151
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Macdonald JD, Simon SC, Han C, Wang F, Shaw JG, Howes JE, Sai J, Yuh JP, Camper D, Alicie BM, Alvarado J, Nikhar S, Payne W, Aho ER, Bauer JA, Zhao B, Phan J, Thomas LR, Rossanese OW, Tansey WP, Waterson AG, Stauffer SR, Fesik SW. Discovery and Optimization of Salicylic Acid-Derived Sulfonamide Inhibitors of the WD Repeat-Containing Protein 5-MYC Protein-Protein Interaction. J Med Chem 2019; 62:11232-11259. [PMID: 31724864 PMCID: PMC6933084 DOI: 10.1021/acs.jmedchem.9b01411] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The treatment of tumors driven by overexpression or amplification of MYC oncogenes remains a significant challenge in drug discovery. Here, we present a new strategy toward the inhibition of MYC via the disruption of the protein-protein interaction between MYC and its chromatin cofactor WD Repeat-Containing Protein 5. Blocking the association of these proteins is hypothesized to disrupt the localization of MYC to chromatin, thus disrupting the ability of MYC to sustain tumorigenesis. Utilizing a high-throughput screening campaign and subsequent structure-guided design, we identify small-molecule inhibitors of this interaction with potent in vitro binding affinity and report structurally related negative controls that can be used to study the effect of this disruption. Our work suggests that disruption of this protein-protein interaction may provide a path toward an effective approach for the treatment of multiple tumors and anticipate that the molecules disclosed can be used as starting points for future efforts toward compounds with improved drug-like properties.
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Affiliation(s)
- Jonathan D. Macdonald
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Selena Chacón Simon
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Changho Han
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Feng Wang
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - J. Grace Shaw
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Jennifer E. Howes
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Jiqing Sai
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Joannes P. Yuh
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Demarco Camper
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Bethany M. Alicie
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Joseph Alvarado
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Sameer Nikhar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - William Payne
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Erin R. Aho
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Joshua A. Bauer
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Bin Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Jason Phan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Lance R. Thomas
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Olivia W. Rossanese
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - William P. Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
| | - Alex G. Waterson
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37232
| | - Shaun R. Stauffer
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37232
| | - Stephen W. Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, 37232
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, 37232
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152
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Farahmand S, O’Connor C, Macoska JA, Zarringhalam K. Causal Inference Engine: a platform for directional gene set enrichment analysis and inference of active transcriptional regulators. Nucleic Acids Res 2019; 47:11563-11573. [PMID: 31701125 PMCID: PMC7145661 DOI: 10.1093/nar/gkz1046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/19/2019] [Accepted: 10/28/2019] [Indexed: 02/07/2023] Open
Abstract
Inference of active regulatory mechanisms underlying specific molecular and environmental perturbations is essential for understanding cellular response. The success of inference algorithms relies on the quality and coverage of the underlying network of regulator-gene interactions. Several commercial platforms provide large and manually curated regulatory networks and functionality to perform inference on these networks. Adaptation of such platforms for open-source academic applications has been hindered by the lack of availability of accurate, high-coverage networks of regulatory interactions and integration of efficient causal inference algorithms. In this work, we present CIE, an integrated platform for causal inference of active regulatory mechanisms form differential gene expression data. Using a regularized Gaussian Graphical Model, we construct a transcriptional regulatory network by integrating publicly available ChIP-seq experiments with gene-expression data from tissue-specific RNA-seq experiments. Our GGM approach identifies high confidence transcription factor (TF)-gene interactions and annotates the interactions with information on mode of regulation (activation vs. repression). Benchmarks against manually curated databases of TF-gene interactions show that our method can accurately detect mode of regulation. We demonstrate the ability of our platform to identify active transcriptional regulators by using controlled in vitro overexpression and stem-cell differentiation studies and utilize our method to investigate transcriptional mechanisms of fibroblast phenotypic plasticity.
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Affiliation(s)
- Saman Farahmand
- Computational Sciences PhD program, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Corey O’Connor
- Department of Computer Science, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Jill A Macoska
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Kourosh Zarringhalam
- Computational Sciences PhD program, University of Massachusetts Boston, Boston, MA 02125, USA
- Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
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153
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Shuai Y, Ma Z, Lu J, Feng J. LncRNA SNHG15: A new budding star in human cancers. Cell Prolif 2019; 53:e12716. [PMID: 31774607 PMCID: PMC6985667 DOI: 10.1111/cpr.12716] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/16/2019] [Accepted: 10/07/2019] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES Long non-coding RNAs (lncRNAs) represent an important group of non-coding RNAs (ncRNAs) with more than 200 nucleotides in length that are transcribed from the so-called genomic "dark matter." Mounting evidence has shown that lncRNAs have manifested a paramount function in the pathophysiology of human diseases, especially in the pathogenesis and progression of cancers. Despite the exponential growth in lncRNA publications, our understanding of regulatory mechanism of lncRNAs is still limited, and a lot of controversies remain in the current lncRNA knowledge.The purpose of this article is to explore the clinical significance and molecular mechanism of SNHG15 in tumors. MATERIALS & METHODS We have systematically searched the Pubmed, Web of Science, Embase and Cochrane databases. We provide an overview of current evidence concerning the functional role, mechanistic models and clinical utilities of SNHG15 in human cancers in this review. RESULTS Small nucleolar RNA host gene 15 (SNHG15), a novel lncRNA, is identified as a key regulator in tumorigenesis and progression of various human cancers, including colorectal cancer (CRC), gastric cancer (GC), pancreatic cancer (PC) and hepatocellular carcinoma (HCC). Dysregulation of SNHG15 has been revealed to be dramatically correlated with advanced clinicopathological factors and predicts poor prognosis, suggesting its potential clinical value as a promising biomarker and therapeutic target for cancer patients. CONCLUSIONS LncRNA SNHG15 may serve as a prospective and novel biomarker for molecular diagnosis and therapeutics in patients with cancer.
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Affiliation(s)
- You Shuai
- Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Zhonghua Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital and Institute, Beijing, China.,Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Beijing, China
| | - Jianwei Lu
- Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jifeng Feng
- Department of Medical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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154
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ZFP281 Recruits MYC to Active Promoters in Regulating Transcriptional Initiation and Elongation. Mol Cell Biol 2019; 39:MCB.00329-19. [PMID: 31570506 DOI: 10.1128/mcb.00329-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 09/24/2019] [Indexed: 02/02/2023] Open
Abstract
The roles of the MYC transcription factor in transcriptional regulation have been studied intensively. However, the general mechanism underlying the recruitment of MYC to chromatin is less clear. Here, we found that the Krüppel-like transcription factor ZFP281 plays important roles in recruiting MYC to active promoters in mouse embryonic stem cells. At the genome scale, ZFP281 is broadly associated with MYC, and the depletion of ZFP281 significantly reduces the levels of MYC and RNA polymerase II at the ZFP281- and MYC-cobound genes. Specially, we found that recruitment is required for the regulation of the Lin28a oncogene and pri-let-7 transcription. Our results therefore suggest a major role of ZFP281 in recruiting MYC to chromatin and the integration of ZFP281 and the MYC/LIN28A/Let-7 loop into a multilevel circuit.
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155
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Interaction of the oncoprotein transcription factor MYC with its chromatin cofactor WDR5 is essential for tumor maintenance. Proc Natl Acad Sci U S A 2019; 116:25260-25268. [PMID: 31767764 PMCID: PMC6911241 DOI: 10.1073/pnas.1910391116] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The oncoprotein transcription factor MYC is a validated but challenging anticancer target. In this work, we show that WDR5—a well-structured protein with druggable pockets—could be a focal point for effective anti-MYC therapies. We demonstrate that WDR5 recruits MYC to chromatin to control the expression of genes connected to protein synthesis, a process that is arguably deregulated in all cancers. We also show that disrupting the interaction between MYC and WDR5 causes existing tumors to regress. These findings raise the possibility that the MYC–WDR5 nexus could be targeted to treat cancer. The oncoprotein transcription factor MYC is overexpressed in the majority of cancers. Key to its oncogenic activity is the ability of MYC to regulate gene expression patterns that drive and maintain the malignant state. MYC is also considered a validated anticancer target, but efforts to pharmacologically inhibit MYC have failed. The dependence of MYC on cofactors creates opportunities for therapeutic intervention, but for any cofactor this requires structural understanding of how the cofactor interacts with MYC, knowledge of the role it plays in MYC function, and demonstration that disrupting the cofactor interaction will cause existing cancers to regress. One cofactor for which structural information is available is WDR5, which interacts with MYC to facilitate its recruitment to chromatin. To explore whether disruption of the MYC–WDR5 interaction could potentially become a viable anticancer strategy, we developed a Burkitt's lymphoma system that allows replacement of wild-type MYC for mutants that are defective for WDR5 binding or all known nuclear MYC functions. Using this system, we show that WDR5 recruits MYC to chromatin to control the expression of genes linked to biomass accumulation. We further show that disrupting the MYC–WDR5 interaction within the context of an existing cancer promotes rapid and comprehensive tumor regression in vivo. These observations connect WDR5 to a core tumorigenic function of MYC and establish that, if a therapeutic window can be established, MYC–WDR5 inhibitors could be developed as anticancer agents.
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156
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PTENα and PTENβ promote carcinogenesis through WDR5 and H3K4 trimethylation. Nat Cell Biol 2019; 21:1436-1448. [DOI: 10.1038/s41556-019-0409-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 09/20/2019] [Indexed: 12/18/2022]
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157
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Dennis ML, Morrow BJ, Dolezal O, Cuzzupe AN, Stupple AE, Newman J, Bentley J, Hattarki M, Nuttall SD, Foitzik RC, Street IP, Stupple PA, Monahan BJ, Peat TS. Fragment screening for a protein-protein interaction inhibitor to WDR5. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:064701. [PMID: 31768400 PMCID: PMC6859963 DOI: 10.1063/1.5122849] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/30/2019] [Indexed: 05/03/2023]
Abstract
The WD40-repeat protein WDR5 scaffolds various epigenetic writers and is a critical component of the mammalian SET/MLL histone methyltransferase complex. Dysregulation of the MLL1 catalytic function is associated with mixed-lineage leukemia, and antagonism of the WDR5-MLL1 interaction by small molecules has been proposed as a therapeutic strategy for MLL-rearranged cancers. Small molecule binders of the "WIN" site of WDR5 that cause displacement from chromatin have been additionally implicated to be of broader use in cancer treatment. In this study, a fragment screen with Surface Plasmon Resonance (SPR) was used to identify a highly ligand-efficient imidazole-containing compound that is bound in the WIN site. The subsequent medicinal chemistry campaign-guided by a suite of high-resolution cocrystal structures with WDR5-progressed the initial hit to a low micromolar binder. One outcome from this study is a moiety that substitutes well for the side chain of arginine; a tripeptide containing one such substitution was resolved in a high resolution structure (1.5 Å) with a binding mode analogous to the native tripeptide. SPR furthermore indicates a similar residence time (k d = ∼0.06 s-1) for these two analogs. This novel scaffold therefore represents a possible means to overcome the potential permeability issues of WDR5 ligands that possess highly basic groups like guanidine. The series reported here furthers the understanding of the WDR5 WIN site and functions as a starting point for the development of more potent WDR5 inhibitors that may serve as cancer therapeutics.
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Affiliation(s)
- Matthew L. Dennis
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria 3052, Australia
| | | | - Olan Dolezal
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria 3052, Australia
| | - Anthony N. Cuzzupe
- SYNthesis med chem (Australia) Pty Ltd, Bio21 Institute, 30 Flemington Road, Parkville, Victoria 3052, Australia
| | | | - Janet Newman
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria 3052, Australia
| | - John Bentley
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria 3052, Australia
| | - Meghan Hattarki
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria 3052, Australia
| | - Stewart D. Nuttall
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria 3052, Australia
| | | | | | | | | | - Thomas. S. Peat
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria 3052, Australia
- Author to whom correspondence should be addressed:
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158
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Omomyc Reveals New Mechanisms To Inhibit the MYC Oncogene. Mol Cell Biol 2019; 39:MCB.00248-19. [PMID: 31501275 PMCID: PMC6817756 DOI: 10.1128/mcb.00248-19] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/07/2019] [Indexed: 11/21/2022] Open
Abstract
The MYC oncogene is upregulated in human cancers by translocation, amplification, and mutation of cellular pathways that regulate Myc. Myc/Max heterodimers bind to E box sequences in the promoter regions of genes and activate transcription. The MYC oncogene is upregulated in human cancers by translocation, amplification, and mutation of cellular pathways that regulate Myc. Myc/Max heterodimers bind to E box sequences in the promoter regions of genes and activate transcription. The MYC inhibitor Omomyc can reduce the ability of MYC to bind specific box sequences in promoters of MYC target genes by binding directly to E box sequences as demonstrated by chromatin immunoprecipitation (CHIP). Here, we demonstrate by both a proximity ligation assay (PLA) and double chromatin immunoprecipitation (ReCHIP) that Omomyc preferentially binds to Max, not Myc, to mediate inhibition of MYC-mediated transcription by replacing MYC/MAX heterodimers with Omomyc/MAX heterodimers. The formation of Myc/Max and Omomyc/Max heterodimers occurs cotranslationally; Myc, Max, and Omomyc can interact with ribosomes and Max RNA under conditions in which ribosomes are intact. Taken together, our data suggest that the mechanism of action of Omomyc is to bind DNA as either a homodimer or a heterodimer with Max that is formed cotranslationally, revealing a novel mechanism to inhibit the MYC oncogene. We find that in vivo, Omomyc distributes quickly to kidneys and liver and has a short effective half-life in plasma, which could limit its use in vivo.
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159
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Filip D, Mraz M. The role of MYC in the transformation and aggressiveness of ‘indolent’ B-cell malignancies. Leuk Lymphoma 2019; 61:510-524. [DOI: 10.1080/10428194.2019.1675877] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Daniel Filip
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Haematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marek Mraz
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Haematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
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160
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Tesi A, de Pretis S, Furlan M, Filipuzzi M, Morelli MJ, Andronache A, Doni M, Verrecchia A, Pelizzola M, Amati B, Sabò A. An early Myc-dependent transcriptional program orchestrates cell growth during B-cell activation. EMBO Rep 2019; 20:e47987. [PMID: 31334602 PMCID: PMC6726900 DOI: 10.15252/embr.201947987] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 06/18/2019] [Accepted: 06/27/2019] [Indexed: 12/18/2022] Open
Abstract
Upon activation, lymphocytes exit quiescence and undergo substantial increases in cell size, accompanied by activation of energy-producing and anabolic pathways, widespread chromatin decompaction, and elevated transcriptional activity. These changes depend upon prior induction of the Myc transcription factor, but how Myc controls them remains unclear. We addressed this issue by profiling the response to LPS stimulation in wild-type and c-myc-deleted primary mouse B-cells. Myc is rapidly induced, becomes detectable on virtually all active promoters and enhancers, but has no direct impact on global transcriptional activity. Instead, Myc contributes to the swift up- and down-regulation of several hundred genes, including many known regulators of the aforementioned cellular processes. Myc-activated promoters are enriched for E-box consensus motifs, bind Myc at the highest levels, and show enhanced RNA Polymerase II recruitment, the opposite being true at down-regulated loci. Remarkably, the Myc-dependent signature identified in activated B-cells is also enriched in Myc-driven B-cell lymphomas: hence, besides modulation of new cancer-specific programs, the oncogenic action of Myc may largely rely on sustained deregulation of its normal physiological targets.
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Affiliation(s)
- Alessandra Tesi
- Center for Genomic Science of IIT@SEMMFondazione Istituto Italiano di Tecnologia (IIT)MilanItaly
| | - Stefano de Pretis
- Center for Genomic Science of IIT@SEMMFondazione Istituto Italiano di Tecnologia (IIT)MilanItaly
| | - Mattia Furlan
- Center for Genomic Science of IIT@SEMMFondazione Istituto Italiano di Tecnologia (IIT)MilanItaly
| | - Marco Filipuzzi
- Department of Experimental OncologyEuropean Institute of Oncology (IEO)‐IRCCSMilanItaly
| | - Marco J Morelli
- Center for Genomic Science of IIT@SEMMFondazione Istituto Italiano di Tecnologia (IIT)MilanItaly
- Present address:
Center for Translational Genomics and BioinformaticsIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Adrian Andronache
- Center for Genomic Science of IIT@SEMMFondazione Istituto Italiano di Tecnologia (IIT)MilanItaly
- Present address:
Experimental Therapeutics Program of IFOM ‐ The FIRC Institute of Molecular OncologyMilanItaly
| | - Mirko Doni
- Department of Experimental OncologyEuropean Institute of Oncology (IEO)‐IRCCSMilanItaly
| | - Alessandro Verrecchia
- Department of Experimental OncologyEuropean Institute of Oncology (IEO)‐IRCCSMilanItaly
| | - Mattia Pelizzola
- Center for Genomic Science of IIT@SEMMFondazione Istituto Italiano di Tecnologia (IIT)MilanItaly
| | - Bruno Amati
- Department of Experimental OncologyEuropean Institute of Oncology (IEO)‐IRCCSMilanItaly
| | - Arianna Sabò
- Department of Experimental OncologyEuropean Institute of Oncology (IEO)‐IRCCSMilanItaly
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161
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Yeganeh M, Praz V, Carmeli C, Villeneuve D, Rib L, Guex N, Herr W, Delorenzi M, Hernandez N. Differential regulation of RNA polymerase III genes during liver regeneration. Nucleic Acids Res 2019; 47:1786-1796. [PMID: 30597109 PMCID: PMC6393285 DOI: 10.1093/nar/gky1282] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/22/2018] [Accepted: 12/14/2018] [Indexed: 12/23/2022] Open
Abstract
Mouse liver regeneration after partial hepatectomy involves cells in the remaining tissue synchronously entering the cell division cycle. We have used this system and H3K4me3, Pol II and Pol III profiling to characterize adaptations in Pol III transcription. Our results broadly define a class of genes close to H3K4me3 and Pol II peaks, whose Pol III occupancy is high and stable, and another class, distant from Pol II peaks, whose Pol III occupancy strongly increases after partial hepatectomy. Pol III regulation in the liver thus entails both highly expressed housekeeping genes and genes whose expression can adapt to increased demand.
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Affiliation(s)
- Meghdad Yeganeh
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Viviane Praz
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Cristian Carmeli
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland.,Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Dominic Villeneuve
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Leonor Rib
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nicolas Guex
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Winship Herr
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Mauro Delorenzi
- Bioinformatics Core Facility, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Fundamental Oncology and the Ludwig Center for Cancer research, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
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162
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Hung KH, Woo YH, Lin IY, Liu CH, Wang LC, Chen HY, Chiang BL, Lin KI. The KDM4A/KDM4C/NF-κB and WDR5 epigenetic cascade regulates the activation of B cells. Nucleic Acids Res 2019; 46:5547-5560. [PMID: 29718303 PMCID: PMC6009645 DOI: 10.1093/nar/gky281] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 04/04/2018] [Indexed: 12/13/2022] Open
Abstract
T follicular helper (Tfh) cell-derived signals promote activation and proliferation of antigen-primed B cells. It remains unclear whether epigenetic regulation is involved in the B cell responses to Tfh cell-derived signals. Here, we demonstrate that Tfh cell-mimicking signals induce the expression of histone demethylases KDM4A and KDM4C, and the concomitant global down-regulation of their substrates, H3K9me3/me2, in B cells. Depletion of KDM4A and KDM4C potentiates B cell activation and proliferation in response to Tfh cell-derived signals. ChIP-seq and de novo motif analysis reveals NF-κB p65 as a binding partner of KDM4A and KDM4C. Their co-targeting to Wdr5, a MLL complex member promoting H3K4 methylation, up-regulates cell cycle inhibitors Cdkn2c and Cdkn3. Thus, Tfh cell-derived signals trigger KDM4A/KDM4C - WDR5 - Cdkn2c/Cdkn3 cascade in vitro, an epigenetic mechanism regulating proper proliferation of activated B cells. This pathway is dysregulated in B cells from systemic lupus erythematosus patients and may represent a pathological link.
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Affiliation(s)
- Kuo-Hsuan Hung
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yong H Woo
- Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - I-Ying Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chin-Hsiu Liu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.,PhD Program in Translational Medicine, Kaohsiung Medical University and Academia Sinica, Division of Allergy, Immunology and Rheumatology, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City 231, Taiwan
| | - Li-Chieh Wang
- Department of Pediatrics, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Hsin-Yu Chen
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Bor-Luen Chiang
- Department of Pediatrics, National Taiwan University Hospital, Taipei 100, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Kuo-I Lin
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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163
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Aho ER, Weissmiller AM, Fesik SW, Tansey WP. Targeting WDR5: A WINning Anti-Cancer Strategy? Epigenet Insights 2019; 12:2516865719865282. [PMID: 31360909 PMCID: PMC6640055 DOI: 10.1177/2516865719865282] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 07/01/2019] [Indexed: 12/11/2022] Open
Abstract
WDR5 is a component of multiple epigenetic regulatory complexes, including the mixed lineage leukemia (MLL)/SET complexes that deposit histone H3 lysine 4 methylation. Inhibitors of an arginine-binding cavity in WDR5, known as the WDR5-interaction (WIN) site, have been proposed to selectively kill MLL-rearranged malignancies via an epigenetic mechanism. We discovered potent WIN site inhibitors and found that they kill MLL cancer cells not through changes in histone methylation, but by displacing WDR5 from chromatin at protein synthesis genes, choking the translational capacity of these cells, and inducing death via a nucleolar stress response. The mechanism of action of WIN site inhibitors reveals new aspects of WDR5 function and forecasts broad therapeutic utility as anti-cancer agents.
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Affiliation(s)
- Erin R Aho
- Department of Cell and Developmental Biology, School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - April M Weissmiller
- Department of Cell and Developmental Biology, School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Stephen W Fesik
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - William P Tansey
- Department of Cell and Developmental Biology, School of Medicine, Vanderbilt University, Nashville, TN, USA
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Stewart-Morgan KR, Reverón-Gómez N, Groth A. Transcription Restart Establishes Chromatin Accessibility after DNA Replication. Mol Cell 2019; 75:284-297.e6. [DOI: 10.1016/j.molcel.2019.04.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/29/2019] [Accepted: 04/29/2019] [Indexed: 12/20/2022]
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165
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Hematopoietic stem and progenitor cell proliferation and differentiation requires the trithorax protein Ash2l. Sci Rep 2019; 9:8262. [PMID: 31164666 PMCID: PMC6547667 DOI: 10.1038/s41598-019-44720-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 05/20/2019] [Indexed: 12/18/2022] Open
Abstract
Post-translational modifications of core histones participate in controlling the expression of genes. Methylation of lysine 4 of histone H3 (H3K4), together with acetylation of H3K27, is closely associated with open chromatin and gene transcription. H3K4 methylation is catalyzed by KMT2 lysine methyltransferases that include the mixed-lineage leukemia 1–4 (MLL1-4) and SET1A and B enzymes. For efficient catalysis, all six require a core complex of four proteins, WDR5, RBBP5, ASH2L, and DPY30. We report that targeted disruption of Ash2l in the murine hematopoietic system results in the death of the mice due to a rapid loss of mature hematopoietic cells. However, lin−Sca1+Kit+ (LSK) cells, which are highly enriched in hematopoietic stem and multi-potent progenitor cells, accumulated in the bone marrow. The loss of Ash2l resulted in global reduction of H3K4 methylation and deregulated gene expression, including down-regulation of many mitosis-associated genes. As a consequence, LSK cells accumulated in the G2-phase of the cell cycle and were unable to proliferate and differentiate. In conclusion, Ash2l is essential for balanced gene expression and for hematopoietic stem and multi-potent progenitor cell physiology.
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166
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Xu W, Wang L, An Y, Ye J. Expression of WD Repeat Domain 5 (WDR5) is Associated with Progression and Reduced Prognosis in Papillary Thyroid Carcinoma. Med Sci Monit 2019; 25:3762-3770. [PMID: 31107859 PMCID: PMC6540649 DOI: 10.12659/msm.915847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background The WD repeat domain 5 (WDR5) is an essential component of methyltransferase complexes. The expression of WDR5 has been reported in several types of malignancy. This study aimed to investigate the expression of the WDR5 gene and protein in a human papillary carcinoma cell line in vitro, including the use WDR5 gene silencing, and the expression of the WDR5 protein in papillary thyroid carcinoma tissue, and clinicopathological characteristics including overall survival (OS). Material/Methods The role of WDR5 in proliferation and migration of the human papillary thyroid carcinoma cell line, KTC-1, was investigated using the cell counting kit-8 (CCK-8) assay and transwell assay after silencing WDR5 expression. Expression levels of WDR5 in 84 patients with papillary thyroid carcinoma were detected using immunohistochemistry. The correlation between WDR5 expression and clinicopathological features was analyzed using the chi-squared test. The prognostic role of WDR5 was evaluated by univariate analysis with the log-rank test, and by multivariate analysis with the Cox regression model. Results WDR5 expression promoted the proliferation and migration of the KTC-1 cells. In tumor tissue from patients with papillary thyroid carcinoma, low expression and high expression levels of WDR5 were found in 72.6% and 27.4%, respectively. Increased expression of WDR5 was significantly associated with lymphatic invasion and reduced survival rates. WDR5 expression was an independent negative prognostic biomarker. Conclusions Expression of WDR5 promoted cell proliferation and migration in vitro and was associated with reduced prognosis in patients with papillary thyroid carcinoma.
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Affiliation(s)
- Wenchao Xu
- Department of Endocrinology, Yidu Central Hospital of Weifang City, Weifang, Shandong, China (mainland)
| | - Lingling Wang
- Department of Endocrinology, Yidu Central Hospital of Weifang City, Weifang, Shandong, China (mainland)
| | - Ying An
- Department of Endocrinology, Yidu Central Hospital of Weifang City, Weifang, Shandong, China (mainland)
| | - Jing Ye
- Department of Oncology, Tong De Hospital of Zhejiang Province, Hangzhou, Zhejiang, China (mainland)
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167
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Wang XN, Su XX, Cheng SQ, Sun ZY, Huang ZS, Ou TM. MYC modulators in cancer: a patent review. Expert Opin Ther Pat 2019; 29:353-367. [PMID: 31068032 DOI: 10.1080/13543776.2019.1612878] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
INTRODUCTION The important role of MYC in tumorigenesis makes it particularly important to design MYC modulators. Over the past decade, researchers have raised a number of strategies for designing MYC modulators, some of which are already in clinical trials. This paper aims to review the patents of MYC modulators. AREAS COVERED The important biological relevance of c-MYC and the regulation pathways related to c-MYC are briefly introduced. Base on that, the MYC modulators reported in published patents and references primarily for cancer treatment are outlined, highlighting the structures and biological activities. EXPERT OPINION There has been a growing awareness of finding and designing MYC modulators as novel anticancer drugs over recent years. Patents involving the discovery, synthesis, and application of MYC modulators are particularly important for further development in this field. Although finding direct MYC inhibitors or binders is challenging, MYC cannot be simply defined as an undruggable target. There is still substantial evidence proving the concept that MYC modulators can benefit to the treatment of both human hematological malignancies and solid tumors. More efforts should be taken to improve the activity and specificity of MYC modulators.
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Affiliation(s)
- Xiao-Na Wang
- a School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou , Guangdong , China
| | - Xiao-Xuan Su
- a School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou , Guangdong , China
| | - Sui-Qi Cheng
- a School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou , Guangdong , China
| | - Zhi-Yin Sun
- a School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou , Guangdong , China
| | - Zhi-Shu Huang
- a School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou , Guangdong , China
| | - Tian-Miao Ou
- a School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou , Guangdong , China
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168
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Weissmiller AM, Wang J, Lorey SL, Howard GC, Martinez E, Liu Q, Tansey WP. Inhibition of MYC by the SMARCB1 tumor suppressor. Nat Commun 2019; 10:2014. [PMID: 31043611 PMCID: PMC6494882 DOI: 10.1038/s41467-019-10022-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/12/2019] [Indexed: 01/22/2023] Open
Abstract
SMARCB1 encodes the SNF5 subunit of the SWI/SNF chromatin remodeler. SNF5 also interacts with the oncoprotein transcription factor MYC and is proposed to stimulate MYC activity. The concept that SNF5 is a coactivator for MYC, however, is at odds with its role as a tumor-suppressor, and with observations that loss of SNF5 leads to activation of MYC target genes. Here, we reexamine the relationship between MYC and SNF5 using biochemical and genome-wide approaches. We show that SNF5 inhibits the DNA-binding ability of MYC and impedes target gene recognition by MYC in cells. We further show that MYC regulation by SNF5 is separable from its role in chromatin remodeling, and that reintroduction of SNF5 into SMARCB1-null cells mimics the primary transcriptional effects of MYC inhibition. These observations reveal that SNF5 antagonizes MYC and provide a mechanism to explain how loss of SNF5 can drive malignancy.
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Affiliation(s)
- April M Weissmiller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Jing Wang
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Shelly L Lorey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Gregory C Howard
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Ernest Martinez
- Department of Biochemistry, University of California at Riverside, Riverside, CA, 92521, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.
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169
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SNHG15 is a bifunctional MYC-regulated noncoding locus encoding a lncRNA that promotes cell proliferation, invasion and drug resistance in colorectal cancer by interacting with AIF. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:172. [PMID: 31014355 PMCID: PMC6480895 DOI: 10.1186/s13046-019-1169-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 04/07/2019] [Indexed: 02/08/2023]
Abstract
Background Thousands of long noncoding RNAs (lncRNAs) are aberrantly expressed in various types of cancers, however our understanding of their role in the disease is still very limited. Methods We applied RNAseq analysis from patient-derived data with validation in independent cohort of patients. We followed these studies with gene regulation analysis as well as experimental dissection of the role of the identified lncRNA by multiple in vitro and in vivo methods. Results We analyzed RNA-seq data from tumors of 456 CRC patients compared to normal samples, and identified SNHG15 as a potentially oncogenic lncRNA that encodes a snoRNA in one of its introns. The processed SNHG15 is overexpressed in CRC tumors and its expression is highly correlated with poor survival of patients. Interestingly, SNHG15 is more highly expressed in tumors with high levels of MYC expression, while MYC protein binds to two E-box motifs on SNHG15 sequence, indicating that SNHG15 transcription is directly regulated by the oncogene MYC. The depletion of SNHG15 by siRNA or CRISPR-Cas9 inhibits cell proliferation and invasion, decreases colony formation as well as the tumorigenic capacity of CRC cells, whereas its overexpression leads to opposite effects. Gene expression analysis performed upon SNHG15 inhibition showed changes in multiple relevant genes implicated in cancer progression, including MYC, NRAS, BAG3 or ERBB3. Several of these genes are functionally related to AIF, a protein that we found to specifically interact with SNHG15, suggesting that the SNHG15 acts, at least in part, by regulating the activity of AIF. Interestingly, ROS levels, which are directly regulated by AIF, show a significant reduction in SNHG15-depleted cells. Moreover, knockdown of SNHG15 increases the sensitiveness of the cells to 5-FU, while its overexpression renders them more resistant to the chemotherapeutic drug. Conclusion Altogether, these results describe an important role of SNHG15 in promoting colon cancer and mediating drug resistance, suggesting its potential as prognostic marker and target for RNA-based therapies. Electronic supplementary material The online version of this article (10.1186/s13046-019-1169-0) contains supplementary material, which is available to authorized users.
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170
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Aho ER, Wang J, Gogliotti RD, Howard GC, Phan J, Acharya P, Macdonald JD, Cheng K, Lorey SL, Lu B, Wenzel S, Foshage AM, Alvarado J, Wang F, Shaw JG, Zhao B, Weissmiller AM, Thomas LR, Vakoc CR, Hall MD, Hiebert SW, Liu Q, Stauffer SR, Fesik SW, Tansey WP. Displacement of WDR5 from Chromatin by a WIN Site Inhibitor with Picomolar Affinity. Cell Rep 2019; 26:2916-2928.e13. [PMID: 30865883 PMCID: PMC6448596 DOI: 10.1016/j.celrep.2019.02.047] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/17/2019] [Accepted: 02/12/2019] [Indexed: 01/09/2023] Open
Abstract
The chromatin-associated protein WDR5 is a promising target for pharmacological inhibition in cancer. Drug discovery efforts center on the blockade of the "WIN site" of WDR5, a well-defined pocket that is amenable to small molecule inhibition. Various cancer contexts have been proposed to be targets for WIN site inhibitors, but a lack of understanding of WDR5 target genes and of the primary effects of WIN site inhibitors hampers their utility. Here, by the discovery of potent WIN site inhibitors, we demonstrate that the WIN site links WDR5 to chromatin at a small cohort of loci, including a specific subset of ribosome protein genes. WIN site inhibitors rapidly displace WDR5 from chromatin and decrease the expression of associated genes, causing translational inhibition, nucleolar stress, and p53 induction. Our studies define a mode by which WDR5 engages chromatin and forecast that WIN site blockade could have utility against multiple cancer types.
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Affiliation(s)
- Erin R Aho
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rocco D Gogliotti
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Gregory C Howard
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jason Phan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Pankaj Acharya
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jonathan D Macdonald
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Ken Cheng
- National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Shelly L Lorey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Bin Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sabine Wenzel
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Audra M Foshage
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Joseph Alvarado
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Feng Wang
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - J Grace Shaw
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Bin Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - April M Weissmiller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Lance R Thomas
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | | | - Matthew D Hall
- National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Shaun R Stauffer
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Stephen W Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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Carabet LA, Rennie PS, Cherkasov A. Therapeutic Inhibition of Myc in Cancer. Structural Bases and Computer-Aided Drug Discovery Approaches. Int J Mol Sci 2018; 20:E120. [PMID: 30597997 PMCID: PMC6337544 DOI: 10.3390/ijms20010120] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/08/2018] [Accepted: 12/21/2018] [Indexed: 12/23/2022] Open
Abstract
Myc (avian myelocytomatosis viral oncogene homolog) represents one of the most sought after drug targets in cancer. Myc transcription factor is an essential regulator of cell growth, but in most cancers it is overexpressed and associated with treatment-resistance and lethal outcomes. Over 40 years of research and drug development efforts did not yield a clinically useful Myc inhibitor. Drugging the "undruggable" is problematic, as Myc inactivation may negatively impact its physiological functions. Moreover, Myc is a disordered protein that lacks effective binding pockets on its surface. It is well established that the Myc function is dependent on dimerization with its obligate partner, Max (Myc associated factor X), which together form a functional DNA-binding domain to activate genomic targets. Herein, we provide an overview of the knowledge accumulated to date on Myc regulation and function, its critical role in cancer, and summarize various strategies that are employed to tackle Myc-driven malignant transformation. We focus on important structure-function relationships of Myc with its interactome, elaborating structural determinants of Myc-Max dimer formation and DNA recognition exploited for therapeutic inhibition. Chronological development of small-molecule Myc-Max prototype inhibitors and corresponding binding sites are comprehensively reviewed and particular emphasis is placed on modern computational drug design methods. On the outlook, technological advancements may soon provide the so long-awaited Myc-Max clinical candidate.
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Affiliation(s)
- Lavinia A Carabet
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada.
| | - Paul S Rennie
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada.
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada.
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172
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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: 8.0] [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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173
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Kalkat M, Resetca D, Lourenco C, Chan PK, Wei Y, Shiah YJ, Vitkin N, Tong Y, Sunnerhagen M, Done SJ, Boutros PC, Raught B, Penn LZ. MYC Protein Interactome Profiling Reveals Functionally Distinct Regions that Cooperate to Drive Tumorigenesis. Mol Cell 2018; 72:836-848.e7. [PMID: 30415952 DOI: 10.1016/j.molcel.2018.09.031] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/09/2018] [Accepted: 09/21/2018] [Indexed: 12/14/2022]
Abstract
Transforming members of the MYC family (MYC, MYCL1, and MYCN) encode transcription factors containing six highly conserved regions, termed MYC homology boxes (MBs). By conducting proteomic profiling of the MB interactomes, we demonstrate that half of the MYC interactors require one or more MBs for binding. Comprehensive phenotypic analyses reveal that two MBs, MB0 and MBII, are universally required for transformation. MBII mediates interactions with acetyltransferase-containing complexes, enabling histone acetylation, and is essential for MYC-dependent tumor initiation. By contrast, MB0 mediates interactions with transcription elongation factors via direct binding to the general transcription factor TFIIF. MB0 is dispensable for tumor initiation but is a major accelerator of tumor growth. Notably, the full transforming activity of MYC can be restored by co-expression of the non-transforming MB0 and MBII deletion proteins, indicating that these two regions confer separate molecular functions, both of which are required for oncogenic MYC activity.
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Affiliation(s)
- Manpreet Kalkat
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Diana Resetca
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Corey Lourenco
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Pak-Kei Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Yong Wei
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Structural Genomics Consortium, Toronto, ON M5G 1L7, Canada
| | - Yu-Jia Shiah
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Natasha Vitkin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Yufeng Tong
- Structural Genomics Consortium, Toronto, ON M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5A 1A8, Canada
| | - Maria Sunnerhagen
- Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
| | - Susan J Done
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Brian Raught
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
| | - Linda Z Penn
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
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174
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Chen LL, Lin HP, Zhou WJ, He CX, Zhang ZY, Cheng ZL, Song JB, Liu P, Chen XY, Xia YK, Chen XF, Sun RQ, Zhang JY, Sun YP, Song L, Liu BJ, Du RK, Ding C, Lan F, Huang SL, Zhou F, Liu S, Xiong Y, Ye D, Guan KL. SNIP1 Recruits TET2 to Regulate c-MYC Target Genes and Cellular DNA Damage Response. Cell Rep 2018; 25:1485-1500.e4. [PMID: 30404004 PMCID: PMC6317994 DOI: 10.1016/j.celrep.2018.10.028] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 09/21/2018] [Accepted: 10/04/2018] [Indexed: 12/17/2022] Open
Abstract
The TET2 DNA dioxygenase regulates gene expression by catalyzing demethylation of 5-methylcytosine, thus epigenetically modulating the genome. TET2 does not contain a sequence-specific DNA-binding domain, and how it is recruited to specific genomic sites is not fully understood. Here we carried out a mammalian two-hybrid screen and identified multiple transcriptional regulators potentially interacting with TET2. The SMAD nuclear interacting protein 1 (SNIP1) physically interacts with TET2 and bridges TET2 to bind several transcription factors, including c-MYC. SNIP1 recruits TET2 to the promoters of c-MYC target genes, including those involved in DNA damage response and cell viability. TET2 protects cells from DNA damage-induced apoptosis dependending on SNIP1. Our observations uncover a mechanism for targeting TET2 to specific promoters through a ternary interaction with a co-activator and many sequence-specific DNA-binding factors. This study also reveals a TET2-SNIP1-c-MYC pathway in mediating DNA damage response, thereby connecting epigenetic control to maintenance of genome stability.
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Affiliation(s)
- Lei-Lei Chen
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Huai-Peng Lin
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Medical College of Xiamen University, Xiamen 361102, China
| | - Wen-Jie Zhou
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Chen-Xi He
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhi-Yong Zhang
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhou-Li Cheng
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jun-Bin Song
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Peng Liu
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xin-Yu Chen
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yu-Kun Xia
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xiu-Fei Chen
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ren-Qiang Sun
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jing-Ye Zhang
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yi-Ping Sun
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Lei Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for National Center for Protein Science (The PHOENIX Center), Beijing, China
| | - Bing-Jie Liu
- Fudan University Shanghai Cancer Center, Key Laboratory of Breast Cancer in Shanghai, Innovation Center for Cell Signaling Network, Cancer Institutes, Fudan University, Shanghai, China
| | - Rui-Kai Du
- Fudan University Shanghai Cancer Center, Key Laboratory of Breast Cancer in Shanghai, Innovation Center for Cell Signaling Network, Cancer Institutes, Fudan University, Shanghai, China
| | - Chen Ding
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for National Center for Protein Science (The PHOENIX Center), Beijing, China
| | - Fei Lan
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Sheng-Lin Huang
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Feng Zhou
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Suling Liu
- Fudan University Shanghai Cancer Center, Key Laboratory of Breast Cancer in Shanghai, Innovation Center for Cell Signaling Network, Cancer Institutes, Fudan University, Shanghai, China
| | - Yue Xiong
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Dan Ye
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of General Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China.
| | - Kun-Liang Guan
- Huashan Hospital and Key Laboratory of Medical Epigenetics and Metabolism and Molecular and Cell Biology Lab, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
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175
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Sammak S, Allen MD, Hamdani N, Bycroft M, Zinzalla G. The structure of INI1/hSNF5 RPT1 and its interactions with the c-MYC:MAX heterodimer provide insights into the interplay between MYC and the SWI/SNF chromatin remodeling complex. FEBS J 2018; 285:4165-4180. [PMID: 30222246 PMCID: PMC6398391 DOI: 10.1111/febs.14660] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 08/11/2018] [Accepted: 09/14/2018] [Indexed: 12/14/2022]
Abstract
c‐MYC and the SWI/SNF chromatin remodeling complex act as master regulators of transcription, and play a key role in human cancer. Although they are known to interact, the molecular details of their interaction are lacking. We have determined the structure of the RPT1 region of the INI1/hSNF5/BAF47/SMARCB1 subunit of the SWI/SNF complex that acts as a c‐MYC‐binding domain, and have localized the interaction regions on both INI1 and on the c‐MYC:MAX heterodimer. c‐MYC interacts with a highly conserved groove on INI1, while INI1 binds to the c‐MYC helix‐loop‐helix region. The binding site overlaps with the c‐MYC DNA‐binding region, and we show that binding of INI1 and E‐box DNA to c‐MYC:MAX are mutually exclusive.
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Affiliation(s)
- Susan Sammak
- Microbiology, Tumor and Cell Biology (MTC) Department, Karolinska Institutet, Stockholm, Sweden
| | - Mark D Allen
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Najoua Hamdani
- Microbiology, Tumor and Cell Biology (MTC) Department, Karolinska Institutet, Stockholm, Sweden
| | - Mark Bycroft
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Giovanna Zinzalla
- Microbiology, Tumor and Cell Biology (MTC) Department, Karolinska Institutet, Stockholm, Sweden
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176
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Schuette D, Moore LM, Robert ME, Taddei TH, Ehrlich BE. Hepatocellular Carcinoma Outcome Is Predicted by Expression of Neuronal Calcium Sensor 1. Cancer Epidemiol Biomarkers Prev 2018; 27:1091-1100. [PMID: 29789326 PMCID: PMC8465775 DOI: 10.1158/1055-9965.epi-18-0167] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/06/2018] [Accepted: 05/17/2018] [Indexed: 11/16/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related death worldwide. There is an urgent demand for prognostic biomarkers that facilitate early tumor detection, as the incidence of HCC has tripled in the United States in the last three decades. Biomarkers to identify populations at risk would have significant impact on survival. We recently found that expression of Neuronal Calcium Sensor 1 (NCS1), a Ca2+-dependent signaling molecule, predicted disease outcome in breast cancer, but its predictive value in other cancer types is unknown. This protein is potentially useful because increased NCS1 regulates Ca2+ signaling and increased Ca2+ signaling is a hallmark of metastatic cancers, conferring cellular motility and an increasingly aggressive phenotype to tumors.Methods: We explored the relationship between NCS1 expression levels and patient survival in two publicly available liver cancer cohorts and a tumor microarray using data mining strategies.Results: High NCS1 expression levels are significantly associated with worse disease outcome in Asian patients within these cohorts. In addition, a variety of Ca2+-dependent and tumor growth-promoting genes are transcriptionally coregulated with NCS1 and many of them are involved in cytoskeleton organization, suggesting that NCS1 induced dysregulated Ca2+ signaling facilitates cellular motility and metastasis.Conclusions: We found NCS1 to be a novel biomarker in HCC. Furthermore, our study identified a pharmacologically targetable signaling complex that can influence tumor progression in HCC.Impact: These results lay the foundation for using NCS1 as a prognostic biomarker in prospective cohorts of HCC patients and for further functional assessment of the characterized signaling axis. Cancer Epidemiol Biomarkers Prev; 27(9); 1091-100. ©2018 AACR.
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Affiliation(s)
- Daniel Schuette
- Department of Pharmacology, Yale University, New Haven, Connecticut
| | - Lauren M Moore
- Department of Pharmacology, Yale University, New Haven, Connecticut
| | - Marie E Robert
- Department of Pathology, Yale University, New Haven, Connecticut
| | - Tamar H Taddei
- Department of Medicine (Digestive Diseases), Yale University, New Haven, Connecticut
| | - Barbara E Ehrlich
- Department of Pharmacology, Yale University, New Haven, Connecticut.
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177
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Dingar D, Tu WB, Resetca D, Lourenco C, Tamachi A, De Melo J, Houlahan KE, Kalkat M, Chan PK, Boutros PC, Raught B, Penn LZ. MYC dephosphorylation by the PP1/PNUTS phosphatase complex regulates chromatin binding and protein stability. Nat Commun 2018; 9:3502. [PMID: 30158517 PMCID: PMC6115416 DOI: 10.1038/s41467-018-05660-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 07/06/2018] [Indexed: 01/08/2023] Open
Abstract
The c-MYC (MYC) oncoprotein is deregulated in over 50% of cancers, yet regulatory mechanisms controlling MYC remain unclear. To this end, we interrogated the MYC interactome using BioID mass spectrometry (MS) and identified PP1 (protein phosphatase 1) and its regulatory subunit PNUTS (protein phosphatase-1 nuclear-targeting subunit) as MYC interactors. We demonstrate that endogenous MYC and PNUTS interact across multiple cell types and that they co-occupy MYC target gene promoters. Inhibiting PP1 by RNAi or pharmacological inhibition results in MYC hyperphosphorylation at multiple serine and threonine residues, leading to a decrease in MYC protein levels due to proteasomal degradation through the canonical SCFFBXW7 pathway. MYC hyperphosphorylation can be rescued specifically with exogenous PP1, but not other phosphatases. Hyperphosphorylated MYC retained interaction with its transcriptional partner MAX, but binding to chromatin is significantly compromised. Our work demonstrates that PP1/PNUTS stabilizes chromatin-bound MYC in proliferating cells. Deregulated MYC activity is oncogenic and is deregulated in a large fraction of human cancers. Here the authors find that protein phosphatase 1 and its regulatory subunit PNUTS controls MYC stability and its interaction with chromatin.
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Affiliation(s)
- Dharmendra Dingar
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | - William B Tu
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
| | - Diana Resetca
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
| | - Corey Lourenco
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
| | - Aaliya Tamachi
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | - Jason De Melo
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | - Kathleen E Houlahan
- Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada.,Ontario Institute for Cancer Research, Toronto, ON Canada M5G 0A3, Canada
| | - Manpreet Kalkat
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
| | - Pak-Kei Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada.,Ontario Institute for Cancer Research, Toronto, ON Canada M5G 0A3, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada M5S 1A8, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada
| | - Linda Z Penn
- Princess Margaret Cancer Centre, University Health Network, Toronto, M5G 1L7, ON, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7, Canada.
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178
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The MYC transcription factor network: balancing metabolism, proliferation and oncogenesis. Front Med 2018; 12:412-425. [PMID: 30054853 PMCID: PMC7358075 DOI: 10.1007/s11684-018-0650-z] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/21/2018] [Indexed: 12/28/2022]
Abstract
Transcription factor networks have evolved in order to control, coordinate, and separate, the functions of distinct network modules spatially and temporally. In this review we focus on the MYC network (also known as the MAX-MLX Network), a highly conserved super-family of related basic-helix-loop-helix-zipper (bHLHZ) proteins that functions to integrate extracellular and intracellular signals and modulate global gene expression. Importantly the MYC network has been shown to be deeply involved in a broad spectrum of human and other animal cancers. Here we summarize molecular and biological properties of the network modules with emphasis on functional interactions among network members. We suggest that these network interactions serve to modulate growth and metabolism at the transcriptional level in order to balance nutrient demand with supply, to maintain growth homeostasis, and to influence cell fate. Moreover, oncogenic activation of MYC and/or loss of a MYC antagonist, results in an imbalance in the activity of the network as a whole, leading to tumor initiation, progression and maintenance.
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179
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Yang Z, Shah K, Busby T, Giles K, Khodadadi-Jamayran A, Li W, Jiang H. Hijacking a key chromatin modulator creates epigenetic vulnerability for MYC-driven cancer. J Clin Invest 2018; 128:3605-3618. [PMID: 29870403 DOI: 10.1172/jci97072] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 05/29/2018] [Indexed: 12/14/2022] Open
Abstract
While the genomic binding of MYC protein correlates with active epigenetic marks on chromatin, it remains largely unclear how major epigenetic mechanisms functionally impact the tumorigenic potential of MYC. Here, we show that, compared with the catalytic subunits, the core subunits, including DPY30, of the major H3K4 methyltransferase complexes were frequently amplified in human cancers and selectively upregulated in Burkitt lymphoma. We show that DPY30 promoted the expression of endogenous MYC and was also functionally important for efficient binding of MYC to its genomic targets by regulating chromatin accessibility. Dpy30 heterozygosity did not affect normal animal physiology including lifespan, but significantly suppressed Myc-driven lymphomagenesis, as cells failed to combat oncogene-triggered apoptosis as a result of insufficient epigenetic modulation and expression of a subset of antiapoptotic genes. Dpy30 reduction also greatly impeded MYC-dependent cellular transformation, without affecting normal cell growth. These results suggest that MYC hijacks a major epigenetic pathway - H3K4 methylation - to facilitate its molecular activity in target binding and to coordinate its oncogenic program for efficient tumorigenesis, meanwhile creating "epigenetic vulnerability." DPY30 and the H3K4 methylation pathway are thus potential epigenetic targets for treating certain MYC-driven cancers.
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Affiliation(s)
- Zhenhua Yang
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Kushani Shah
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Theodore Busby
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Keith Giles
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Alireza Khodadadi-Jamayran
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Wei Li
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, UAB Stem Cell Institute, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA.,Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
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180
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Wang F, Jeon KO, Salovich JM, Macdonald JD, Alvarado J, Gogliotti RD, Phan J, Olejniczak ET, Sun Q, Wang S, Camper D, Yuh JP, Shaw JG, Sai J, Rossanese OW, Tansey WP, Stauffer SR, Fesik SW. Discovery of Potent 2-Aryl-6,7-dihydro-5 H-pyrrolo[1,2- a]imidazoles as WDR5-WIN-Site Inhibitors Using Fragment-Based Methods and Structure-Based Design. J Med Chem 2018; 61:5623-5642. [PMID: 29889518 PMCID: PMC6842305 DOI: 10.1021/acs.jmedchem.8b00375] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
WDR5 is a chromatin-regulatory scaffold protein overexpressed in various cancers and a potential epigenetic drug target for the treatment of mixed-lineage leukemia. Here, we describe the discovery of potent and selective WDR5-WIN-site inhibitors using fragment-based methods and structure-based design. NMR-based screening of a large fragment library identified several chemically distinct hit series that bind to the WIN site within WDR5. Members of a 6,7-dihydro-5 H-pyrrolo[1,2- a]imidazole fragment class were expanded using a structure-based design approach to arrive at lead compounds with dissociation constants <10 nM and micromolar cellular activity against an AML-leukemia cell line. These compounds represent starting points for the discovery of clinically useful WDR5 inhibitors for the treatment of cancer.
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Affiliation(s)
- Feng Wang
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232
| | - Kyu Ok Jeon
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232
| | - James M. Salovich
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232
| | | | - Joseph Alvarado
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232
| | - Rocco D. Gogliotti
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232
| | - Jason Phan
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232
| | | | - Qi Sun
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232
| | - Shidong Wang
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232
| | - DeMarco Camper
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232
| | - Joannes P. Yuh
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232
| | - J. Grace Shaw
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232
| | - Jiqing Sai
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232
| | - Olivia W. Rossanese
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232
| | - William P. Tansey
- Department of Cell and Developmental Biology Vanderbilt University, Nashville, Tennessee 37232
| | - Shaun R. Stauffer
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232
| | - Stephen W. Fesik
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee 37232
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232
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181
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Neilsen BK, Chakraborty B, McCall JL, Frodyma DE, Sleightholm RL, Fisher KW, Lewis RE. WDR5 supports colon cancer cells by promoting methylation of H3K4 and suppressing DNA damage. BMC Cancer 2018; 18:673. [PMID: 29925347 PMCID: PMC6011590 DOI: 10.1186/s12885-018-4580-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/08/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND KMT2/MLL proteins are commonly overexpressed or mutated in cancer and have been shown to support cancer maintenance. These proteins are responsible for methylating histone 3 at lysine 4 and promoting transcription and DNA synthesis; however, they are inactive outside of a multi-protein complex that requires WDR5. WDR5 has been implicated in cancer for its role in the COMPASS complex and its interaction with Myc; however, the role of WDR5 in colon cancer has not yet been elucidated. METHODS WDR5 expression was evaluated using RT-qPCR and western blot analysis. Cell viability and colony forming assays were utilized to evaluate the effects of WDR5 depletion or inhibition in colon cancer cells. Downstream effects of WDR5 depletion and inhibition were observed by western blot. RESULTS WDR5 is overexpressed in colon tumors and colon cancer cell lines at the mRNA and protein level. WDR5 depletion reduces cell viability in HCT116, LoVo, RKO, HCT15, SW480, SW620, and T84 colon cancer cells. Inhibition of the WDR5:KMT2/MLL interaction using OICR-9429 reduces cell viability in the same panel of cell lines albeit not to the same extent as RNAi-mediated WDR5 depletion. WDR5 depletion reduced H3K4Me3 and increased phosphorylation of H2AX in HCT116, SW620, and RKO colon cancer cells; however, OICR-9429 treatment did not recapitulate these effects in all cell lines potentially explaining the reduced toxicity of OICR-9429 treatment as compared to WDR5 depletion. WDR5 depletion also sensitized colon cancer cells to radiation-induced DNA damage. CONCLUSIONS These data demonstrate a clear role for WDR5 in colon cancer and future studies should examine its potential to serve as a therapeutic target in cancer. Additional studies are needed to fully elucidate if the requirement for WDR5 is independent of or consistent with its role within the COMPASS complex. OICR-9429 treatment was particularly toxic to SW620 and T84 colon cancer cells, two cell lines without mutations in WDR5 and KMT2/MLL proteins suggesting COMPASS complex inhibition may be particularly effective in tumors lacking KMT2 mutations. Additionally, the ability of WDR5 depletion to amplify the toxic effects of radiation presents the possibility of targeting WDR5 to sensitize cells to DNA-damaging therapies.
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Affiliation(s)
- Beth K Neilsen
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Binita Chakraborty
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,Present address: Department of Pharmacology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Jamie L McCall
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,Present address: Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Danielle E Frodyma
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Richard L Sleightholm
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Kurt W Fisher
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Robert E Lewis
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
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182
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Wolpaw AJ, Dang CV. MYC-induced metabolic stress and tumorigenesis. Biochim Biophys Acta Rev Cancer 2018; 1870:43-50. [PMID: 29791870 DOI: 10.1016/j.bbcan.2018.05.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 12/25/2022]
Abstract
The MYC oncogene is commonly altered across human cancers. Distinct from the normal MYC proto-oncogene, which is under tight transcriptional, translational, and post-translational control, deregulated oncogenic MYC drives imbalanced, non-linear amplification of transcription that results in oncogenic 'stress.' The term 'stress' had been a euphemism for our lack of mechanistic understanding, but synthesis of many studies over the past decade provides a more coherent picture of oncogenic MYC driving metastable cellular states, particularly altered metabolism, that activate and depend on cellular stress response pathways to allow for continued growth and survival. Both deregulated metabolism and these stress response pathways represent vulnerabilities that can be exploited therapeutically.
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Affiliation(s)
- Adam J Wolpaw
- Divisions of Hematology and Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; The Wistar Institute, Philadelphia, PA 19104, USA
| | - Chi V Dang
- The Wistar Institute, Philadelphia, PA 19104, USA; Ludwig Institute for Cancer Research, New York, NY 10017, USA.
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183
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Wu Y, Diao P, Li Z, Zhang W, Wang D, Wang Y, Cheng J. Overexpression of WD repeat domain 5 associates with aggressive clinicopathological features and unfavorable prognosis in head neck squamous cell carcinoma. J Oral Pathol Med 2018; 47:502-510. [PMID: 29569374 DOI: 10.1111/jop.12708] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND WD repeat domain 5 (WDR5), a core member of Mixed lineage leukemia (MLL) and SET1 histone H3 lysine 4 (H3K4) methyltransferase complexes, is involved in multiple biological and pathological processes. Its deregulation in cancer and pro-tumorigenic roles has been increasingly appreciated. However, the expression pattern of WDR5 and its biological functions in head neck squamous cell carcinoma (HNSCC) have not been well established. METHODS The expression of WDR5 mRNA in HNSCC was determined by data mining and interrogation using publicly available databases. Its protein expression was measured by immunohistochemistry in a retrospective cohort of primary HNSCC samples. Moreover, the associations between WDR5 expression and various clinicopathological parameters and patient survival were assessed. The pro-tumorigenic roles of WDR5 in HNSCC were further delineated in vitro by loss-of-function assay. RESULTS Our bioinformatics analyses revealed that WDR5 mRNA was significantly overexpressed in 3 HNSCC cohorts. WDR5 protein was markedly upregulated in HNSCC samples as compared to normal counterparts and its overexpression significantly associated with large tumor size, advanced clinical stage (chi-square test, P = .048, .006) and reduced overall and disease-free survival (Kaplan-Mier analyses, Log-rank test, P = .0137, .0154). Univariate and multivariate survival analyses further revealed WDR5 protein abundance as an independent prognostic factor for patients' overall survival. Moreover, WDR5 knockdown significantly inhibited cell proliferation, migration and invasion, and induced cell apoptosis in HNSCC cells. CONCLUSIONS Our findings reveal that WDR5 is aberrantly overexpressed in HNSCC and associates with aggressiveness and unfavorable prognosis, thus representing a novel diagnostic and prognostic biomarker for HNSCC.
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Affiliation(s)
- Yaping Wu
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, China
| | - Pengfei Diao
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, China
| | - Zhongwu Li
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
| | - Wei Zhang
- Department of Oral Pathology, School of Stomatology, Nanjing Medical University, Nanjing, China
| | - Dongmiao Wang
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, China.,Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital, Nanjing Medical University, Nanjing, China
| | - Yanling Wang
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, China
| | - Jie Cheng
- Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, China
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184
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Abstract
Small cell lung cancer (SCLC) is a devastating and aggressive neuroendocrine carcinoma of the lung. It accounts for ~15% of lung cancer mortality and has had no improvement in standard treatment options for nearly 30 years. However, there is now hope for change with new therapies and modalities of therapy. Immunotherapies and checkpoint inhibitors are entering clinical practice, selected targeted therapies show promise, and "smart bomb"-based drug/radioconjugates have led to good response in early clinical trials. Additionally, new research insights into the genetics and tumor heterogeneity of SCLC alongside the availability of new tools such as patient-derived or circulating tumor cell xenografts offer the potential to shine light on this beshadowed cancer.
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185
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Modes of Interaction of KMT2 Histone H3 Lysine 4 Methyltransferase/COMPASS Complexes with Chromatin. Cells 2018; 7:cells7030017. [PMID: 29498679 PMCID: PMC5870349 DOI: 10.3390/cells7030017] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/22/2018] [Accepted: 02/27/2018] [Indexed: 02/07/2023] Open
Abstract
Regulation of gene expression is achieved by sequence-specific transcriptional regulators, which convey the information that is contained in the sequence of DNA into RNA polymerase activity. This is achieved by the recruitment of transcriptional co-factors. One of the consequences of co-factor recruitment is the control of specific properties of nucleosomes, the basic units of chromatin, and their protein components, the core histones. The main principles are to regulate the position and the characteristics of nucleosomes. The latter includes modulating the composition of core histones and their variants that are integrated into nucleosomes, and the post-translational modification of these histones referred to as histone marks. One of these marks is the methylation of lysine 4 of the core histone H3 (H3K4). While mono-methylation of H3K4 (H3K4me1) is located preferentially at active enhancers, tri-methylation (H3K4me3) is a mark found at open and potentially active promoters. Thus, H3K4 methylation is typically associated with gene transcription. The class 2 lysine methyltransferases (KMTs) are the main enzymes that methylate H3K4. KMT2 enzymes function in complexes that contain a necessary core complex composed of WDR5, RBBP5, ASH2L, and DPY30, the so-called WRAD complex. Here we discuss recent findings that try to elucidate the important question of how KMT2 complexes are recruited to specific sites on chromatin. This is embedded into short overviews of the biological functions of KMT2 complexes and the consequences of H3K4 methylation.
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186
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Moonlighting with WDR5: A Cellular Multitasker. J Clin Med 2018; 7:jcm7020021. [PMID: 29385767 PMCID: PMC5852437 DOI: 10.3390/jcm7020021] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/16/2018] [Accepted: 01/18/2018] [Indexed: 11/17/2022] Open
Abstract
WDR5 is a highly conserved WD40 repeat-containing protein that is essential for proper regulation of multiple cellular processes. WDR5 is best characterized as a core scaffolding component of histone methyltransferase complexes, but emerging evidence demonstrates that it does much more, ranging from expanded functions in the nucleus through to controlling the integrity of cell division. The purpose of this review is to describe the current molecular understandings of WDR5, discuss how it participates in diverse cellular processes, and highlight drug discovery efforts around WDR5 that may form the basis of new anti-cancer therapies.
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187
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Rickman DS, Schulte JH, Eilers M. The Expanding World of N-MYC–Driven Tumors. Cancer Discov 2018; 8:150-163. [DOI: 10.1158/2159-8290.cd-17-0273] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 08/04/2017] [Accepted: 10/18/2017] [Indexed: 11/16/2022]
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188
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189
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PAF1 complex component Leo1 helps recruit Drosophila Myc to promoters. Proc Natl Acad Sci U S A 2017; 114:E9224-E9232. [PMID: 29078288 DOI: 10.1073/pnas.1705816114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The Myc oncogene is a transcription factor with a powerful grip on cellular growth and proliferation. The physical interaction of Myc with the E-box DNA motif has been extensively characterized, but it is less clear whether this sequence-specific interaction is sufficient for Myc's binding to its transcriptional targets. Here we identify the PAF1 complex, and specifically its component Leo1, as a factor that helps recruit Myc to target genes. Since the PAF1 complex is typically associated with active genes, this interaction with Leo1 contributes to Myc targeting to open promoters.
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190
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Cheng J, Park DE, Berrios C, White EA, Arora R, Yoon R, Branigan T, Xiao T, Westerling T, Federation A, Zeid R, Strober B, Swanson SK, Florens L, Bradner JE, Brown M, Howley PM, Padi M, Washburn MP, DeCaprio JA. Merkel cell polyomavirus recruits MYCL to the EP400 complex to promote oncogenesis. PLoS Pathog 2017; 13:e1006668. [PMID: 29028833 PMCID: PMC5640240 DOI: 10.1371/journal.ppat.1006668] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/25/2017] [Indexed: 11/19/2022] Open
Abstract
Merkel cell carcinoma (MCC) frequently contains integrated copies of Merkel cell polyomavirus DNA that express a truncated form of Large T antigen (LT) and an intact Small T antigen (ST). While LT binds RB and inactivates its tumor suppressor function, it is less clear how ST contributes to MCC tumorigenesis. Here we show that ST binds specifically to the MYC homolog MYCL (L-MYC) and recruits it to the 15-component EP400 histone acetyltransferase and chromatin remodeling complex. We performed a large-scale immunoprecipitation for ST and identified co-precipitating proteins by mass spectrometry. In addition to protein phosphatase 2A (PP2A) subunits, we identified MYCL and its heterodimeric partner MAX plus the EP400 complex. Immunoprecipitation for MAX and EP400 complex components confirmed their association with ST. We determined that the ST-MYCL-EP400 complex binds together to specific gene promoters and activates their expression by integrating chromatin immunoprecipitation with sequencing (ChIP-seq) and RNA-seq. MYCL and EP400 were required for maintenance of cell viability and cooperated with ST to promote gene expression in MCC cell lines. A genome-wide CRISPR-Cas9 screen confirmed the requirement for MYCL and EP400 in MCPyV-positive MCC cell lines. We demonstrate that ST can activate gene expression in a EP400 and MYCL dependent manner and this activity contributes to cellular transformation and generation of induced pluripotent stem cells.
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Affiliation(s)
- Jingwei Cheng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Donglim Esther Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Graduate School of Arts and Sciences, Harvard University, Boston, Massachusetts, United States of America
| | - Christian Berrios
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Microbiology and Immunobiology, Harvard Medical School; Boston, Massachusetts, United States of America
| | - Elizabeth A. White
- Department of Microbiology and Immunobiology, Harvard Medical School; Boston, Massachusetts, United States of America
| | - Reety Arora
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Rosa Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Graduate School of Arts and Sciences, Harvard University, Boston, Massachusetts, United States of America
| | - Timothy Branigan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Graduate School of Arts and Sciences, Harvard University, Boston, Massachusetts, United States of America
| | - Tengfei Xiao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Thomas Westerling
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alexander Federation
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Graduate School of Arts and Sciences, Harvard University, Boston, Massachusetts, United States of America
| | - Rhamy Zeid
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Graduate School of Arts and Sciences, Harvard University, Boston, Massachusetts, United States of America
| | - Benjamin Strober
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Selene K. Swanson
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - James E. Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Peter M. Howley
- Department of Microbiology and Immunobiology, Harvard Medical School; Boston, Massachusetts, United States of America
| | - Megha Padi
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Michael P. Washburn
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - James A. DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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191
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Wang D, Hashimoto H, Zhang X, Barwick BG, Lonial S, Boise LH, Vertino PM, Cheng X. MAX is an epigenetic sensor of 5-carboxylcytosine and is altered in multiple myeloma. Nucleic Acids Res 2017; 45:2396-2407. [PMID: 27903915 PMCID: PMC5389568 DOI: 10.1093/nar/gkw1184] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/15/2016] [Indexed: 12/31/2022] Open
Abstract
The oncogenic transcription factor MYC and its binding partner MAX regulate gene expression by binding to DNA at enhancer-box (E-box) elements 5΄-CACGTG-3΄. In mammalian genomes, the central E-box CpG has the potential to be methylated at the 5-position of cytosine (5mC), or to undergo further oxidation to the 5-hydroxymethyl (5hmC), 5-formyl (5fC), or 5-carboxyl (5caC) forms. We find that MAX exhibits the greatest affinity for a 5caC or unmodified C-containing E-box, and much reduced affinities for the corresponding 5mC, 5hmC or 5fC forms. Crystallization of MAX with a 5caC modified E-box oligonucleotide revealed that MAX Arg36 recognizes 5caC using a 5caC–Arg–Guanine triad, with the next nearest residue to the carboxylate group being Arg60. In an analysis of >800 primary multiple myelomas, MAX alterations occurred at a frequency of ∼3%, more than half of which were single nucleotide substitutions affecting a basic clamp-like interface important for DNA interaction. Among these, arginines 35, 36 and 60 were the most frequently altered. In vitro binding studies showed that whereas mutation of Arg36 (R36W) or Arg35 (R35H/L) completely abolished DNA binding, mutation of Arg60 (R60Q) significantly reduced DNA binding, but retained a preference for the 5caC modified E-box. Interestingly, MAX alterations define a subset of myeloma patients with lower MYC expression and a better overall prognosis. Together these data indicate that MAX can act as a direct epigenetic sensor of E-box cytosine modification states and that local CpG modification and MAX variants converge to modulate the MAX-MYC transcriptional network.
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Affiliation(s)
- Dongxue Wang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hideharu Hashimoto
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Benjamin G Barwick
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA.,The Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Lawrence H Boise
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA.,The Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Paula M Vertino
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA.,The Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,The Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
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192
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Brägelmann J, Böhm S, Guthrie MR, Mollaoglu G, Oliver TG, Sos ML. Family matters: How MYC family oncogenes impact small cell lung cancer. Cell Cycle 2017; 16:1489-1498. [PMID: 28737478 DOI: 10.1080/15384101.2017.1339849] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Small cell lung cancer (SCLC) is one of the most deadly cancers and currently lacks effective targeted treatment options. Recent advances in the molecular characterization of SCLC has provided novel insight into the biology of this disease and raises hope for a paradigm shift in the treatment of SCLC. We and others have identified activation of MYC as a driver of susceptibility to Aurora kinase inhibition in SCLC cells and tumors that translates into a therapeutic option for the targeted treatment of MYC-driven SCLC. While MYC shares major features with its paralogs MYCN and MYCL, the sensitivity to Aurora kinase inhibitors is unique for MYC-driven SCLC. In this review, we will compare the distinct molecular features of the 3 MYC family members and address the potential implications for targeted therapy of SCLC.
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Affiliation(s)
- Johannes Brägelmann
- a Molecular Pathology, Institute of Pathology, University of Cologne , Cologne , Germany.,b Department of Translational Genomics , Medical Faculty, University of Cologne , Cologne , Germany
| | - Stefanie Böhm
- a Molecular Pathology, Institute of Pathology, University of Cologne , Cologne , Germany.,b Department of Translational Genomics , Medical Faculty, University of Cologne , Cologne , Germany
| | - Matthew R Guthrie
- c Department of Oncological Sciences , University of Utah, Huntsman Cancer Institute , Salt Lake City , UT , USA
| | - Gurkan Mollaoglu
- c Department of Oncological Sciences , University of Utah, Huntsman Cancer Institute , Salt Lake City , UT , USA
| | - Trudy G Oliver
- c Department of Oncological Sciences , University of Utah, Huntsman Cancer Institute , Salt Lake City , UT , USA
| | - Martin L Sos
- a Molecular Pathology, Institute of Pathology, University of Cologne , Cologne , Germany.,b Department of Translational Genomics , Medical Faculty, University of Cologne , Cologne , Germany.,d Center for Molecular Medicine Cologne , University of Cologne , Cologne , Germany
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193
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Allevato M, Bolotin E, Grossman M, Mane-Padros D, Sladek FM, Martinez E. Sequence-specific DNA binding by MYC/MAX to low-affinity non-E-box motifs. PLoS One 2017; 12:e0180147. [PMID: 28719624 PMCID: PMC5515408 DOI: 10.1371/journal.pone.0180147] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/09/2017] [Indexed: 01/07/2023] Open
Abstract
The MYC oncoprotein regulates transcription of a large fraction of the genome as an obligatory heterodimer with the transcription factor MAX. The MYC:MAX heterodimer and MAX:MAX homodimer (hereafter MYC/MAX) bind Enhancer box (E-box) DNA elements (CANNTG) and have the greatest affinity for the canonical MYC E-box (CME) CACGTG. However, MYC:MAX also recognizes E-box variants and was reported to bind DNA in a “non-specific” fashion in vitro and in vivo. Here, in order to identify potential additional non-canonical binding sites for MYC/MAX, we employed high throughput in vitro protein-binding microarrays, along with electrophoretic mobility-shift assays and bioinformatic analyses of MYC-bound genomic loci in vivo. We identified all hexameric motifs preferentially bound by MYC/MAX in vitro, which include the low-affinity non-E-box sequence AACGTT, and found that the vast majority (87%) of MYC-bound genomic sites in a human B cell line contain at least one of the top 21 motifs bound by MYC:MAX in vitro. We further show that high MYC/MAX concentrations are needed for specific binding to the low-affinity sequence AACGTT in vitro and that elevated MYC levels in vivo more markedly increase the occupancy of AACGTT sites relative to CME sites, especially at distal intergenic and intragenic loci. Hence, MYC binds diverse DNA motifs with a broad range of affinities in a sequence-specific and dose-dependent manner, suggesting that MYC overexpression has more selective effects on the tumor transcriptome than previously thought.
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Affiliation(s)
- Michael Allevato
- Department of Biochemistry, University of California Riverside, Riverside, California, United States of America
| | - Eugene Bolotin
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, California, United States of America
| | - Mark Grossman
- Department of Biochemistry, University of California Riverside, Riverside, California, United States of America
| | - Daniel Mane-Padros
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, California, United States of America
| | - Frances M. Sladek
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, California, United States of America
- * E-mail: (E.M.); (F.M.S.)
| | - Ernest Martinez
- Department of Biochemistry, University of California Riverside, Riverside, California, United States of America
- * E-mail: (E.M.); (F.M.S.)
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194
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MYC Modulation around the CDK2/p27/SKP2 Axis. Genes (Basel) 2017; 8:genes8070174. [PMID: 28665315 PMCID: PMC5541307 DOI: 10.3390/genes8070174] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 06/23/2017] [Accepted: 06/24/2017] [Indexed: 12/20/2022] Open
Abstract
MYC is a pleiotropic transcription factor that controls a number of fundamental cellular processes required for the proliferation and survival of normal and malignant cells, including the cell cycle. MYC interacts with several central cell cycle regulators that control the balance between cell cycle progression and temporary or permanent cell cycle arrest (cellular senescence). Among these are the cyclin E/A/cyclin-dependent kinase 2 (CDK2) complexes, the CDK inhibitor p27KIP1 (p27) and the E3 ubiquitin ligase component S-phase kinase-associated protein 2 (SKP2), which control each other by forming a triangular network. MYC is engaged in bidirectional crosstalk with each of these players; while MYC regulates their expression and/or activity, these factors in turn modulate MYC through protein interactions and post-translational modifications including phosphorylation and ubiquitylation, impacting on MYC's transcriptional output on genes involved in cell cycle progression and senescence. Here we elaborate on these network interactions with MYC and their impact on transcription, cell cycle, replication and stress signaling, and on the role of other players interconnected to this network, such as CDK1, the retinoblastoma protein (pRB), protein phosphatase 2A (PP2A), the F-box proteins FBXW7 and FBXO28, the RAS oncoprotein and the ubiquitin/proteasome system. Finally, we describe how the MYC/CDK2/p27/SKP2 axis impacts on tumor development and discuss possible ways to interfere therapeutically with this system to improve cancer treatment.
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195
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Bayliss R, Burgess SG, Leen E, Richards MW. A moving target: structure and disorder in pursuit of Myc inhibitors. Biochem Soc Trans 2017; 45:709-717. [PMID: 28620032 DOI: 10.1042/bst20160328] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/27/2017] [Accepted: 03/28/2017] [Indexed: 02/11/2024]
Abstract
The Myc proteins comprise a family of ubiquitous regulators of gene expression implicated in over half of all human cancers. They interact with a large number of other proteins, such as transcription factors, chromatin-modifying enzymes and kinases. Remarkably, few of these interactions have been characterized structurally. This is at least in part due to the intrinsically disordered nature of Myc proteins, which adopt a defined conformation only in the presence of binding partners. Owing to this behaviour, crystallographic studies on Myc proteins have been limited to short fragments in complex with other proteins. Most recently, we determined the crystal structure of Aurora-A kinase domain bound to a 28-amino acid fragment of the N-Myc transactivation domain. The structure reveals an α-helical segment within N-Myc capped by two tryptophan residues that recognize the surface of Aurora-A. The kinase domain acts as a molecular scaffold, independently of its catalytic activity, upon which this region of N-Myc becomes ordered. The binding site for N-Myc on Aurora-A is disrupted by certain ATP-competitive inhibitors, such as MLN8237 (alisertib) and CD532, and explains how these kinase inhibitors are able to disrupt the protein-protein interaction to affect Myc destabilization. Structural studies on this and other Myc complexes will lead to the design of protein-protein interaction inhibitors as chemical tools to dissect the complex pathways of Myc regulation and function, which may be developed into Myc inhibitors for the treatment of cancer.
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Affiliation(s)
- Richard Bayliss
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Selena G Burgess
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Eoin Leen
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Mark W Richards
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K
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196
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Liu Z, Bai J, Zhang L, Lou F, Ke F, Cai W, Wang H. Conditional knockout of microRNA-31 promotes the development of colitis associated cancer. Biochem Biophys Res Commun 2017; 490:62-68. [PMID: 28600172 DOI: 10.1016/j.bbrc.2017.06.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 06/05/2017] [Indexed: 02/04/2023]
Abstract
MicroRNA-31 (miR-31) is an evolutionarily conserved microRNA, and its biological function in colorectal cancer and other cancers is controversial. In this study, we identified the host gene of mouse miR-31 and found that miR-31 was over-expressed in both human colorectal cancer and mouse colon cancer models. We here developed a miR-31 conditional knockout mouse model that allows for colon epithelium specific deletion of miR-31 to investigate its functionality in colon cancer development. We demonstrated that mice with miR-31 conditional deletion resulted in more severe colitis-associated cancer than wild-type, and we further identified Wdr5 as an important target of miR-31.
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Affiliation(s)
- Zhaoyuan Liu
- Shanghai Institute of Immunology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jing Bai
- Shanghai Institute of Immunology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lingyun Zhang
- Shanghai Institute of Immunology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Fangzhou Lou
- Shanghai Institute of Immunology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Fang Ke
- Shanghai Institute of Immunology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wei Cai
- Shanghai Institute of Immunology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Honglin Wang
- Shanghai Institute of Immunology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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197
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Qu Y, Yang Q, Liu J, Shi B, Ji M, Li G, Hou P. c-Myc is Required for BRAF V600E-Induced Epigenetic Silencing by H3K27me3 in Tumorigenesis. Theranostics 2017; 7:2092-2107. [PMID: 28656062 PMCID: PMC5485424 DOI: 10.7150/thno.19884] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 03/31/2017] [Indexed: 12/16/2022] Open
Abstract
BRAFV600E mutation is frequently found in human cancers particularly thyroid cancer and melanoma, and is involved in the regulation of gene expression through activating MAPK/Erk signaling. Trimethylation of histone 3 lysine 27 (H3K27me3) is a critical epigenetic mark for the maintenance of gene silencing in tumorigenesis. However, molecular mechanism underlying the complex interplay between these two molecular events remains to be explored. In the present study, we conducted chromatin immunoprecipitation combined with next-generation sequencing (ChIP-Seq) and expression microarray analysis in NIH3T3 cells to explore the relationship between H3K27me3 and transcriptional regulation by BRAFV600E mutation. Our results showed that activated MAPK/Erk signaling by BRAFV600E mutation was a trigger of this epigenetic processing at many downstream target genes in cancer cell lines and BrafV600E-induced thyroid cancer of transgenetic mice. By integrating ChIP-Seq and gene expression microarray data, we identified 150 down-regulated loci with increased levels of H3K27me3 in BRAF-mutant cells relative to BRAF wild-type cells. Our data also demonstrated that c-Myc, a downstream key effector of BRAFV600E signaling, was required for BRAFV600E-induced changes in H3K27me3 through regulating the components of the polycomb repressive complex 2 (PRC2) genes Ezh2, Suz12 and Jarid2 at both transcriptional levels via direct binding to their regulatory elements and post-transcriptional levels via repressing the miR-26a, miR-200b and miR-155. In addition, BRAFV600E also caused gene silencing through Erk1/2-induced RNA polymerase II (RNAPII) poising and chromatin architecture. Collectively, our data uncover a previously unknown epigenetic mechanism in the tumorigenesis of BRAFV600E-driven cancers.
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198
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Poole CJ, van Riggelen J. MYC-Master Regulator of the Cancer Epigenome and Transcriptome. Genes (Basel) 2017; 8:genes8050142. [PMID: 28505071 PMCID: PMC5448016 DOI: 10.3390/genes8050142] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 01/03/2023] Open
Abstract
Overexpression of MYC is a hallmark of many human cancers. The MYC oncogene has long been thought to execute its neoplastic functions by acting as a classic transcription factor, deregulating the expression of a large number of specific target genes. However, MYC’s influence on many of these target genes is rather modest and there is little overlap between MYC regulated genes in different cell types, leaving many mechanistic questions unanswered. Recent advances in the field challenge the dogma further, revealing a role for MYC that extends beyond the traditional concept of a sequence-specific transcription factor. In this article, we review MYC’s function as a regulator of the cancer epigenome and transcriptome. We outline our current understanding of how MYC regulates chromatin structure in both a site-specific and genome-wide fashion, and highlight the implications for therapeutic strategies for cancers with high MYC expression.
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Affiliation(s)
- Candace J Poole
- Augusta University, Department of Biochemistry and Molecular Biology, 1410 Laney-Walker Blvd., Augusta, GA 30912, USA.
| | - Jan van Riggelen
- Augusta University, Department of Biochemistry and Molecular Biology, 1410 Laney-Walker Blvd., Augusta, GA 30912, USA.
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199
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Menin enhances c-Myc-mediated transcription to promote cancer progression. Nat Commun 2017; 8:15278. [PMID: 28474697 PMCID: PMC5424160 DOI: 10.1038/ncomms15278] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 03/14/2017] [Indexed: 12/14/2022] Open
Abstract
Menin is an enigmatic protein that displays unique ability to either suppress or promote tumorigenesis in a context-dependent manner. The role for Menin to promote oncogenic functions has been largely attributed to its essential role in forming the MLL methyltransferase complex, which mediates H3K4me3. Here, we identify an unexpected role of Menin in enhancing the transactivity of oncogene MYC in a way independent of H3K4me3 activity. Intriguingly, we find that Menin interacts directly with the TAD domain of MYC and co-localizes with MYC to E-Box to enhance the transcription of MYC target genes in a P-TEFb-dependent manner. We further demonstrate that, by transcriptionally promoting the expression of MYC target genes in cancer cells, Menin stimulates cell proliferation and cellular metabolism both in vitro and in vivo. Our results uncover a previously unappreciated mechanism by which Menin functions as an oncogenic regulatory factor that is critical for MYC-mediated gene transcription. Menin is a protein with context-dependent oncogenic or oncosuppressive roles; the oncogenic activity is mainly due to its function as a cofactor of the MLL1 histone methyltransferase complex. Here the authors show that Menin regulates c-Myc-dependent transformation independently of the MLL complex.
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200
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Xie Q, Li Z, Chen J. WDR5 positively regulates p53 stability by inhibiting p53 ubiquitination. Biochem Biophys Res Commun 2017; 487:333-338. [PMID: 28412363 DOI: 10.1016/j.bbrc.2017.04.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 04/12/2017] [Indexed: 12/13/2022]
Abstract
WD40 repeat protein WDR5 is a core component of the Set/MLL histone methyltransferase complex which catalyzes histone H3 Lys4 trimethylation and activates gene transcription in human cells. WDR5 promotes Set/MLL complex assembly and mediates the complex binding to Lys4-dimethylated histone H3 tail. Most earlier studies report that WDR5 exerts profound effects on various cellular and organismal processes mainly through epigenetic regulation of gene transcription. However, the functions of WDR5 in lung cancer remain largely unknown. Here, we report that WDR5 positively regulates p53 stability by inhibiting p53 ubiquitination in human lung cancer A549 cells. Overexpression of WDR5 dramatically increases p53 protein levels and its half-life in A549 cells, while depletion of WDR5 with WDR5-specific siRNAs significantly decreases p53 protein levels. We also observe that WDR5 is required for p53 induction in response to cisplatin treatment. Mechanistically, WDR5 colocalizes with p53 and inhibits p53 ubiquitination, resulting in p53 stabilization. Consequently, overexpression of WDR5 induces G1 phase arrest in A549 cells, and knocking down WDR5 by siRNAs reduces the population at G1 phase. Furthermore, p53 expression levels is at least in part determined by the p53 positive regulator WDR5 in some cancer cells. Taken together, these data suggest that WDR5 is directly involved in p53 signaling pathway. Our studies provide a new insight into WDR5 functions in A549 cells.
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Affiliation(s)
- Qingqing Xie
- School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Zengpeng Li
- School of Life Sciences, Xiamen University, Xiamen 361102, Fujian, China
| | - Jianming Chen
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, Fujian, China.
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