201
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Jung LA, Gebhardt A, Koelmel W, Ade CP, Walz S, Kuper J, von Eyss B, Letschert S, Redel C, d'Artista L, Biankin A, Zender L, Sauer M, Wolf E, Evan G, Kisker C, Eilers M. OmoMYC blunts promoter invasion by oncogenic MYC to inhibit gene expression characteristic of MYC-dependent tumors. Oncogene 2017; 36:1911-1924. [PMID: 27748763 DOI: 10.1038/onc.2016.354] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 07/15/2016] [Accepted: 08/15/2016] [Indexed: 01/01/2023]
Abstract
MYC genes have both essential roles during normal development and exert oncogenic functions during tumorigenesis. Expression of a dominant-negative allele of MYC, termed OmoMYC, can induce rapid tumor regression in mouse models with little toxicity for normal tissues. How OmoMYC discriminates between physiological and oncogenic functions of MYC is unclear. We have solved the crystal structure of OmoMYC and show that it forms a stable homodimer and as such recognizes DNA in the same manner as the MYC/MAX heterodimer. OmoMYC attenuates both MYC-dependent activation and repression by competing with MYC/MAX for binding to chromatin, effectively lowering MYC/MAX occupancy at its cognate binding sites. OmoMYC causes the largest decreases in promoter occupancy and changes in expression on genes that are invaded by oncogenic MYC levels. A signature of OmoMYC-regulated genes defines subgroups with high MYC levels in multiple tumor entities and identifies novel targets for the eradication of MYC-driven tumors.
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Affiliation(s)
- L A Jung
- Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - A Gebhardt
- Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - W Koelmel
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - C P Ade
- Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - S Walz
- Comprehensive Cancer Center, Core Unit Bioinformatics, Biocenter, Würzburg, Germany
| | - J Kuper
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - B von Eyss
- Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - S Letschert
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Würzburg, Germany
| | - C Redel
- Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - L d'Artista
- Division of Translational Gastrointestinal Oncology, Department of Internal Medicine I, University of Tübingen, Tübingen, Germany
| | - A Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
- South Western Sydney Clinical School, Faculty of Medicine, University of NSW, Liverpool, New South Wales, Australia
| | - L Zender
- Division of Translational Gastrointestinal Oncology, Department of Internal Medicine I, University of Tübingen, Tübingen, Germany
| | - M Sauer
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Würzburg, Germany
| | - E Wolf
- Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - G Evan
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - C Kisker
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - M Eilers
- Theodor Boveri Institute, Biocenter, University of Würzburg, Würzburg, Germany
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202
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Tang Y, Wang J, Lian Y, Fan C, Zhang P, Wu Y, Li X, Xiong F, Li X, Li G, Xiong W, Zeng Z. Linking long non-coding RNAs and SWI/SNF complexes to chromatin remodeling in cancer. Mol Cancer 2017; 16:42. [PMID: 28212646 PMCID: PMC5316185 DOI: 10.1186/s12943-017-0612-0] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 02/06/2017] [Indexed: 02/08/2023] Open
Abstract
Chromatin remodeling controls gene expression and signaling pathway activation, and aberrant chromatin structure and gene dysregulation are primary characteristics of human cancer progression. Recent reports have shown that long non-coding RNAs (lncRNAs) are tightly associated with chromatin remodeling. In this review, we focused on important chromatin remodelers called the switching defective/sucrose nonfermenting (SWI/SNF) complexes, which use the energy of ATP hydrolysis to control gene transcription by altering chromatin structure. We summarize a link between lncRNAs and the SWI/SNF complexes and their role in chromatin remodeling and gene expression regulation in cancer, thereby providing systematic information and a better understanding of carcinogenesis.
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Affiliation(s)
- Yanyan Tang
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jinpeng Wang
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Yu Lian
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Chunmei Fan
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Ping Zhang
- School of Information Science and Engineering, Central South University, Changsha, Hunan, China
| | - Yingfen Wu
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Xiayu Li
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fang Xiong
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaoling Li
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guiyuan Li
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wei Xiong
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China. .,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Zhaoyang Zeng
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China. .,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China.
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203
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Wong M, Tee AEL, Milazzo G, Bell JL, Poulos RC, Atmadibrata B, Sun Y, Jing D, Ho N, Ling D, Liu PY, Zhang XD, Hüttelmaier S, Wong JWH, Wang J, Polly P, Perini G, Scarlett CJ, Liu T. The Histone Methyltransferase DOT1L Promotes Neuroblastoma by Regulating Gene Transcription. Cancer Res 2017; 77:2522-2533. [PMID: 28209620 DOI: 10.1158/0008-5472.can-16-1663] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/08/2016] [Accepted: 01/17/2017] [Indexed: 11/16/2022]
Abstract
Myc oncoproteins exert tumorigenic effects by regulating expression of target oncogenes. Histone H3 lysine 79 (H3K79) methylation at Myc-responsive elements of target gene promoters is a strict prerequisite for Myc-induced transcriptional activation, and DOT1L is the only known histone methyltransferase that catalyzes H3K79 methylation. Here, we show that N-Myc upregulates DOT1L mRNA and protein expression by binding to the DOT1L gene promoter. shRNA-mediated depletion of DOT1L reduced mRNA and protein expression of N-Myc target genes ODC1 and E2F2 DOT1L bound to the Myc Box II domain of N-Myc protein, and knockdown of DOT1L reduced histone H3K79 methylation and N-Myc protein binding at the ODC1 and E2F2 gene promoters and reduced neuroblastoma cell proliferation. Treatment with the small-molecule DOT1L inhibitor SGC0946 reduced H3K79 methylation and proliferation of MYCN gene-amplified neuroblastoma cells. In mice xenografts of neuroblastoma cells stably expressing doxycycline-inducible DOT1L shRNA, ablating DOT1L expression with doxycycline significantly reduced ODC1 and E2F2 expression, reduced tumor progression, and improved overall survival. In addition, high levels of DOT1L gene expression in human neuroblastoma tissues correlated with high levels of MYCN, ODC1, and E2F2 gene expression and independently correlated with poor patient survival. Taken together, our results identify DOT1L as a novel cofactor in N-Myc-mediated transcriptional activation of target genes and neuroblastoma oncogenesis. Furthermore, they characterize DOT1L inhibitors as novel anticancer agents against MYCN-amplified neuroblastoma. Cancer Res; 77(9); 2522-33. ©2017 AACR.
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Affiliation(s)
| | - Andrew E L Tee
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Giorgio Milazzo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Jessica L Bell
- Institute of Molecular Medicine, Martin Luther University, ZAMED, Halle, Germany
| | - Rebecca C Poulos
- Prince of Wales Clinical School and Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Bernard Atmadibrata
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Yuting Sun
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Duohui Jing
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Nicholas Ho
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Dora Ling
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Pei Yan Liu
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Xu Dong Zhang
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Martin Luther University, ZAMED, Halle, Germany
| | - Jason W H Wong
- Prince of Wales Clinical School and Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Jenny Wang
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia.,Centre for Childhood Cancer Research, UNSW Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Patsie Polly
- Department of Pathology and Mechanisms of Disease and Translational Research, University of New South Wales, Sydney, New South Wales, Australia
| | - Giovanni Perini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Christopher J Scarlett
- School of Environmental & Life Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
| | - Tao Liu
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia. .,Centre for Childhood Cancer Research, UNSW Medicine, University of New South Wales, Sydney, New South Wales, Australia
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204
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Abstract
Targeting the transcription factor c-Myc via one of its coactivator proteins is a promising strategy for cancer therapy.
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Affiliation(s)
- Linchong Sun
- CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei, China
| | - Ping Gao
- CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei, China
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205
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Stefan E, Bister K. MYC and RAF: Key Effectors in Cellular Signaling and Major Drivers in Human Cancer. Curr Top Microbiol Immunol 2017; 407:117-151. [PMID: 28466200 DOI: 10.1007/82_2017_4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The prototypes of the human MYC and RAF gene families are orthologs of animal proto-oncogenes that were originally identified as transduced alleles in the genomes of highly oncogenic retroviruses. MYC and RAF genes are now established as key regulatory elements in normal cellular physiology, but also as major cancer driver genes. Although the predominantly nuclear MYC proteins and the cytoplasmic RAF proteins have different biochemical functions, they are functionally linked in pivotal signaling cascades and circuits. The MYC protein is a transcription factor and together with its dimerization partner MAX holds a central position in a regulatory network of bHLH-LZ proteins. MYC regulates transcription conducted by all RNA polymerases and controls virtually the entire transcriptome. Fundamental cellular processes including distinct catabolic and anabolic branches of metabolism, cell cycle regulation, cell growth and proliferation, differentiation, stem cell regulation, and apoptosis are under MYC control. Deregulation of MYC expression by rearrangement or amplification of the MYC locus or by defects in kinase-mediated upstream signaling, accompanied by loss of apoptotic checkpoints, leads to tumorigenesis and is a hallmark of most human cancers. The critically controlled serine/threonine RAF kinases are central nodes of the cytoplasmic MAPK signaling cascade transducing converted extracellular signals to the nucleus for reshaping transcription factor controlled gene expression profiles. Specific mutations of RAF kinases, such as the prevalent BRAF(V600E) mutation in melanoma, or defects in upstream signaling or feedback loops cause decoupled kinase activities which lead to tumorigenesis. Different strategies for pharmacological interference with MYC- or RAF-induced tumorigenesis are being developed and several RAF kinase inhibitors are already in clinical use.
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Affiliation(s)
- Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Klaus Bister
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria.
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206
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Wu J, Tan X, Lin J, Yuan L, Chen J, Qiu L, Huang W. Minicircle-oriP-miR-31 as a Novel EBNA1-Specific miRNA Therapy Approach for Nasopharyngeal Carcinoma. Hum Gene Ther 2016; 28:415-427. [PMID: 28042945 DOI: 10.1089/hum.2016.136] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
MicroRNAs (miRNAs) are important post-transcriptional regulators that control cancer development and progression. However, the application of miRNA therapy in cancer has been hampered by a lack of an efficient and targeted delivery system. In our previous studies, an oriP promoter-based minicircle system successfully mediated targeted foreign gene expression in EBNA1-positive nasopharyngeal carcinoma (NPC). However, it remains to be evaluated whether this system can be applied for tumor miRNA therapy. miR-31-5p, a tumor suppressive miRNA involved in the tumorigenesis of EBV-positive NPC, was selected as the therapeutic miRNA to be transferred. In this work, we constructed a novel EBNA1-specific miRNA expression system, minicircle-oriP-miR-31. The results indicated that mc-oriP-miR-31 mediated selective miR-31-5p expression in EBNA1-positive NPC cells. Both the proliferation and migration of EBNA1-positive NPC cell lines were inhibited by mc-oriP-miR-31 treatment in vitro. Furthermore, mc-oriP-miR-31 treatment inhibited xenograft growth and lung metastasis in vivo. We also identified WDR5 as a novel miR-31-5p target. Knockdown of WDR5 inhibited NPC cell proliferation and migration and was associated with downregulation of Notch1. Reintroduction of WDR5 partially abrogated the suppressive effects induced by miR-31-5p. In conclusion, we demonstrate for the first time that targeted expression of miR-31-5p using a nonviral minicircle vector can serve as a novel approach for tumor miRNA therapy. Moreover, WDR5 may be a promising therapeutic target for NPC treatment.
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Affiliation(s)
- Jiangxue Wu
- 1 State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center , Guangzhou, China
- 2 Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center , Guangzhou, China
| | - Xin Tan
- 1 State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center , Guangzhou, China
- 2 Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center , Guangzhou, China
| | - Jiaxin Lin
- 1 State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center , Guangzhou, China
- 2 Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center , Guangzhou, China
| | - Luping Yuan
- 1 State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center , Guangzhou, China
- 2 Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center , Guangzhou, China
| | - Jiemin Chen
- 1 State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center , Guangzhou, China
- 2 Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center , Guangzhou, China
| | - Lin Qiu
- 1 State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center , Guangzhou, China
- 2 Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center , Guangzhou, China
| | - Wenlin Huang
- 1 State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center , Guangzhou, China
- 2 Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center , Guangzhou, China
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207
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Willmer T, Peres J, Mowla S, Abrahams A, Prince S. The T-Box factor TBX3 is important in S-phase and is regulated by c-Myc and cyclin A-CDK2. Cell Cycle 2016; 14:3173-83. [PMID: 26266831 DOI: 10.1080/15384101.2015.1080398] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The transcription factor, TBX3, is critical for the formation of, among other structures, the heart, limbs and mammary glands and haploinsufficiency of the human TBX3 gene result in ulnar-mammary syndrome which is characterized by hypoplasia of these structures. On the other hand, the overexpression of TBX3 is a feature of a wide range of cancers and it has been implicated in several aspects of the oncogenic process. This includes its ability to function as an immortalizing gene and to promote proliferation through actively repressing negative cell cycle regulators. Together this suggests that TBX3 levels may need to be tightly regulated during the cell cycle. Here we demonstrate that this is indeed the case and that TBX3 mRNA and protein levels peak at S-phase and that the TBX3 protein is predominantly localized to the nucleus of S-phase cells. The increased levels of TBX3 in S-phase are shown to occur transcriptionally through activation by c-Myc at E-box motifs located at -1210 and -701 bps and post-translationally by cyclin A-CDK2 phosphorylation. Importantly, when TBX3 is depleted by shRNA the cells accumulate in S-phase. These results suggest that TBX3 is required for cells to transit through S-phase and that this function may be linked to its role as a pro-proliferative factor.
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Affiliation(s)
- Tarryn Willmer
- a Department of Human Biology ; Faculty of Health Sciences; University of Cape Town ; Cape Town , South Africa
| | - Jade Peres
- a Department of Human Biology ; Faculty of Health Sciences; University of Cape Town ; Cape Town , South Africa
| | - Shaheen Mowla
- a Department of Human Biology ; Faculty of Health Sciences; University of Cape Town ; Cape Town , South Africa
| | - Amaal Abrahams
- a Department of Human Biology ; Faculty of Health Sciences; University of Cape Town ; Cape Town , South Africa
| | - Sharon Prince
- a Department of Human Biology ; Faculty of Health Sciences; University of Cape Town ; Cape Town , South Africa
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208
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Alicea-Velázquez NL, Shinsky SA, Loh DM, Lee JH, Skalnik DG, Cosgrove MS. Targeted Disruption of the Interaction between WD-40 Repeat Protein 5 (WDR5) and Mixed Lineage Leukemia (MLL)/SET1 Family Proteins Specifically Inhibits MLL1 and SETd1A Methyltransferase Complexes. J Biol Chem 2016; 291:22357-22372. [PMID: 27563068 DOI: 10.1074/jbc.m116.752626] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 08/23/2016] [Indexed: 11/06/2022] Open
Abstract
MLL1 belongs to the SET1 family of histone H3 lysine 4 (H3K4) methyltransferases, composed of MLL1-4 and SETd1A/B. MLL1 translocations are present in acute leukemias, and mutations in several family members are associated with cancer and developmental disorders. MLL1 associates with a subcomplex containing WDR5, RbBP5, ASH2L, and DPY-30 (WRAD), forming the MLL1 core complex required for H3K4 mono- and dimethylation and transcriptional activation. Core complex assembly requires interaction of WDR5 with the MLL1 Win (WDR5 interaction) motif, which is conserved across the SET1 family. Agents that mimic the SET1 family Win motif inhibit the MLL1 core complex and have become an attractive approach for targeting MLL1 in cancers. Like MLL1, other SET1 family members interact with WRAD, but the roles of the Win motif in complex assembly and enzymatic activity remain unexplored. Here, we show that the Win motif is necessary for interaction of WDR5 with all members of the human SET1 family. Mutation of the Win motif-WDR5 interface severely disrupts assembly and activity of MLL1 and SETd1A complexes but only modestly disrupts MLL2/4 and SETd1B complexes without significantly altering enzymatic activity in vitro Notably, in the absence of WDR5, MLL3 interacts with RAD and shows enhanced activity. To further probe the role of the Win motif-WDR5 interaction, we designed a peptidomimetic that binds WDR5 (Kd ∼3 nm) and selectively inhibits activity of MLL1 and SETd1A core complexes within the SET1 family. Our results reveal that SET1 family complexes with the weakest Win motif-WDR5 interaction are more susceptible to Win motif-based inhibitors.
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Affiliation(s)
- Nilda L Alicea-Velázquez
- From the Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210 and
| | - Stephen A Shinsky
- From the Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210 and
| | - Daniel M Loh
- From the Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210 and
| | - Jeong-Heon Lee
- the Biology Department, School of Science, Indiana University-Purdue University, Indianapolis, Indiana 46202
| | - David G Skalnik
- the Biology Department, School of Science, Indiana University-Purdue University, Indianapolis, Indiana 46202
| | - Michael S Cosgrove
- From the Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210 and
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209
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Lorenzin F, Benary U, Baluapuri A, Walz S, Jung LA, von Eyss B, Kisker C, Wolf J, Eilers M, Wolf E. Different promoter affinities account for specificity in MYC-dependent gene regulation. eLife 2016; 5. [PMID: 27460974 PMCID: PMC4963202 DOI: 10.7554/elife.15161] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/13/2016] [Indexed: 12/21/2022] Open
Abstract
Enhanced expression of the MYC transcription factor is observed in the majority of tumors. Two seemingly conflicting models have been proposed for its function: one proposes that MYC enhances expression of all genes, while the other model suggests gene-specific regulation. Here, we have explored the hypothesis that specific gene expression profiles arise since promoters differ in affinity for MYC and high-affinity promoters are fully occupied by physiological levels of MYC. We determined cellular MYC levels and used RNA- and ChIP-sequencing to correlate promoter occupancy with gene expression at different concentrations of MYC. Mathematical modeling showed that binding affinities for interactions of MYC with DNA and with core promoter-bound factors, such as WDR5, are sufficient to explain promoter occupancies observed in vivo. Importantly, promoter affinity stratifies different biological processes that are regulated by MYC, explaining why tumor-specific MYC levels induce specific gene expression programs and alter defined biological properties of cells. DOI:http://dx.doi.org/10.7554/eLife.15161.001 Genes with the potential to cause tumors and cancer are commonly called oncogenes. One example of an oncogene encodes for a protein called MYC and many tumors contain high levels of this protein. MYC is a transcription factor and studies of aggressive tumors suggested that, like most other transcription factors, MYC binds to and regulates the activity of a small number of genes in tumors. However, other studies went on to show that MYC actually binds to thousands of genes and somehow only regulates a subset of them during tumor development. Lorenzin et al. set out to understand how this process works by generating human cells in which the concentration of MYC protein could be altered. In the experiments, the concentration was varied from normal healthy levels to the high levels found in aggressive tumors. The amount of MYC bound to genes and the extent to which it activated the genes inside these cells was also measured. Lorenzin et al. found that increasing MYC levels from normal to tumor-specific levels did not affect MYC binding at genes where the transcription factor was already strongly bound in normal cells. Rather, MYC binding increased only at genes that were weakly bound in normal cells. Consistent with this observation, only genes at which MYC was weakly bound in normal cells were activated by increasing MYC levels. This observation suggests that increasing the concentration of MYC protein from normal to tumor-specific levels “fills up” previously empty binding sites around these genes with the transcription factor. Lorenzin et al. also used mathematical modeling to understand how the concentrations of MYC in normal and tumor cells might explain how MYC behaves in cells. Together, the results imply that the MYC transcription factor regulates distinct sets of genes in normal and tumor cells according to how much MYC is present. Further studies may show that the altered regulation of a tumor-specific set of genes is important for tumor development and could use this new information to identify new targets for treating MYC-driven tumors. DOI:http://dx.doi.org/10.7554/eLife.15161.002
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Affiliation(s)
- Francesca Lorenzin
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Uwe Benary
- Group Mathematical Modeling of Cellular Processes, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Apoorva Baluapuri
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Susanne Walz
- Core Unit Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | - Lisa Anna Jung
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany.,Rudolf-Virchow-Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Björn von Eyss
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Caroline Kisker
- Rudolf-Virchow-Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Jana Wolf
- Group Mathematical Modeling of Cellular Processes, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | - Elmar Wolf
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Würzburg, Germany
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210
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Carugo A, Genovese G, Seth S, Nezi L, Rose JL, Bossi D, Cicalese A, Shah PK, Viale A, Pettazzoni PF, Akdemir KC, Bristow CA, Robinson FS, Tepper J, Sanchez N, Gupta S, Estecio MR, Giuliani V, Dellino GI, Riva L, Yao W, Di Francesco ME, Green T, D'Alesio C, Corti D, Kang Y, Jones P, Wang H, Fleming JB, Maitra A, Pelicci PG, Chin L, DePinho RA, Lanfrancone L, Heffernan TP, Draetta GF. In Vivo Functional Platform Targeting Patient-Derived Xenografts Identifies WDR5-Myc Association as a Critical Determinant of Pancreatic Cancer. Cell Rep 2016; 16:133-147. [PMID: 27320920 DOI: 10.1016/j.celrep.2016.05.063] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 03/21/2016] [Accepted: 05/16/2016] [Indexed: 12/28/2022] Open
Abstract
Current treatment regimens for pancreatic ductal adenocarcinoma (PDAC) yield poor 5-year survival, emphasizing the critical need to identify druggable targets essential for PDAC maintenance. We developed an unbiased and in vivo target discovery approach to identify molecular vulnerabilities in low-passage and patient-derived PDAC xenografts or genetically engineered mouse model-derived allografts. Focusing on epigenetic regulators, we identified WDR5, a core member of the COMPASS histone H3 Lys4 (H3K4) MLL (1-4) methyltransferase complex, as a top tumor maintenance hit required across multiple human and mouse tumors. Mechanistically, WDR5 functions to sustain proper execution of DNA replication in PDAC cells, as previously suggested by replication stress studies involving MLL1, and c-Myc, also found to interact with WDR5. We indeed demonstrate that interaction with c-Myc is critical for this function. By showing that ATR inhibition mimicked the effects of WDR5 suppression, these data provide rationale to test ATR and WDR5 inhibitors for activity in this disease.
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Affiliation(s)
- Alessandro Carugo
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy.
| | - Giannicola Genovese
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sahil Seth
- Institute for Applied Cancer Science, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Luigi Nezi
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Johnathon Lynn Rose
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Daniela Bossi
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Angelo Cicalese
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | | | - Andrea Viale
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Piergiorgio Francesco Pettazzoni
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kadir Caner Akdemir
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Frederick Scott Robinson
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - James Tepper
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nora Sanchez
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sonal Gupta
- Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marcos Roberto Estecio
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Virginia Giuliani
- Institute for Applied Cancer Science, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy; Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Laura Riva
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), Milan 20139, Italy
| | - Wantong Yao
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria Emilia Di Francesco
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Institute for Applied Cancer Science, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tessa Green
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Carolina D'Alesio
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Denise Corti
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ya'an Kang
- Department of Surgical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Philip Jones
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Institute for Applied Cancer Science, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huamin Wang
- Department of Pathology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jason Bates Fleming
- Department of Surgical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Anirban Maitra
- Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy; Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Lynda Chin
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Institute for Applied Cancer Science, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Luisa Lanfrancone
- Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy.
| | | | - Giulio Francesco Draetta
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Institute for Applied Cancer Science, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
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211
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Lundberg SM, Tu WB, Raught B, Penn LZ, Hoffman MM, Lee SI. ChromNet: Learning the human chromatin network from all ENCODE ChIP-seq data. Genome Biol 2016; 17:82. [PMID: 27139377 PMCID: PMC4852466 DOI: 10.1186/s13059-016-0925-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/15/2016] [Indexed: 01/12/2023] Open
Abstract
A cell's epigenome arises from interactions among regulatory factors-transcription factors and histone modifications-co-localized at particular genomic regions. We developed a novel statistical method, ChromNet, to infer a network of these interactions, the chromatin network, by inferring conditional-dependence relationships among a large number of ChIP-seq data sets. We applied ChromNet to all available 1451 ChIP-seq data sets from the ENCODE Project, and showed that ChromNet revealed previously known physical interactions better than alternative approaches. We experimentally validated one of the previously unreported interactions, MYC-HCFC1. An interactive visualization tool is available at http://chromnet.cs.washington.edu.
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Affiliation(s)
- Scott M Lundberg
- Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - William B Tu
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Brian Raught
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Linda Z Penn
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Michael M Hoffman
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Princess Margaret Cancer Centre, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Su-In Lee
- Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA. .,Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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212
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Xu Y, Zhang M, Li W, Zhu X, Bao X, Qin B, Hutchins AP, Esteban MA. Transcriptional Control of Somatic Cell Reprogramming. Trends Cell Biol 2016; 26:272-288. [DOI: 10.1016/j.tcb.2015.12.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 12/07/2015] [Accepted: 12/16/2015] [Indexed: 01/26/2023]
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213
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Richart L, Real FX, Sanchez-Arevalo Lobo VJ. c-MYC partners with BPTF in human cancer. Mol Cell Oncol 2016; 3:e1152346. [PMID: 27314097 DOI: 10.1080/23723556.2016.1152346] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 10/22/2022]
Abstract
The c-MYC oncogene is deregulated in virtually all human tumors and therefore constitutes an attractive therapeutic target. We found that the chromatin remodeler BPTF is a c-MYC interactor required for c-MYC chromatin recruitment and transcriptional activity. Moreover, inhibition of BPTF delays tumor development both in vitro and in vivo and its levels positively correlate with c-MYC signatures in human tumors. We propose BPTF as a therapeutic target in c-MYC-addicted tumors.
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Affiliation(s)
- Laia Richart
- Epithelial Carcinogenesis Group, Cancer Cell Biology Program, Spanish National Cancer Research Center-CNIO , Madrid, Spain
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Cancer Cell Biology Program, Spanish National Cancer Research Center-CNIO, Madrid, Spain; Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
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214
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BPTF is required for c-MYC transcriptional activity and in vivo tumorigenesis. Nat Commun 2016; 7:10153. [PMID: 26729287 PMCID: PMC4728380 DOI: 10.1038/ncomms10153] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 11/06/2015] [Indexed: 01/06/2023] Open
Abstract
c-MYC oncogene is deregulated in most human tumours. Histone marks associated with transcriptionally active genes define high-affinity c-MYC targets. The mechanisms involved in their recognition by c-MYC are unknown. Here we report that c-MYC interacts with BPTF, a core subunit of the NURF chromatin-remodelling complex. BPTF is required for the activation of the full c-MYC transcriptional programme in fibroblasts. BPTF knockdown leads to decreased c-MYC recruitment to DNA and changes in chromatin accessibility. In Bptf-null MEFs, BPTF is necessary for c-MYC-driven proliferation, G1–S progression and replication stress, but not for c-MYC-driven apoptosis. Bioinformatics analyses unveil that BPTF levels correlate positively with c-MYC-driven transcriptional signatures. In vivo, Bptf inactivation in pre-neoplastic pancreatic acinar cells significantly delays tumour development and extends survival. Our findings uncover BPTF as a crucial c-MYC co-factor required for its biological activity and suggest that the BPTF-c-MYC axis is a potential therapeutic target in cancer. c-MYC genomic distribution is dictated by the epigenetic context but the mechanisms are unknown. Here, the authors show that c-MYC requires the chromatin reader BPTF to activate its transcriptional program and promote tumour development in vivo, suggesting that BPTF is a potential target for cancer therapy.
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215
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Abstract
The MYC oncogene plays a pivotal role in the development and progression of human cancers. It encodes a transcription factor that has broad reaching effects on many cellular functions, most importantly in driving cell growth through regulation of genes involved in ribosome biogenesis, metabolism, and cell cycle. Upon binding DNA with its partner MAX, MYC recruits factors that release paused RNA polymerases to drive transcription and amplify gene expression. At physiologic levels of MYC, occupancy of high-affinity DNA-binding sites drives 'house-keeping' metabolic genes and those involved in ribosome and mitochondrial biogenesis for biomass accumulation. At high oncogenic levels of MYC, invasion of low-affinity sites and enhancer sequences alter the transcriptome and cause metabolic imbalances, which activates stress response and checkpoints such as p53. Loss of checkpoints unleashes MYC's full oncogenic potential to couple metabolism with neoplastic cell growth and division. Cells that overexpress MYC, however, are vulnerable to metabolic perturbations that provide potential new avenues for cancer therapy.
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216
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Jaenicke LA, von Eyss B, Carstensen A, Wolf E, Xu W, Greifenberg AK, Geyer M, Eilers M, Popov N. Ubiquitin-Dependent Turnover of MYC Antagonizes MYC/PAF1C Complex Accumulation to Drive Transcriptional Elongation. Mol Cell 2015; 61:54-67. [PMID: 26687678 DOI: 10.1016/j.molcel.2015.11.007] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 10/06/2015] [Accepted: 11/04/2015] [Indexed: 12/31/2022]
Abstract
MYC is an unstable protein, and its turnover is controlled by the ubiquitin system. Ubiquitination enhances MYC-dependent transactivation, but the underlying mechanism remains unresolved. Here we show that MYC proteasomal turnover is dispensable for loading of RNA polymerase II (RNAPII). In contrast, MYC turnover is essential for recruitment of TRRAP, histone acetylation, and binding of BRD4 and P-TEFb to target promoters, leading to phosphorylation of RNAPII and transcriptional elongation. In the absence of histone acetylation and P-TEFb recruitment, MYC associates with the PAF1 complex (PAF1C) through a conserved domain in the MYC amino terminus ("MYC box I"). Depletion of the PAF1C subunit CDC73 enhances expression of MYC target genes, suggesting that the MYC/PAF1C complex can inhibit transcription. Because several ubiquitin ligases bind to MYC via the same domain ("MYC box II") that interacts with TRRAP, we propose that degradation of MYC limits the accumulation of MYC/PAF1C complexes during transcriptional activation.
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Affiliation(s)
- Laura A Jaenicke
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Björn von Eyss
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Anne Carstensen
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Elmar Wolf
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Wenshan Xu
- Comprehensive Cancer Center Mainfranken, Versbacher Straße 5, 97078 Würzburg, Germany
| | - Ann Katrin Greifenberg
- Department of Structural Immunology, Institute of Innate Immunity, University Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Matthias Geyer
- Department of Structural Immunology, Institute of Innate Immunity, University Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; Comprehensive Cancer Center Mainfranken, Versbacher Straße 5, 97078 Würzburg, Germany.
| | - Nikita Popov
- Comprehensive Cancer Center Mainfranken, Versbacher Straße 5, 97078 Würzburg, Germany; Department of Radiation Oncology, University Hospital Würzburg, Josef-Schneider-Straße 11, 97080 Würzburg, Germany.
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217
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Harikumar A, Meshorer E. Chromatin remodeling and bivalent histone modifications in embryonic stem cells. EMBO Rep 2015; 16:1609-19. [PMID: 26553936 DOI: 10.15252/embr.201541011] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/05/2015] [Indexed: 11/09/2022] Open
Abstract
Pluripotent embryonic stem cells (ESCs) are characterized by distinct epigenetic features including a relative enrichment of histone modifications related to active chromatin. Among these is tri-methylation of lysine 4 on histone H3 (H3K4me3). Several thousands of the H3K4me3-enriched promoters in pluripotent cells also contain a repressive histone mark, namely H3K27me3, a situation referred to as "bivalency". While bivalent promoters are not unique to pluripotent cells, they are relatively enriched in these cell types, largely marking developmental and lineage-specific genes which are silent but poised for immediate action. The H3K4me3 and H3K27me3 modifications are catalyzed by lysine methyltransferases which are usually found within, although not entirely limited to, the Trithorax group (TrxG) and Polycomb group (PcG) protein complexes, respectively, but these do not provide selective bivalent specificity. Recent studies highlight the family of ATP-dependent chromatin remodeling proteins as regulators of bivalent domains. Here, we discuss bivalency in general, describe the machineries that catalyze bivalent chromatin domains, and portray the emerging connection between bivalency and the action of different families of chromatin remodelers, namely INO80, esBAF, and NuRD, in pluripotent cells. We posit that chromatin remodeling proteins may enable "bivalent specificity", often selectively acting on, or selectively depleted from, bivalent domains.
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Affiliation(s)
- Arigela Harikumar
- Department of Genetics, Institute of Life Sciences and The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eran Meshorer
- Department of Genetics, Institute of Life Sciences and The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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218
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Thomas LR, Foshage AM, Weissmiller AM, Popay TM, Grieb BC, Qualls SJ, Ng V, Carboneau B, Lorey S, Eischen CM, Tansey WP. Interaction of MYC with host cell factor-1 is mediated by the evolutionarily conserved Myc box IV motif. Oncogene 2015; 35:3613-8. [PMID: 26522729 PMCID: PMC4853269 DOI: 10.1038/onc.2015.416] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 09/23/2015] [Accepted: 09/28/2015] [Indexed: 01/04/2023]
Abstract
The MYC family of oncogenes encodes a set of three related transcription factors that are overexpressed in many human tumors and contribute to the cancer-related deaths of more than 70,000 Americans every year. MYC proteins drive tumorigenesis by interacting with co-factors that enable them to regulate the expression of thousands of genes linked to cell growth, proliferation, metabolism, and genome stability. One effective way to identify critical cofactors required for MYC function has been to focus on sequence motifs within MYC that are conserved throughout evolution, on the assumption that their conservation is driven by protein-protein interactions that are vital for MYC activity. In addition to their DNA-binding domains, MYC proteins carry five regions of high sequence conservation known as Myc boxes (Mb). To date, four of the Myc box motifs (MbI, MbII, MbIIIa, and MbIIIb) have had a molecular function assigned to them, but the precise role of the remaining Myc box, MbIV, and the reason for its preservation in vertebrate Myc proteins, is unknown. Here, we show that MbIV is required for the association of MYC with the abundant transcriptional coregulator host cell factor 1 (HCF-1). We show that the invariant core of MbIV resembles the tetrapeptide HCF-binding motif (HBM) found in many HCF-interaction partners, and demonstrate that MYC interacts with HCF in a manner indistinguishable from the prototypical HBM-containing protein VP16. Finally, we show that rationalized point mutations in MYC that disrupt interaction with HCF-1 attenuate the ability of MYC to drive tumorigenesis in mice. Together, these data expose a molecular function for MbIV and indicate that HCF-1 is an important co-factor for MYC.
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Affiliation(s)
- L R Thomas
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - A M Foshage
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - A M Weissmiller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - T M Popay
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.,Vanderbilt International Scholar Program, Vanderbilt University, Nashville, TN, USA
| | - B C Grieb
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - S J Qualls
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - V Ng
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - B Carboneau
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - S Lorey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - C M Eischen
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - W P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
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219
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Abstract
Two opposing models have been proposed to describe the function of the MYC oncoprotein in shaping cellular transcriptomes: one posits that MYC amplifies transcription at all active loci; the other that MYC differentially controls discrete sets of genes, the products of which affect global transcript levels. Here, we argue that differential gene regulation by MYC is the sole unifying model that is consistent with all available data. Among other effects, MYC endows cells with physiological and metabolic changes that have the potential to feed back on global RNA production, processing and turnover. The field is progressing steadily towards a full characterization of the MYC-regulated genes and pathways that mediate these biological effects and - by the same token - endow MYC with its pervasive oncogenic potential.
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Affiliation(s)
- Theresia R Kress
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT) and Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy
| | - Arianna Sabò
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT) and Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy
| | - Bruno Amati
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT) and Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy
- Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy
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220
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Genomic Determinants of THAP11/ZNF143/HCFC1 Complex Recruitment to Chromatin. Mol Cell Biol 2015; 35:4135-46. [PMID: 26416877 DOI: 10.1128/mcb.00477-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 09/21/2015] [Indexed: 01/10/2023] Open
Abstract
The THAP11 and ZNF143 transcription factors recognize overlapping DNA sequences and are reported to exhibit signs of both competitive and cooperative binding. HCFC1 serves as a scaffold protein, bridging interactions between transcription factors, including THAP11 and ZNF143, and transcriptional coregulators. The exact mechanism of how DNA sequences guide the recruitment of the THAP11/ZNF143/HCFC1 complex to chromatin is still controversial. In this study, we use chromosomally integrated synthetic constructs and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9-mediated approaches in intact cells to elucidate the role of the DNA sequence in the recruitment of this complex and to establish its biological relevance. We show that the ACTACA submotif, shared by both THAP11 and ZNF143, directs the recruitment of THAP11 and HCFC1 to ZNF143-occupied loci. Importantly, its position, spacing, and orientation relative to the ZNF143 core motif are critical for this action. CRISPR-Cas9-mediated alterations of the ACTACA submotif at endogenous promoters recapitulated results obtained with synthetic constructs and resulted in altered gene transcription and histone modifications at targeted promoters. Our in vivo approaches provide strong evidence for the molecular role of the ACTACA submotif in THAP11, ZNF143, and HCFC1 cooperative recruitment to chromatin and its biological role in target gene expression.
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221
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Thomas LR, Foshage AM, Weissmiller AM, Tansey WP. The MYC-WDR5 Nexus and Cancer. Cancer Res 2015; 75:4012-5. [PMID: 26383167 DOI: 10.1158/0008-5472.can-15-1216] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/10/2015] [Indexed: 02/05/2023]
Abstract
The MYC oncogenes encode a family of transcription factors that feature prominently in cancer. MYC proteins are overexpressed or deregulated in a majority of malignancies and drive tumorigenesis by inducing widespread transcriptional reprogramming that promotes cell proliferation, metabolism, and genomic instability. The ability of MYC to regulate transcription depends on its dimerization with MAX, which creates a DNA-binding domain that recognizes specific sequences in the regulatory elements of MYC target genes. Recently, we discovered that recognition of target genes by MYC also depends on its interaction with WDR5, a WD40-repeat protein that exists as part of several chromatin-regulatory complexes. Here, we discuss how interaction of MYC with WDR5 could create an avidity-based chromatin recognition mechanism that allows MYC to select its target genes in response to both genetic and epigenetic determinants. We rationalize how the MYC-WDR5 interaction provides plasticity in target gene selection by MYC and speculate on the biochemical and genomic contexts in which this interaction occurs. Finally, we discuss how properties of the MYC-WDR5 interface make it an attractive point for discovery of small-molecule inhibitors of MYC function in cancer cells.
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Affiliation(s)
- Lance R Thomas
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Audra M Foshage
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - April M Weissmiller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee.
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222
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Stine ZE, Walton ZE, Altman BJ, Hsieh AL, Dang CV. MYC, Metabolism, and Cancer. Cancer Discov 2015; 5:1024-39. [PMID: 26382145 DOI: 10.1158/2159-8290.cd-15-0507] [Citation(s) in RCA: 939] [Impact Index Per Article: 93.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/10/2015] [Indexed: 02/07/2023]
Abstract
UNLABELLED The MYC oncogene encodes a transcription factor, MYC, whose broad effects make its precise oncogenic role enigmatically elusive. The evidence to date suggests that MYC triggers selective gene expression amplification to promote cell growth and proliferation. Through its targets, MYC coordinates nutrient acquisition to produce ATP and key cellular building blocks that increase cell mass and trigger DNA replication and cell division. In cancer, genetic and epigenetic derangements silence checkpoints and unleash MYC's cell growth- and proliferation-promoting metabolic activities. Unbridled growth in response to deregulated MYC expression creates dependence on MYC-driven metabolic pathways, such that reliance on specific metabolic enzymes provides novel targets for cancer therapy. SIGNIFICANCE MYC's expression and activity are tightly regulated in normal cells by multiple mechanisms, including a dependence upon growth factor stimulation and replete nutrient status. In cancer, genetic deregulation of MYC expression and loss of checkpoint components, such as TP53, permit MYC to drive malignant transformation. However, because of the reliance of MYC-driven cancers on specific metabolic pathways, synthetic lethal interactions between MYC overexpression and specific enzyme inhibitors provide novel cancer therapeutic opportunities.
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Affiliation(s)
- Zachary E Stine
- Abramson Family Cancer Research Institute, Abramson Cancer Center of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Zandra E Walton
- Abramson Family Cancer Research Institute, Abramson Cancer Center of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Brian J Altman
- Abramson Family Cancer Research Institute, Abramson Cancer Center of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Annie L Hsieh
- Abramson Family Cancer Research Institute, Abramson Cancer Center of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Chi V Dang
- Abramson Family Cancer Research Institute, Abramson Cancer Center of the University of Pennsylvania, Philadelphia, Pennsylvania.
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Affiliation(s)
- Patrick Trojer
- Constellation Pharmaceuticals Inc., Cambridge, Massachusetts, USA
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