory Biology, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Dongyan Han
- Shanghai Tenth People's Hospital of Tongji University, School of Medicine and School of Life Science and Technology, Tongji University, Shanghai 200072, China
| | - Cheng Li
- Shanghai Tenth People's Hospital of Tongji University, School of Medicine and School of Life Science and Technology, Tongji University, Shanghai 200072, China
| | - Xueling Jin
- Obstetrics and Gynecology Hospital of Fudan University, Fudan University, Shanghai 200032, China
| | - Shihao Zhang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Zhongchen Liu
- Shanghai Tenth People's Hospital of Tongji University, School of Medicine and School of Life Science and Technology, Tongji University, Shanghai 200072, China
| | - Min Liu
- Institute of Biomedical Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Shandong Collaborative Innovation Center of Cell Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, China
| | - Qing Wei
- Shanghai Tenth People's Hospital of Tongji University, School of Medicine and School of Life Science and Technology, Tongji University, Shanghai 200072, China
| | - Lujian Liao
- Shanghai Key Laboratory of Regulatory Biology, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
| | - Xin Ge
- Shanghai Tenth People's Hospital of Tongji University, School of Medicine and School of Life Science and Technology, Tongji University, Shanghai 200072, China
| | - Bin Zhao
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Zhejiang 310058, China
| | - Dawang Zhou
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Huan-Long Qin
- Shanghai Tenth People's Hospital of Tongji University, School of Medicine and School of Life Science and Technology, Tongji University, Shanghai 200072, China
| | - Jun Zhou
- Institute of Biomedical Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Shandong Collaborative Innovation Center of Cell Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, China
| | - Ping Wang
- Shanghai Tenth People's Hospital of Tongji University, School of Medicine and School of Life Science and Technology, Tongji University, Shanghai 200072, China.
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50
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WDR5 Facilitates Human Cytomegalovirus Replication by Promoting Capsid Nuclear Egress. J Virol 2018; 92:JVI.00207-18. [PMID: 29437978 DOI: 10.1128/jvi.00207-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 02/05/2018] [Indexed: 01/27/2023] Open
Abstract
WD repeat-containing protein 5 (WDR5) is essential for assembling the VISA-associated complex to induce a type I interferon antiviral response to Sendai virus infection. However, the roles of WDR5 in DNA virus infections are not well described. Here, we report that human cytomegalovirus exploits WDR5 to facilitate capsid nuclear egress. Overexpression of WDR5 in fibroblasts slightly enhanced the infectious virus yield. However, WDR5 knockdown dramatically reduced infectious virus titers with only a small decrease in viral genome replication or gene expression. Further investigation of late steps of viral replication found that WDR5 knockdown significantly impaired formation of the viral nuclear egress complex and induced substantially fewer infoldings of the inner nuclear membrane. In addition, fewer capsids were associated with these infoldings, and there were fewer capsids in the cytoplasm. Restoration of WDR5 partially reversed these effects. These results suggest that WDR5 knockdown impairs the nuclear egress of capsids, which in turn decreases virus titers. These findings reveal an important role for a host factor whose function(s) is usurped by a viral pathogen to promote efficient replication. Thus, WDR5 represents an interesting regulatory mechanism and a potential antiviral target.IMPORTANCE Human cytomegalovirus (HCMV) has a large (∼235-kb) genome with over 170 open reading frames and exploits numerous cellular factors to facilitate its replication. HCMV infection increases protein levels of WD repeat-containing protein 5 (WDR5) during infection, overexpression of WDR5 enhances viral replication, and knockdown of WDR5 dramatically attenuates viral replication. Our results indicate that WDR5 promotes the nuclear egress of viral capsids, the depletion of WDR5 resulting in a significant decrease in production of infectious virions. This is the first report that WDR5 favors HCMV, a DNA virus, replication and highlights a novel target for antiviral therapy.
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