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Herranz-Montoya I, Angulo-Aguado M, Perna C, Zagorac S, García-Jimeno L, Park S, Djouder N. p53 protein degradation redefines the initiation mechanisms and drives transitional mutations in colorectal cancer. Nat Commun 2025; 16:3934. [PMID: 40287431 PMCID: PMC12033273 DOI: 10.1038/s41467-025-59282-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 04/16/2025] [Indexed: 04/29/2025] Open
Abstract
Incidence of colorectal cancer (CRC) is increasing likely due to different mechanisms driving initiation and progression. The initial model proposed by Fearon and Vogelstein posits it as a multi-hit neoplasia, originating from adenomatous-polyps induced by WNT activation, ultimately progressing to aggressiveness through p53 loss. Integrating human data with mouse genetics, we redefine this paradigm, highlighting pivotal roles of MYC, oncogenic URI and p53 degradation to initiate CRC. Early APC loss activates MYC to transcriptionally upregulate URI, which modulates MDM2 activity, triggering p53 proteasomal degradation, essential for tumour initiation and mutation burden accrual in CRC mice. Remarkably, reinstating p53 levels via genetic URI depletion or p53 super-expression in CRC mice with WNT pathway activation prevents tumour initiation and extends lifespan. Our data reveal a "two-hit" genetic model central to APC loss-driven CRC initiation, wherein MYC/URI axis intricately controls p53 degradation, offering mechanistic insights into transitional mutation acquisition essential for CRC progression.
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Affiliation(s)
- Irene Herranz-Montoya
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Centro Nacional Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - Mariana Angulo-Aguado
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Centro Nacional Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - Cristian Perna
- Department of Pathology, Hospital Universitario Ramón y Cajal, IRYCIS, 28034, Madrid, Spain
- Universidad de Alcalá, 28801, Madrid, Spain
| | - Sladjana Zagorac
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Centro Nacional Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - Luis García-Jimeno
- Computational Cancer Genomics Group, Structural Biology Programme, Centro Nacional Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - Solip Park
- Computational Cancer Genomics Group, Structural Biology Programme, Centro Nacional Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain
| | - Nabil Djouder
- Growth Factors, Nutrients and Cancer Group, Molecular Oncology Programme, Centro Nacional Investigaciones Oncológicas (CNIO), 28029, Madrid, Spain.
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2
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Jones JE, Gunderson CE, Wigdahl B, Nonnemacher MR. Impact of chromatin on HIV-1 latency: a multi-dimensional perspective. Epigenetics Chromatin 2025; 18:9. [PMID: 40055755 PMCID: PMC11889793 DOI: 10.1186/s13072-025-00573-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2025] [Accepted: 02/04/2025] [Indexed: 05/13/2025] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) is a retrovirus that infects multiple immune cell types and integrates into host cell DNA termed provirus. Under antiretroviral control, provirus in cells is able to evade targeting by both host immune surveillance and antiretroviral drug regimens. Additionally, the provirus remains integrated for the life of the cell, and clonal expansion establishes a persistent reservoir. As host cells become quiescent following the acute stage of infection, the provirus also enters a latent state characterized by low levels of transcription and virion production. Proviral latency may last years or even decades, but stimuli such as immune activation, accumulation of viral proteins, and certain medications can trigger reactivation of proviral gene expression. Left untreated, this can lead to virema, development of pathogenic out comes, and even death as the immune system becomes weakened and dysregulated. Over the last few decades, the role of chromatin in both HIV-1 latency and reactivation has been characterized in-depth, and a number of host factors have been identified as key players in modifying the local (2D) chromatin environment of the provirus. Here, the impact of the 2D chromatin environment and its related factors are reviewed. Enzymes that catalyze the addition or removal of covalent groups from histone proteins, such as histone deacetylase complexes (HDACs) and methyltransferases (HMTs) are of particular interest, as they both alter the affinity of histones for proviral DNA and function to recruit other proteins that contribute to chromatin remodeling and gene expression from the provirus. More recently, advances in next-generation sequencing and imaging technology has enabled the study of how the higher-order (3D) chromatin environment relates to proviral latency, including the impacts of integration site and cell type. All together, these multi-dimensional factors regulate latency by influencing the degree of accessibility to the proviral DNA by transcription machinery. Finally, additional implications for therapeutics and functional studies are proposed and discussed.
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Affiliation(s)
- Joanna E Jones
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Chelsea E Gunderson
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA
- Sidney Kimmel Comprehensive Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19102, USA.
- Center for Molecular Virology and Gene Therapy, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, 19102, USA.
- Sidney Kimmel Comprehensive Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
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3
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Babaei-Abraki S, Karamali F, Nasr-Esfahani MH. The Role of Endoplasmic Reticulum and Mitochondria in Maintaining Redox Status and Glycolytic Metabolism in Pluripotent Stem Cells. Stem Cell Rev Rep 2022; 18:1789-1808. [PMID: 35141862 DOI: 10.1007/s12015-022-10338-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2022] [Indexed: 10/19/2022]
Abstract
Pluripotent stem cells (PSCs), including embryonic stem cells and induced pluripotent stem cells (iPSCs), can be applicable for regenerative medicine. They strangely rely on glycolysis metabolism akin to aerobic glycolysis in cancer cells. Upon differentiation, PSCs undergo a metabolic shift from glycolysis to oxidative phosphorylation (OXPHOS). The metabolic shift depends on organelles maturation, transcriptome modification, and metabolic switching. Besides, metabolism-driven chromatin regulation is necessary for cell survival, self-renewal, proliferation, senescence, and differentiation. In this respect, mitochondria may serve as key organelle to adapt environmental changes with metabolic intermediates which are necessary for maintaining PSCs identity. The endoplasmic reticulum (ER) is another organelle whose role in cellular identity remains under-explored. The purpose of our article is to highlight the recent progress on these two organelles' role in maintaining PSCs redox status focusing on metabolism. Topics include redox status, metabolism regulation, mitochondrial dynamics, and ER stress in PSCs. They relate to the maintenance of stem cell properties and subsequent differentiation of stem cells into specific cell types.
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Affiliation(s)
- Shahnaz Babaei-Abraki
- Department of Plant and Animal Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.,Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Fereshteh Karamali
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Mohammad Hossein Nasr-Esfahani
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
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4
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Sradhanjali S, Rout P, Tripathy D, Kaliki S, Rath S, Modak R, Mittal R, Chowdary TK, Reddy MM. The Oncogene MYCN Modulates Glycolytic and Invasive Genes to Enhance Cell Viability and Migration in Human Retinoblastoma. Cancers (Basel) 2021; 13:cancers13205248. [PMID: 34680394 PMCID: PMC8533785 DOI: 10.3390/cancers13205248] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/21/2022] Open
Abstract
Retinoblastoma is usually initiated by biallelic RB1 gene inactivation. In addition, MYCN copy number alterations also contribute to RB pathogenesis. However, MYCN expression, its role in disease progression and correlation with RB histological risk factors are not well understood. We studied the expression of MYCN in enucleated RB patient specimens by immunohistochemistry. MYCN is overexpressed in RB compared to control retina. Our microarray gene expression analysis followed by qRT-PCR validation revealed that genes involved in glucose metabolism and migration are significantly downregulated in MYCN knockdown cells. Further, targeting MYCN in RB cells using small molecule compounds or shRNAs led to decreased cell survival and migration, increased apoptosis and cell cycle arrest, suggesting that MYCN inhibition can be a potential therapeutic strategy. We also noted that MYCN inhibition results in reduction in glucose uptake, lactate production, ROS levels and gelatinolytic activity of active-MMP9, explaining a possible mechanism of MYCN in RB. Taking clues from our findings, we tested a combination treatment of RB cells with carboplatin and MYCN inhibitors to find enhanced therapeutic efficacy compared to single drug treatment. Thus, MYCN inhibition can be a potential therapeutic strategy in combination with existing chemotherapy drugs to restrict tumor cell growth in RB.
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Affiliation(s)
- Swatishree Sradhanjali
- The Operation Eyesight Universal Institute for Eye Cancer, LV Prasad Eye Institute, Bhubaneswar 751024, Odisha, India; (S.S.); (P.R.)
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar 751024, Odisha, India;
| | - Padmalochan Rout
- The Operation Eyesight Universal Institute for Eye Cancer, LV Prasad Eye Institute, Bhubaneswar 751024, Odisha, India; (S.S.); (P.R.)
- Novo Nordisk, Bangalore 560066, Karnataka, India
| | - Devjyoti Tripathy
- Ophthalmic Plastics, Orbit and Ocular Oncology Service, LV Prasad Eye Institute, Bhubaneswar 751024, Odisha, India; (D.T.); (S.R.)
| | - Swathi Kaliki
- The Operation Eyesight Universal Institute for Eye Cancer, LV Prasad Eye Institute, Hyderabad 500034, Telangana, India;
| | - Suryasnata Rath
- Ophthalmic Plastics, Orbit and Ocular Oncology Service, LV Prasad Eye Institute, Bhubaneswar 751024, Odisha, India; (D.T.); (S.R.)
| | - Rahul Modak
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar 751024, Odisha, India;
| | - Ruchi Mittal
- Kanupriya Dalmia Ophthalmic Pathology Laboratory, LV Prasad Eye Institute, Bhubaneswar 751024, Odisha, India;
- Department of Pathology, Kalinga Institute of Medical Sciences, Bhubaneswar 751024, Odisha, India
| | - Tirumala Kumar Chowdary
- School of Biological Sciences, National Institute of Science Education and Research, Homi Bhabha National Institute, Bhubaneswar 752050, Odisha, India;
| | - Mamatha M. Reddy
- The Operation Eyesight Universal Institute for Eye Cancer, LV Prasad Eye Institute, Bhubaneswar 751024, Odisha, India; (S.S.); (P.R.)
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar 751024, Odisha, India;
- Correspondence: or ; Tel.: +91-674-3987175
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5
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Mechanisms of Binding Specificity among bHLH Transcription Factors. Int J Mol Sci 2021; 22:ijms22179150. [PMID: 34502060 PMCID: PMC8431614 DOI: 10.3390/ijms22179150] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/14/2021] [Accepted: 08/18/2021] [Indexed: 12/25/2022] Open
Abstract
The transcriptome of every cell is orchestrated by the complex network of interaction between transcription factors (TFs) and their binding sites on DNA. Disruption of this network can result in many forms of organism malfunction but also can be the substrate of positive natural selection. However, understanding the specific determinants of each of these individual TF-DNA interactions is a challenging task as it requires integrating the multiple possible mechanisms by which a given TF ends up interacting with a specific genomic region. These mechanisms include DNA motif preferences, which can be determined by nucleotide sequence but also by DNA’s shape; post-translational modifications of the TF, such as phosphorylation; and dimerization partners and co-factors, which can mediate multiple forms of direct or indirect cooperative binding. Binding can also be affected by epigenetic modifications of putative target regions, including DNA methylation and nucleosome occupancy. In this review, we describe how all these mechanisms have a role and crosstalk in one specific family of TFs, the basic helix-loop-helix (bHLH), with a very conserved DNA binding domain and a similar DNA preferred motif, the E-box. Here, we compile and discuss a rich catalog of strategies used by bHLH to acquire TF-specific genome-wide landscapes of binding sites.
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6
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Shrestha S, Morcavallo A, Gorrini C, Chesler L. Biological Role of MYCN in Medulloblastoma: Novel Therapeutic Opportunities and Challenges Ahead. Front Oncol 2021; 11:694320. [PMID: 34195095 PMCID: PMC8236857 DOI: 10.3389/fonc.2021.694320] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/19/2021] [Indexed: 12/13/2022] Open
Abstract
The constitutive and dysregulated expression of the transcription factor MYCN has a central role in the pathogenesis of the paediatric brain tumour medulloblastoma, with an increased expression of this oncogene correlating with a worse prognosis. Consequently, the genomic and functional alterations of MYCN represent a major therapeutic target to attenuate tumour growth in medulloblastoma. This review will provide a comprehensive synopsis of the biological role of MYCN and its family components, their interaction with distinct signalling pathways, and the implications of this network in medulloblastoma development. We will then summarise the current toolbox for targeting MYCN and highlight novel therapeutic avenues that have the potential to results in better-tailored clinical treatments.
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Affiliation(s)
- Sumana Shrestha
- Division of Clinical Studies, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Alaide Morcavallo
- Division of Clinical Studies, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Chiara Gorrini
- Division of Clinical Studies, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom
| | - Louis Chesler
- Division of Clinical Studies, Institute of Cancer Research (ICR), London and Royal Marsden NHS Trust, Sutton, United Kingdom.,Division of Cancer Therapeutics, The Institute of Cancer Research (ICR), and The Royal Marsden NHS Trust, Sutton, United Kingdom
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7
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Pellanda P, Dalsass M, Filipuzzi M, Loffreda A, Verrecchia A, Castillo Cano V, Thabussot H, Doni M, Morelli MJ, Soucek L, Kress T, Mazza D, Mapelli M, Beaulieu ME, Amati B, Sabò A. Integrated requirement of non-specific and sequence-specific DNA binding in Myc-driven transcription. EMBO J 2021; 40:e105464. [PMID: 33792944 DOI: 10.15252/embj.2020105464] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 02/15/2021] [Accepted: 02/24/2021] [Indexed: 12/17/2022] Open
Abstract
Eukaryotic transcription factors recognize specific DNA sequence motifs, but are also endowed with generic, non-specific DNA-binding activity. How these binding modes are integrated to determine select transcriptional outputs remains unresolved. We addressed this question by site-directed mutagenesis of the Myc transcription factor. Impairment of non-specific DNA backbone contacts caused pervasive loss of genome interactions and gene regulation, associated with increased intra-nuclear mobility of the Myc protein in murine cells. In contrast, a mutant lacking base-specific contacts retained DNA-binding and mobility profiles comparable to those of the wild-type protein, but failed to recognize its consensus binding motif (E-box) and could not activate Myc-target genes. Incidentally, this mutant gained weak affinity for an alternative motif, driving aberrant activation of different genes. Altogether, our data show that non-specific DNA binding is required to engage onto genomic regulatory regions; sequence recognition in turn contributes to transcriptional activation, acting at distinct levels: stabilization and positioning of Myc onto DNA, and-unexpectedly-promotion of its transcriptional activity. Hence, seemingly pervasive genome interaction profiles, as detected by ChIP-seq, actually encompass diverse DNA-binding modalities, driving defined, sequence-dependent transcriptional responses.
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Affiliation(s)
- Paola Pellanda
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy.,Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Mattia Dalsass
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | | | - Alessia Loffreda
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Virginia Castillo Cano
- Peptomyc S.L., Barcelona, Spain.,Vall d'Hebron Institute of Oncology (VHIO), Edifici Cellex, Barcelona, Spain
| | | | - Mirko Doni
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Marco J Morelli
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Laura Soucek
- Peptomyc S.L., Barcelona, Spain.,Vall d'Hebron Institute of Oncology (VHIO), Edifici Cellex, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Theresia Kress
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Davide Mazza
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marina Mapelli
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | | | - Bruno Amati
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Arianna Sabò
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
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8
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Liu R, Shi P, Wang Z, Yuan C, Cui H. Molecular Mechanisms of MYCN Dysregulation in Cancers. Front Oncol 2021; 10:625332. [PMID: 33614505 PMCID: PMC7886978 DOI: 10.3389/fonc.2020.625332] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/18/2020] [Indexed: 12/17/2022] Open
Abstract
MYCN, a member of MYC proto-oncogene family, encodes a basic helix-loop-helix transcription factor N-MYC. Abnormal expression of N-MYC is correlated with high-risk cancers and poor prognosis. Initially identified as an amplified oncogene in neuroblastoma in 1983, the oncogenic effect of N-MYC is expanded to multiple neuronal and nonneuronal tumors. Direct targeting N-MYC remains challenge due to its "undruggable" features. Therefore, alternative therapeutic approaches for targeting MYCN-driven tumors have been focused on the disruption of transcription, translation, protein stability as well as synthetic lethality of MYCN. In this review, we summarize the latest advances in understanding the molecular mechanisms of MYCN dysregulation in cancers.
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Affiliation(s)
- Ruochen Liu
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
- NHC Key Laboratory of Birth Defects and Reproductive Health (Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute), Chongqing, China
| | - Pengfei Shi
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
- NHC Key Laboratory of Birth Defects and Reproductive Health (Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute), Chongqing, China
| | - Zhongze Wang
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Chaoyu Yuan
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
- Cancer Center, Reproductive Medicine Center, Medical Research Institute, Southwest University, Chongqing, China
- NHC Key Laboratory of Birth Defects and Reproductive Health (Chongqing Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute), Chongqing, China
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9
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Inamoto I, Sheoran I, Popa SC, Hussain M, Shin JA. Combining Rational Design and Continuous Evolution on Minimalist Proteins That Target the E-box DNA Site. ACS Chem Biol 2021; 16:35-44. [PMID: 33370105 DOI: 10.1021/acschembio.0c00684] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein-based therapeutics are part of the next-generation arsenal of drugs being developed against proto-oncoprotein Myc. We designed protein MEF to mimic the basic region/helix-loop-helix/leucine zipper (bHLHZ) domain of Max and Myc, which bind to the E-box motif (enhancer box, CACGTG). To make MEF, we started with our rationally designed ME47, a hybrid of the Max basic region and E47 HLH, that effectively inhibited tumor growth in a mouse model of breast cancer. We used phage-assisted continuous evolution (PACE), which uncovered mutations at Arg12 that contact the DNA phosphodiester backbone. The Arg12 mutations improved ME47's stability. We replaced Cys29 with Ala to eliminate potential undesired disulfide formation and fused the designed FosW leucine zipper to mutated ME47 to increase the dimerization interface and E-box targeting activity. This "franken-protein" MEF comprises the Max basic region, E47 HLH, and FosW leucine zipper. Compared with ME47, MEF gives 2-fold stronger binding to E-box and 4-fold increased specificity for E-box over nonspecific DNA. The synergistic combination of rational design and PACE allowed us to make MEF and demonstrates the power and utility of our two-pronged approach toward development of promising protein drugs with robust structure and DNA-binding function.
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Affiliation(s)
- Ichiro Inamoto
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Inder Sheoran
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Serban C. Popa
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Montdher Hussain
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
| | - Jumi A. Shin
- Department of Chemistry, University of Toronto, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada
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10
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Popay TM, Wang J, Adams CM, Howard GC, Codreanu SG, Sherrod SD, McLean JA, Thomas LR, Lorey SL, Machida YJ, Weissmiller AM, Eischen CM, Liu Q, Tansey WP. MYC regulates ribosome biogenesis and mitochondrial gene expression programs through its interaction with host cell factor-1. eLife 2021; 10:e60191. [PMID: 33416496 PMCID: PMC7793627 DOI: 10.7554/elife.60191] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 12/05/2020] [Indexed: 12/11/2022] Open
Abstract
The oncoprotein transcription factor MYC is a major driver of malignancy and a highly validated but challenging target for the development of anticancer therapies. Novel strategies to inhibit MYC may come from understanding the co-factors it uses to drive pro-tumorigenic gene expression programs, providing their role in MYC activity is understood. Here we interrogate how one MYC co-factor, host cell factor (HCF)-1, contributes to MYC activity in a human Burkitt lymphoma setting. We identify genes connected to mitochondrial function and ribosome biogenesis as direct MYC/HCF-1 targets and demonstrate how modulation of the MYC-HCF-1 interaction influences cell growth, metabolite profiles, global gene expression patterns, and tumor growth in vivo. This work defines HCF-1 as a critical MYC co-factor, places the MYC-HCF-1 interaction in biological context, and highlights HCF-1 as a focal point for development of novel anti-MYC therapies.
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Affiliation(s)
- Tessa M Popay
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University Medical CenterNashvilleUnited States
- Center for Quantitative Sciences, Vanderbilt University Medical CenterNashvilleUnited States
| | - Clare M Adams
- Department of Cancer Biology, Thomas Jefferson UniversityPhiladelphiaUnited States
| | - Gregory Caleb Howard
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Simona G Codreanu
- Center for Innovative Technology (CIT), Vanderbilt UniversityNashvilleUnited States
- Department of Chemistry, Vanderbilt UniversityNashvilleUnited States
| | - Stacy D Sherrod
- Center for Innovative Technology (CIT), Vanderbilt UniversityNashvilleUnited States
- Department of Chemistry, Vanderbilt UniversityNashvilleUnited States
| | - John A McLean
- Center for Innovative Technology (CIT), Vanderbilt UniversityNashvilleUnited States
- Department of Chemistry, Vanderbilt UniversityNashvilleUnited States
| | - Lance R Thomas
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Shelly L Lorey
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | | | - April M Weissmiller
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Christine M Eischen
- Department of Cancer Biology, Thomas Jefferson UniversityPhiladelphiaUnited States
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical CenterNashvilleUnited States
- Center for Quantitative Sciences, Vanderbilt University Medical CenterNashvilleUnited States
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
- Department of Biochemistry, Vanderbilt University School of MedicineNashvilleUnited States
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11
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Tu R, Chen Z, Bao Q, Liu H, Qing G. Crosstalk between oncogenic MYC and noncoding RNAs in cancer. Semin Cancer Biol 2020; 75:62-71. [PMID: 33160022 DOI: 10.1016/j.semcancer.2020.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/09/2020] [Accepted: 10/24/2020] [Indexed: 12/19/2022]
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12
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Qian W, Li Z, Song W, Zhao T, Wang W, Peng J, Wei L, Xia Q, Cheng D. A novel transcriptional cascade is involved in Fzr-mediated endoreplication. Nucleic Acids Res 2020; 48:4214-4229. [PMID: 32182338 PMCID: PMC7192621 DOI: 10.1093/nar/gkaa158] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/29/2020] [Indexed: 01/08/2023] Open
Abstract
Endoreplication, known as endocycle, is a variant of the cell cycle that differs from mitosis and occurs in specific tissues of different organisms. Endoreplicating cells generally undergo multiple rounds of genome replication without chromosome segregation. Previous studies demonstrated that Drosophila fizzy-related protein (Fzr) and its mammalian homolog Cdh1 function as key regulators of endoreplication entrance by activating the anaphase-promoting complex/cyclosome to initiate the ubiquitination and subsequent degradation of cell cycle factors such as Cyclin B (CycB). However, the molecular mechanism underlying Fzr-mediated endoreplication is not completely understood. In this study, we demonstrated that the transcription factor Myc acts downstream of Fzr during endoreplication in Drosophila salivary gland. Mechanistically, Fzr interacts with chromatin-associated histone H2B to enhance H2B ubiquitination in the Myc promoter and promotes Myc transcription. In addition to negatively regulating CycB transcription, the Fzr-ubiquitinated H2B (H2Bub)-Myc signaling cascade also positively regulates the transcription of the MCM6 gene that is involved in DNA replication by directly binding to specific motifs within their promoters. We further found that the Fzr-H2Bub-Myc signaling cascade regulating endoreplication progression is conserved between insects and mammalian cells. Altogether, our work uncovers a novel transcriptional cascade that is involved in Fzr-mediated endoreplication.
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Affiliation(s)
- Wenliang Qian
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Zheng Li
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Wei Song
- Medical Research Institute, Wuhan University, Wuhan 430071, China.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Tujing Zhao
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Weina Wang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Jian Peng
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Ling Wei
- School of Life Science, Southwest University, Chongqing 400715, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Daojun Cheng
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
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13
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Yoshida GJ. Beyond the Warburg Effect: N-Myc Contributes to Metabolic Reprogramming in Cancer Cells. Front Oncol 2020; 10:791. [PMID: 32547946 PMCID: PMC7269178 DOI: 10.3389/fonc.2020.00791] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022] Open
Abstract
Cancer cells generate large amounts of lactate derived from glucose regardless of the available oxygen level. Cancer cells finely control ATP synthesis by modulating the uptake of substrates and the activity of enzymes involved in aerobic glycolysis (Warburg effect), which enables them to adapt to the tumor microenvironment. However, increasing evidence suggests that mitochondrial metabolism, including the tricarboxylic acid (TCA) cycle, oxidative phosphorylation (OXPHOS), and glutaminolysis, is paradoxically activated in MYCN-amplified malignancies. Unlike non-amplified cells, MYCN-amplified cancer cells significantly promote OXPHOS-dependent ATP synthesis. Furthermore, tumor cells are differentially dependent on fatty acid β-oxidation (FAO) according to N-Myc status. Therefore, upregulation of FAO-associated enzymes is positively correlated with both N-Myc expression level and poor clinical outcome. This review explores therapeutic strategies targeting cancer stem-like cells for the treatment of tumors associated with MYCN amplification.
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Affiliation(s)
- Go J Yoshida
- Department of Pathology and Oncology, Juntendo University School of Medicine, Tokyo, Japan.,Department of Immunological Diagnosis, Juntendo University School of Medicine, Tokyo, Japan
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14
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Beaulieu ME, Castillo F, Soucek L. Structural and Biophysical Insights into the Function of the Intrinsically Disordered Myc Oncoprotein. Cells 2020; 9:E1038. [PMID: 32331235 PMCID: PMC7226237 DOI: 10.3390/cells9041038] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/13/2022] Open
Abstract
Myc is a transcription factor driving growth and proliferation of cells and involved in the majority of human tumors. Despite a huge body of literature on this critical oncogene, our understanding of the exact molecular determinants and mechanisms that underlie its function is still surprisingly limited. Indubitably though, its crucial and non-redundant role in cancer biology makes it an attractive target. However, achieving successful clinical Myc inhibition has proven challenging so far, as this nuclear protein is an intrinsically disordered polypeptide devoid of any classical ligand binding pockets. Indeed, Myc only adopts a (partially) folded structure in some contexts and upon interacting with some protein partners, for instance when dimerizing with MAX to bind DNA. Here, we review the cumulative knowledge on Myc structure and biophysics and discuss the implications for its biological function and the development of improved Myc inhibitors. We focus this biophysical walkthrough mainly on the basic region helix-loop-helix leucine zipper motif (bHLHLZ), as it has been the principal target for inhibitory approaches so far.
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Affiliation(s)
| | | | - Laura Soucek
- Peptomyc S.L., Edifici Cellex, 08035 Barcelona, Spain; (F.C.); (L.S.)
- Vall d’Hebron Institute of Oncology (VHIO), Edifici Cellex, 08035 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08035 Barcelona, Spain
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08035 Bellaterra, Spain
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15
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Zhang T, Li N, Sun C, Jin Y, Sheng X. MYC and the unfolded protein response in cancer: synthetic lethal partners in crime? EMBO Mol Med 2020; 12:e11845. [PMID: 32310340 PMCID: PMC7207169 DOI: 10.15252/emmm.201911845] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/07/2020] [Accepted: 03/10/2020] [Indexed: 12/15/2022] Open
Abstract
The transcription factors of the MYC family play pivotal roles in the initiation and progression of human cancers. High oncogenic level of MYC invades low‐affinity sites and enhancer sequences, which subsequently alters the transcriptome, causes metabolic imbalance, and induces stress response. The endoplasmic reticulum (ER) not only plays a central role in maintaining proteostasis, but also contributes to other key biological processes, including Ca2+ metabolism and the synthesis of lipids and glucose. Stress conditions, such as shortage in glucose or oxygen and disruption of Ca2+ homeostasis, may perturb proteostasis and induce the unfolded protein response (UPR), which either restores homeostasis or triggers cell death. Crucial roles of ER stress and UPR signaling have been implicated in various cancers, from oncogenesis to treatment response. Here, we summarize the current knowledge on the interaction between MYC and UPR signaling, and its contribution to cancer development. We also discuss the potential of targeting key UPR signaling nodes as novel synthetic lethal strategies in MYC‐driven cancers.
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Affiliation(s)
- Tingting Zhang
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ningning Li
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Chaoyang Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Jin
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
| | - Xia Sheng
- Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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16
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Popa SC, Shin JA. The Intrinsically Disordered Loop in the USF1 bHLHZ Domain Modulates Its DNA-Binding Sequence Specificity in Hereditary Asthma. J Phys Chem B 2019; 123:9862-9871. [PMID: 31670516 DOI: 10.1021/acs.jpcb.9b06719] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
USF1, a basic region/helix-loop-helix/leucine zipper (bHLHZ) transcription factor, binds to the E-box in the PAI-1 (plasminogen activator inhibitor) promoter. Two alleles containing the E-box control PAI-1 transcription; these alleles are termed "4G" and "5G" based on the G tract flanking E-box. USF1-governed transcription of PAI-1 is elevated in heritable asthma sufferers: the 4G/4G genotype has the highest plasma levels of PAI-1. While USF1 uses its basic region to bind E-box, we found that it uses its 12 amino-acid loop to recognize the flanking sequence and discern the single-nucleotide difference between the alleles. We used the bacterial one-hybrid and electrophoretic mobility shift assays to assess protein-DNA recognition, and circular dichroism to examine protein secondary structure. We mutated Ser233 and Thr234 in the USF1 bHLHZ loop to Ala to generate S233A and T234A. Interestingly, USF1 bHLHZ, S233A, and T234A prefer the 5G sequence (USF1 bHLHZ Kd values 4.1 ± 0.3 nM and 7.0 ± 0.4 nM for 5G and 4G, respectively), whereas studies in stimulated human mast cells showed a preference for 4G. We replaced the 8 amino-acid loop of transcription factor Max bHLHZ with the 12 amino-acid USF1 loop: this mutant now distinguishes the 4G/5G polymorphism-while Max bHLHZ does not-confirming that USF1 differentiation of the 4G/5G is driven by the loop.
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Affiliation(s)
- Serban C Popa
- Department of Chemistry , University of Toronto , 3359 Mississauga Road , Mississauga , Ontario L5L 1C6 , Canada
| | - Jumi A Shin
- Department of Chemistry , University of Toronto , 3359 Mississauga Road , Mississauga , Ontario L5L 1C6 , Canada
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17
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Sammak S, Hamdani N, Gorrec F, Allen MD, Freund SMV, Bycroft M, Zinzalla G. Crystal Structures and Nuclear Magnetic Resonance Studies of the Apo Form of the c-MYC:MAX bHLHZip Complex Reveal a Helical Basic Region in the Absence of DNA. Biochemistry 2019; 58:3144-3154. [PMID: 31260268 PMCID: PMC6791285 DOI: 10.1021/acs.biochem.9b00296] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
The c-MYC transcription
factor is a master regulator of cell growth
and proliferation and is an established target for cancer therapy.
This basic helix–loop–helix Zip protein forms a heterodimer
with its obligatory partner MAX, which binds to DNA via the basic
region. Considerable research efforts are focused on targeting the
heterodimerization interface and the interaction of the complex with
DNA. The only available crystal structure is that of a c-MYC:MAX complex
artificially tethered by an engineered disulfide linker and prebound
to DNA. We have carried out a detailed structural analysis of the
apo form of the c-MYC:MAX complex, with no artificial linker, both
in solution using nuclear magnetic resonance (NMR) spectroscopy and
by X-ray crystallography. We have obtained crystal structures in three
different crystal forms, with resolutions between 1.35 and 2.2 Å,
that show extensive helical structure in the basic region. Determination
of the α-helical propensity using NMR chemical shift analysis
shows that the basic region of c-MYC and, to a lesser extent, that
of MAX populate helical conformations. We have also assigned the NMR
spectra of the c-MYC basic helix–loop–helix Zip motif
in the absence of MAX and showed that the basic region has an intrinsic
helical propensity even in the absence of its dimerization partner.
The presence of helical structure in the basic regions in the absence
of DNA suggests that the molecular recognition occurs via a conformational
selection rather than an induced fit. Our work provides both insight
into the mechanism of DNA binding and structural information to aid
in the development of MYC inhibitors.
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Affiliation(s)
- Susan Sammak
- Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Solnavägen 9 , 171 65 Stockholm , Sweden
| | - Najoua Hamdani
- Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Solnavägen 9 , 171 65 Stockholm , Sweden
| | - Fabrice Gorrec
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Mark D Allen
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Stefan M V Freund
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Mark Bycroft
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Giovanna Zinzalla
- Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Solnavägen 9 , 171 65 Stockholm , Sweden
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18
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Nagasaka M, Tsuzuki K, Ozeki Y, Tokugawa M, Ohoka N, Inoue Y, Hayashi H. Lysine-Specific Demethylase 1 (LSD1/KDM1A) Is a Novel Target Gene of c-Myc. Biol Pharm Bull 2019; 42:481-488. [PMID: 30828079 DOI: 10.1248/bpb.b18-00892] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Lysine-specific demethylase 1 (LSD1/KDM1A) is a histone demethylase and specifically catalyzes the demethylation of mono- and di-methylated histone H3 lysine 4 (H3K4). The LSD1-mediated demethylation of H3K4 promotes the assembly of the c-Myc-induced transcription initiation complex. Although LSD1 and c-Myc are both strongly expressed in human cancers, the mechanisms by which their activities are coordinated remain unclear. We herein demonstrated that LSD1 is a direct target gene of c-Myc. The knockdown of c-Myc decreased the expression of LSD1 in several cancer cell lines. We identified two non-canonical E-boxes in the proximal promoter region of the LSD1 gene. A chromatin immunoprecipitation assay showed that c-Myc bound to these E-boxes in the LSD1 promoter. Importantly, LSD1 mRNA expression correlated with c-Myc expression in human acute myeloid leukemia (AML), glioblastoma, stomach adenocarcinoma, and prostate adenocarcinoma. The present results suggest that LSD1 is induced by c-Myc and forms a positive feedback mechanism in transcription reactions by c-Myc.
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Affiliation(s)
- Mai Nagasaka
- Department of Cell Signaling, Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Kaori Tsuzuki
- Department of Cell Signaling, Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Yu Ozeki
- Department of Cell Signaling, Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Muneshige Tokugawa
- Department of Cell Signaling, Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Nobumichi Ohoka
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences
| | - Yasumichi Inoue
- Department of Cell Signaling, Graduate School of Pharmaceutical Sciences, Nagoya City University.,Department of Innovative Therapeutics Sciences, Cooperative Major in Nanopharmaceutical Sciences, Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Hidetoshi Hayashi
- Department of Cell Signaling, Graduate School of Pharmaceutical Sciences, Nagoya City University.,Department of Innovative Therapeutics Sciences, Cooperative Major in Nanopharmaceutical Sciences, Graduate School of Pharmaceutical Sciences, Nagoya City University
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19
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Disruption of the Myc-PDE4B regulatory circuitry impairs B-cell lymphoma survival. Leukemia 2019; 33:2912-2923. [PMID: 31138843 DOI: 10.1038/s41375-019-0492-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 03/18/2019] [Accepted: 04/11/2019] [Indexed: 01/19/2023]
Abstract
A large body of evidence suggests that B-cell lymphomas with enhanced Myc expression are associated with an aggressive phenotype and poor prognosis, which makes Myc a compelling therapeutic target. Phosphodiesterase 4B (PDE4B), a main hydrolyzer of cyclic AMP (cAMP) in B cells, was shown to be involved in cell survival and drug resistance in diffuse large B cell lymphomas (DLBCL). However, the interrelationship between Myc and PDE4B remains unclear. Here, we first demonstrate the presence of the Myc-PDE4B feed-forward loop, in which Myc and PDE4B mutually reinforce the expression of each other. Next, the combined targeting of Myc and PDE4 synergistically prevented the proliferation and survival of B lymphoma cells in vitro and in a mouse xenograft model. We finally recapitulated this combinatorial effect in Eμ-myc transgenic mice; co-inhibition of Myc and PDE4 suppressed lymphomagenesis and restored B cell development to the wild type level that was associated with marked reduction in Myc levels, unveiling the critical role of the Myc-PDE4B amplification loop in the regulation of Myc expression and the pathogenesis of B cell lymphoma. These findings suggest that the disruption of the Myc-PDE4B circuitry can be exploited in the treatment of B cell malignancies.
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20
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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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21
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EBNA1: Oncogenic Activity, Immune Evasion and Biochemical Functions Provide Targets for Novel Therapeutic Strategies against Epstein-Barr Virus- Associated Cancers. Cancers (Basel) 2018; 10:cancers10040109. [PMID: 29642420 PMCID: PMC5923364 DOI: 10.3390/cancers10040109] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 03/26/2018] [Accepted: 03/29/2018] [Indexed: 12/12/2022] Open
Abstract
The presence of the Epstein-Barr virus (EBV)-encoded nuclear antigen-1 (EBNA1) protein in all EBV-carrying tumours constitutes a marker that distinguishes the virus-associated cancer cells from normal cells and thereby offers opportunities for targeted therapeutic intervention. EBNA1 is essential for viral genome maintenance and also for controlling viral gene expression and without EBNA1, the virus cannot persist. EBNA1 itself has been linked to cell transformation but the underlying mechanism of its oncogenic activity has been unclear. However, recent data are starting to shed light on its growth-promoting pathways, suggesting that targeting EBNA1 can have a direct growth suppressing effect. In order to carry out its tasks, EBNA1 interacts with cellular factors and these interactions are potential therapeutic targets, where the aim would be to cripple the virus and thereby rid the tumour cells of any oncogenic activity related to the virus. Another strategy to target EBNA1 is to interfere with its expression. Controlling the rate of EBNA1 synthesis is critical for the virus to maintain a sufficient level to support viral functions, while at the same time, restricting expression is equally important to prevent the immune system from detecting and destroying EBNA1-positive cells. To achieve this balance EBNA1 has evolved a unique repeat sequence of glycines and alanines that controls its own rate of mRNA translation. As the underlying molecular mechanisms for how this repeat suppresses its own rate of synthesis in cis are starting to be better understood, new therapeutic strategies are emerging that aim to modulate the translation of the EBNA1 mRNA. If translation is induced, it could increase the amount of EBNA1-derived antigenic peptides that are presented to the major histocompatibility (MHC) class I pathway and thus, make EBV-carrying cancers better targets for the immune system. If translation is further suppressed, this would provide another means to cripple the virus.
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22
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Schaub FX, Dhankani V, Berger AC, Trivedi M, Richardson AB, Shaw R, Zhao W, Zhang X, Ventura A, Liu Y, Ayer DE, Hurlin PJ, Cherniack AD, Eisenman RN, Bernard B, Grandori C. Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas. Cell Syst 2018; 6:282-300.e2. [PMID: 29596783 PMCID: PMC5892207 DOI: 10.1016/j.cels.2018.03.003] [Citation(s) in RCA: 278] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 02/06/2018] [Accepted: 03/02/2018] [Indexed: 12/19/2022]
Abstract
Although the MYC oncogene has been implicated in cancer, a systematic assessment of alterations of MYC, related transcription factors, and co-regulatory proteins, forming the proximal MYC network (PMN), across human cancers is lacking. Using computational approaches, we define genomic and proteomic features associated with MYC and the PMN across the 33 cancers of The Cancer Genome Atlas. Pan-cancer, 28% of all samples had at least one of the MYC paralogs amplified. In contrast, the MYC antagonists MGA and MNT were the most frequently mutated or deleted members, proposing a role as tumor suppressors. MYC alterations were mutually exclusive with PIK3CA, PTEN, APC, or BRAF alterations, suggesting that MYC is a distinct oncogenic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such as immune response and growth factor signaling; chromatin, translation, and DNA replication/repair were conserved pan-cancer. This analysis reveals insights into MYC biology and is a reference for biomarkers and therapeutics for cancers with alterations of MYC or the PMN.
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Affiliation(s)
- Franz X Schaub
- Cure First, Seattle, WA, USA; SEngine Precision Medicine, Seattle, WA, USA
| | | | - Ashton C Berger
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | | | | | - Reid Shaw
- SEngine Precision Medicine, Seattle, WA, USA
| | - Wei Zhao
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaoyang Zhang
- Dana-Farber Cancer Institute, the Broad Institute of Harvard and MIT, and Harvard Medical School, Boston, MA, USA
| | - Andrea Ventura
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuexin Liu
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Donald E Ayer
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Peter J Hurlin
- Shriners Hospitals for Children Research Center, Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Andrew D Cherniack
- Dana-Farber Cancer Institute, the Broad Institute of Harvard and MIT, and Harvard Medical School, Boston, MA, USA
| | - Robert N Eisenman
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Brady Bernard
- Institute for Systems Biology, Seattle, WA, USA; Providence Health and Services, Portland, OR, USA.
| | - Carla Grandori
- Cure First, Seattle, WA, USA; SEngine Precision Medicine, Seattle, WA, USA.
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23
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Inamoto I, Shin JA. Peptide therapeutics that directly target transcription factors. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ichiro Inamoto
- Department of Chemistry; University of Toronto, 3359 Mississauga Road; Mississauga Ontario L5L 1C6 Canada
| | - Jumi A. Shin
- Department of Chemistry; University of Toronto, 3359 Mississauga Road; Mississauga Ontario L5L 1C6 Canada
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24
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Antimyeloma activity of bromodomain inhibitors on the human myeloma cell line U266 by downregulation of MYCL. Anticancer Drugs 2017; 27:756-65. [PMID: 27276402 PMCID: PMC4969056 DOI: 10.1097/cad.0000000000000389] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Supplemental Digital Content is available in the text. Bromodomain and extraterminal protein (BET) inhibitors suppress the expression of c-MYC. U266, a human myeloma cell line, expresses the MYCL gene, but not the c-MYC gene. Our aim was to analyse the antimyeloma activity of BET inhibitors on U266 cells. Two BET inhibitors, I-BET151 and JQ1, were tested. U266 cell proliferation decreased to 61.5 and 54.0% of the control after incubation with 500 nmol/l I-BET151 for 72 and 96 h and to 53.5 and 56.4% of control after incubation with 500 nmol/l JQ1 for 72 and 96 h by MTS tetrazolium, respectively. BET inhibitors induced cell cycle arrest at the G1 phase in U266 cells, but did not induce apoptosis by flow cytometry. According to Gene Set Enrichment Analysis, MYC-related genes were significantly downregulated in U266 cells treated with I-BET151 similar to KMS11 cells that expressed c-MYC. The MYCL1 was expressed in U266 cells, whereas c-MYC and MYCN were not by quantitative real-time reverse-transcription-PCR. Incubation with I-BET151 induced downregulation of MYCL1 in U266 cells. BET inhibitors decreased the cell proliferation in U266 cells with overexpression of MYCL less than those without overexpression of MYCL. BET inhibitors induce G1 arrest without apoptosis and interfere with the proliferation of U266 myeloma cells, which express MYCL, but not c-MYC. BET inhibitors might be active in cancers that express MYCL, but not c-MYC.
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Büchel G, Carstensen A, Mak KY, Roeschert I, Leen E, Sumara O, Hofstetter J, Herold S, Kalb J, Baluapuri A, Poon E, Kwok C, Chesler L, Maric HM, Rickman DS, Wolf E, Bayliss R, Walz S, Eilers M. Association with Aurora-A Controls N-MYC-Dependent Promoter Escape and Pause Release of RNA Polymerase II during the Cell Cycle. Cell Rep 2017; 21:3483-3497. [PMID: 29262328 PMCID: PMC5746598 DOI: 10.1016/j.celrep.2017.11.090] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 10/12/2017] [Accepted: 11/27/2017] [Indexed: 12/17/2022] Open
Abstract
MYC proteins bind globally to active promoters and promote transcriptional elongation by RNA polymerase II (Pol II). To identify effector proteins that mediate this function, we performed mass spectrometry on N-MYC complexes in neuroblastoma cells. The analysis shows that N-MYC forms complexes with TFIIIC, TOP2A, and RAD21, a subunit of cohesin. N-MYC and TFIIIC bind to overlapping sites in thousands of Pol II promoters and intergenic regions. TFIIIC promotes association of RAD21 with N-MYC target sites and is required for N-MYC-dependent promoter escape and pause release of Pol II. Aurora-A competes with binding of TFIIIC and RAD21 to N-MYC in vitro and antagonizes association of TOP2A, TFIIIC, and RAD21 with N-MYC during S phase, blocking N-MYC-dependent release of Pol II from the promoter. Inhibition of Aurora-A in S phase restores RAD21 and TFIIIC binding to chromatin and partially restores N-MYC-dependent transcriptional elongation. We propose that complex formation with Aurora-A controls N-MYC function during the cell cycle.
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Affiliation(s)
- Gabriele Büchel
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Anne Carstensen
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Ka-Yan Mak
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Isabelle Roeschert
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Eoin Leen
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; University of Leicester, Leicester LE1 9HN, UK
| | - Olga Sumara
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Julia Hofstetter
- Cancer Systems Biology Group, Biochemistry and Molecular Biology, University of Würzburg, 97074 Würzburg, Germany
| | - Steffi Herold
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jacqueline Kalb
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Apoorva Baluapuri
- Cancer Systems Biology Group, Biochemistry and Molecular Biology, University of Würzburg, 97074 Würzburg, Germany
| | - Evon Poon
- Division of Clinical Studies and Cancer Therapeutics, The Institute of Cancer Research, The Royal Marsden NHS Trust, 15 Cotswold Rd., Belmont, Sutton, Surrey SM2 5NG, UK
| | - Colin Kwok
- Division of Clinical Studies and Cancer Therapeutics, The Institute of Cancer Research, The Royal Marsden NHS Trust, 15 Cotswold Rd., Belmont, Sutton, Surrey SM2 5NG, UK
| | - Louis Chesler
- Division of Clinical Studies and Cancer Therapeutics, The Institute of Cancer Research, The Royal Marsden NHS Trust, 15 Cotswold Rd., Belmont, Sutton, Surrey SM2 5NG, UK
| | - Hans Michael Maric
- Department of Drug Design and Pharmacology, Center for Biopharmaceuticals, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - David S Rickman
- Weill Cornell Medicine, Sandra and Edward Meyer Cancer Center, 413 E. 69(th) Street, New York, NY 10021, USA
| | - Elmar Wolf
- Cancer Systems Biology Group, Biochemistry and Molecular Biology, University of Würzburg, 97074 Würzburg, Germany
| | - Richard Bayliss
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; University of Leicester, Leicester LE1 9HN, UK
| | - Susanne Walz
- Comprehensive Cancer Center Mainfranken, Core Unit Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Martin Eilers
- Theodor Boveri Institute and Comprehensive Cancer Center Mainfranken, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
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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: 36] [Impact Index Per Article: 4.5] [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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Zhang Q, West-Osterfield K, Spears E, Li Z, Panaccione A, Hann SR. MB0 and MBI Are Independent and Distinct Transactivation Domains in MYC that Are Essential for Transformation. Genes (Basel) 2017; 8:genes8050134. [PMID: 28481271 PMCID: PMC5448008 DOI: 10.3390/genes8050134] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/24/2017] [Accepted: 04/28/2017] [Indexed: 01/05/2023] Open
Abstract
MYC is a transcription factor that is essential for cellular proliferation and development. Deregulation or overexpression of MYC occurs in a variety of human cancers. Ectopic expression of MYC causes hyperproliferation and transformation of cells in culture and tumorigenesis in several transgenic mouse models. Deregulation of MYC can also induce apoptosis through activation of p53 and/or ARF tumor suppressors as a safeguard to prevent tumorigenesis. MYC binds to thousands of genomic sites and regulates hundreds of target genes in a context-dependent fashion to mediate these diverse biological roles. The N-terminal region of MYC contains several conserved domains or MYC Boxes (MB), which influence the different MYC transcriptional and biological activities to varying degrees. However, the specific domains that mediate the ability of MYC to activate transcription remain ill defined. In this report, we have identified a new conserved transactivation domain (TAD), MB0, which is essential for MYC transactivation and target gene induction. We demonstrate that MB0 and MBI represent two distinct and independent TADs within the N-terminal 62 amino acids of MYC. In addition, both MB0 and MBI are essential for MYC transformation of primary fibroblasts in cooperation with activated RAS, while MB0 is necessary for efficient MYC-induced p53-independent apoptosis.
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Affiliation(s)
- Qin Zhang
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, 1121 21st Ave., Nashville, TN 37232, USA.
| | - Kimberly West-Osterfield
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, 1121 21st Ave., Nashville, TN 37232, USA.
| | - Erick Spears
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, 1121 21st Ave., Nashville, TN 37232, USA.
| | - Zhaoliang Li
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, 1121 21st Ave., Nashville, TN 37232, USA.
| | - Alexander Panaccione
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, 1121 21st Ave., Nashville, TN 37232, USA.
| | - Stephen R Hann
- Department of Cell and Developmental Biology, Vanderbilt University, School of Medicine, 1121 21st Ave., Nashville, TN 37232, USA.
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Fagnocchi L, Zippo A. Multiple Roles of MYC in Integrating Regulatory Networks of Pluripotent Stem Cells. Front Cell Dev Biol 2017; 5:7. [PMID: 28217689 PMCID: PMC5289991 DOI: 10.3389/fcell.2017.00007] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/20/2017] [Indexed: 12/20/2022] Open
Abstract
Pluripotent stem cells (PSCs) are defined by their self-renewal potential, which permits their unlimited propagation, and their pluripotency, being able to generate cell of the three embryonic lineages. These properties render PSCs a valuable tool for both basic and medical research. To induce and stabilize the pluripotent state, complex circuitries involving signaling pathways, transcription regulators and epigenetic mechanisms converge on a core transcriptional regulatory network of PSCs, thus determining their cell identity. Among the transcription factors, MYC represents a central hub, which modulates and integrates multiple mechanisms involved both in the maintenance of pluripotency and in cell reprogramming. Indeed, it instructs the PSC-specific cell cycle, metabolism and epigenetic landscape, contributes to limit exit from pluripotency and modulates signaling cascades affecting the PSC identity. Moreover, MYC extends its regulation on pluripotency by controlling PSC-specific non-coding RNAs. In this report, we review the MYC-controlled networks, which support the pluripotent state and discuss how their perturbation could affect cell identity. We further discuss recent finding demonstrating a central role of MYC in triggering epigenetic memory in PSCs, which depends on the establishment of a WNT-centered self-reinforcing circuit. Finally, we comment on the therapeutic implications of the role of MYC in affecting PSCs. Indeed, PSCs are used for both disease and cancer modeling and to derive cells for regenerative medicine. For these reasons, unraveling the MYC-mediated mechanism in those cells is fundamental to exploit their full potential and to identify therapeutic targets.
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Affiliation(s)
- Luca Fagnocchi
- Department of Epigenetics, Fondazione Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM)Milan, Italy; Division of Pathology, Fondazione IRCCS Ca' Granda, Ospedale Maggiore PoliclinicoMilan, Italy
| | - Alessio Zippo
- Department of Epigenetics, Fondazione Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM)Milan, Italy; Division of Pathology, Fondazione IRCCS Ca' Granda, Ospedale Maggiore PoliclinicoMilan, Italy
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29
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Vinnakota JM, Gummadi SN. Snail represses the expression of human phospholipid scramblase 4 gene. Gene 2016; 591:433-41. [PMID: 27363667 DOI: 10.1016/j.gene.2016.06.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/09/2016] [Accepted: 06/24/2016] [Indexed: 11/18/2022]
Abstract
Human phospholipid scramblases (hPLSCRs) are a group of transmembrane ATP independent lipid transporters mediating bi-directional transport of phospholipids. There are four homologues hPLSCR1-hPLSCR4 and hPLSCR1 is the extensively studied homologue among them. hPLSCR4 shares 48% homology with hPLSCR1 and mediates scrambling of PLs similar to hPLSCR1 in Ca(2+) dependent manner. Transcriptional regulation helps in better understanding of the function and the expression of a protein. Till date there are no reports suggesting the transcriptional regulation of hPLSCR4. In this study, we identified Snail to be a potent regulator of hPLSCR4. ConSite tool predicted the presence of a putative Snail binding site with a consensus sequence of (-1521)CAGGTG(-1516) on hPLSCR4 promoter. Luciferase assays depicted a dose dependent decrease in hPLSCR4 promoter activity with an increase in amount of Snail. Deletion analysis revealed that the region from -1380 to -2100 to be the regulatory region of hPLSCR4. Knock down studies further confirmed Snail mediated downregulation of hPLSCR4, as the mRNA and the protein levels of hPLSCR4 considerably increased under knock down conditions. The in vivo interaction of Snail with hPLSCR4 promoter was further confirmed by ChIP assay. This is the first report on the transcriptional regulation of hPLSCR4, where Snail was shown to downregulate the expression of hPLSCR4.
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Affiliation(s)
- Janaki Manoja Vinnakota
- Applied and Industrial Microbiology Lab, Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, IIT Madras, Chennai 600036, India.
| | - Sathyanarayana N Gummadi
- Applied and Industrial Microbiology Lab, Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, IIT Madras, Chennai 600036, India.
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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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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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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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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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34
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Two c-Myc binding sites are crucial in upregulating the expression of human phospholipid scramblase 1 gene. Biochem Biophys Res Commun 2015; 469:412-7. [PMID: 26679604 DOI: 10.1016/j.bbrc.2015.11.131] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 11/29/2015] [Indexed: 11/21/2022]
Abstract
Human phospholipid scramblase 1 (hPLSCR1) is a type II endofacial membrane protein which mediates bi-directional transport of phospholipids across the plasma membrane. hPLSCR1, a multifunctional protein with variety of roles in apoptosis, tumor progression, cell signaling and anti-viral defense. The expression of such a multifunctional protein should be under tight regulation. Apart from a single report showing snail mediated down regulation of hPLSCR1, the molecular mechanisms regulating the expression of scramblases are not well elucidated. In this study we identified c-Myc as a transcriptional regulator of hPLSCR1. Transcription factor prediction tool ConSite predicted three binding sites for c-Myc. Reporter gene assays and western blot analysis revealed c-Myc mediated up regulation of hPLSCR1 expression. Deletion construct -790 lacking one c-Myc binding site showed a 27% decrease in promoter activity while deletion construct -469 lacking two c-Myc binding sites showed a 62% decrease in promoter activity. Site directed mutagenesis revealed the importance of c-Myc binding sites from -751 to -756 and -548 to -553 on the promoter of hPLSCR1in transcriptionally regulating the expression of hPLSCR1. The results were further confirmed by shRNA mediated knock down of endogenous c-Myc and in vivo interactions by ChIP assay.
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35
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Fogal V, Babic I, Chao Y, Pastorino S, Mukthavaram R, Jiang P, Cho YJ, Pingle SC, Crawford JR, Piccioni DE, Kesari S. Mitochondrial p32 is upregulated in Myc expressing brain cancers and mediates glutamine addiction. Oncotarget 2015; 6:1157-70. [PMID: 25528767 PMCID: PMC4359224 DOI: 10.18632/oncotarget.2708] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 11/08/2014] [Indexed: 12/22/2022] Open
Abstract
Metabolic reprogramming is a key feature of tumorigenesis that is controlled by oncogenes. Enhanced utilization of glucose and glutamine are the best-established hallmarks of tumor metabolism. The oncogene c-Myc is one of the major players responsible for this metabolic alteration. However, the molecular mechanisms involved in Myc-induced metabolic reprogramming are not well defined. Here we identify p32, a mitochondrial protein known to play a role in the expression of mitochondrial respiratory chain complexes, as a critical player in Myc-induced glutamine addiction. We show that p32 is a direct transcriptional target of Myc and that high level of Myc in malignant brain cancers correlates with high expression of p32. Attenuation of p32 expression reduced growth rate of glioma cells expressing Myc and impaired tumor formation in vivo. Loss of p32 in glutamine addicted glioma cells induced resistance to glutamine deprivation and imparted sensitivity to glucose withdrawal. Finally, we provide evidence that p32 expression contributes to Myc-induced glutamine addiction of cancer cells. Our findings suggest that Myc promotes the expression of p32, which is required to maintain sufficient respiratory capacity to sustain glutamine metabolism in Myc transformed cells.
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Affiliation(s)
- Valentina Fogal
- Translational Neuro-Oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Ivan Babic
- Translational Neuro-Oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Ying Chao
- Translational Neuro-Oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Sandra Pastorino
- Translational Neuro-Oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Rajesh Mukthavaram
- Translational Neuro-Oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Pengfei Jiang
- Translational Neuro-Oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA
| | | | - Sandeep C Pingle
- Translational Neuro-Oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - John R Crawford
- Translational Neuro-Oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA.,Division of Neuro-Oncology, Department of Neurosciences, University of California, San Diego, La Jolla, CA
| | - David E Piccioni
- Translational Neuro-Oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA.,Division of Neuro-Oncology, Department of Neurosciences, University of California, San Diego, La Jolla, CA
| | - Santosh Kesari
- Translational Neuro-Oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA.Division of Neuro-Oncology, Department of Neurosciences, University of California, San Diego, La Jolla, CA.,Translational Neuro-Oncology Laboratories, Moores Cancer Center, University of California San Diego, La Jolla, CA.Division of Neuro-Oncology, Department of Neurosciences, University of California, San Diego, La Jolla, CA
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Wiese KE, Haikala HM, von Eyss B, Wolf E, Esnault C, Rosenwald A, Treisman R, Klefström J, Eilers M. Repression of SRF target genes is critical for Myc-dependent apoptosis of epithelial cells. EMBO J 2015; 34:1554-71. [PMID: 25896507 PMCID: PMC4474530 DOI: 10.15252/embj.201490467] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 03/28/2015] [Accepted: 03/30/2015] [Indexed: 12/22/2022] Open
Abstract
Oncogenic levels of Myc expression sensitize cells to multiple apoptotic stimuli, and this protects long-lived organisms from cancer development. How cells discriminate physiological from supraphysiological levels of Myc is largely unknown. Here, we show that induction of apoptosis by Myc in breast epithelial cells requires association of Myc with Miz1. Gene expression and ChIP-Sequencing experiments show that high levels of Myc invade target sites that lack consensus E-boxes in a complex with Miz1 and repress transcription. Myc/Miz1-repressed genes encode proteins involved in cell adhesion and migration and include several integrins. Promoters of repressed genes are enriched for binding sites of the serum-response factor (SRF). Restoring SRF activity antagonizes Myc repression of SRF target genes, attenuates Myc-induced apoptosis, and reverts a Myc-dependent decrease in Akt phosphorylation and activity, a well-characterized suppressor of Myc-induced apoptosis. We propose that high levels of Myc engage Miz1 in repressive DNA binding complexes and suppress an SRF-dependent transcriptional program that supports survival of epithelial cells.
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Affiliation(s)
- Katrin E Wiese
- Biocenter Theodor Boveri Institute University of Würzburg, Würzburg, Germany
| | - Heidi M Haikala
- Faculty of Medicine, Cancer Cell Circuitry Laboratory, Translational Cancer Biology Research Program and Institute of Biomedicine Biomedicum Helsinki University of Helsinki, Helsinki, Finland
| | - Björn von Eyss
- Biocenter Theodor Boveri Institute University of Würzburg, Würzburg, Germany
| | - Elmar Wolf
- Biocenter Theodor Boveri Institute University of Würzburg, Würzburg, Germany
| | - Cyril Esnault
- Cancer Research UK London Research Institute Lincoln's Inn Fields Laboratories Transcription Laboratory, London, UK
| | - Andreas Rosenwald
- Institute of Pathology University of Würzburg, Würzburg, Germany Comprehensive Cancer Center Mainfranken University of Würzburg, Würzburg, Germany
| | - Richard Treisman
- Cancer Research UK London Research Institute Lincoln's Inn Fields Laboratories Transcription Laboratory, London, UK
| | - Juha Klefström
- Faculty of Medicine, Cancer Cell Circuitry Laboratory, Translational Cancer Biology Research Program and Institute of Biomedicine Biomedicum Helsinki University of Helsinki, Helsinki, Finland
| | - Martin Eilers
- Biocenter Theodor Boveri Institute University of Würzburg, Würzburg, Germany Comprehensive Cancer Center Mainfranken University of Würzburg, Würzburg, Germany
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37
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Zhao Y, Su H, Zhou J, Feng H, Zhang KQ, Yang J. The APSES family proteins in fungi: Characterizations, evolution and functions. Fungal Genet Biol 2014; 81:271-80. [PMID: 25534868 DOI: 10.1016/j.fgb.2014.12.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 12/08/2014] [Accepted: 12/12/2014] [Indexed: 10/24/2022]
Abstract
The APSES protein family belongs to transcriptional factors of the basic helix-loop-helix (bHLH) class, the originally described members (APSES: Asm1p, Phd1p, Sok2p, Efg1p and StuAp) are used to designate this group of proteins, and they have been identified as key regulators of fungal development and other biological processes. APSES proteins share a highly conserved DNA-binding domain (APSES domain) of about 100 amino acids, whose central domain is predicted to form a typical bHLH structure. Besides APSES domain, several APSES proteins also contain additional domains, such as KilA-N and ankyrin repeats. In recent years, an increasing number of APSES proteins have been identified from diverse fungi, and they involve in numerous biological processes, such as sporulation, cellular differentiation, mycelial growth, secondary metabolism and virulence. Most fungi, including Aspergillus fumigatus, Aspergillus nidulans, Candida albicans, Fusarium graminearum, and Neurospora crassa, contain five APSES proteins. However, Cryptococcus neoformans only contains two APSES proteins, and Saccharomyces cerevisiae contains six APSES proteins. The phylogenetic analysis showed the APSES domains from different fungi were grouped into four clades (A, B, C and D), which is consistent with the result of homologous alignment of APSES domains using DNAman. The roles of APSES proteins in clade C have been studied in detail, while little is known about the roles of other APSES proteins in clades A, B and D. In this review, the biochemical properties and functional domains of APSES proteins are predicted and compared, and the phylogenetic relationship among APSES proteins from various fungi are analyzed based on the APSES domains. Moreover, the functions of APSES proteins in different fungi are summarized and discussed.
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Affiliation(s)
- Yong Zhao
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Hao Su
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Jing Zhou
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Huihua Feng
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Ke-Qin Zhang
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Jinkui Yang
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming 650091, PR China.
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Selmi A, de Saint-Jean M, Jallas AC, Garin E, Hogarty MD, Bénard J, Puisieux A, Marabelle A, Valsesia-Wittmann S. TWIST1 is a direct transcriptional target of MYCN and MYC in neuroblastoma. Cancer Lett 2014; 357:412-418. [PMID: 25475555 DOI: 10.1016/j.canlet.2014.11.056] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/20/2014] [Accepted: 11/25/2014] [Indexed: 10/24/2022]
Abstract
In neuroblastoma, MYCN amplification is associated with a worse prognosis and is a criterion used in the clinic to provide intensive treatments to children even with localized disease. In correlation with MYCN amplification, upregulation of TWIST1, a transcription factor playing a crucial role in inhibition of apoptosis and differentiation, was previously reported. Clinical data set analysis of MYCN, MYC and TWIST1 expression permits us to confirm that TWIST1 expression is upregulated in MYCN amplified neuroblastoma but also in a subset of neuroblastoma harboring high expression of MYCN or MYC without gene amplification. In silico analyses reveal the presence of several MYC regulatory motifs (E-Boxes and INR) within the TWIST1 promoter. Using gel shift assay and reporter activity assays, we demonstrate that both N-Myc and c-Myc proteins can bind and activate the TWIST1 promoter. Therefore, we propose TWIST1 as a direct MYC transcriptional target.
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Affiliation(s)
- Abdelkader Selmi
- Université Lyon 1, F-69000 Lyon, France; INSERM UMR-S1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69008 Lyon, France
| | - Maud de Saint-Jean
- Université Lyon 1, F-69000 Lyon, France; INSERM UMR-S1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69008 Lyon, France
| | - Anne-Catherine Jallas
- Centre Léon Bérard, F-69008 Lyon, France; Pôle des Sciences Cliniques, Lyon, F-69008, France
| | - Elisabeth Garin
- Centre Léon Bérard, F-69008 Lyon, France; Pôle des Sciences Cliniques, Lyon, F-69008, France
| | - Michael D Hogarty
- Division of Oncology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104-4318, USA
| | - Jean Bénard
- CNRS UMR8126 Institut Gustave Roussy, Université Paris XI, Villejuif F-94805, France
| | - Alain Puisieux
- Université Lyon 1, F-69000 Lyon, France; INSERM UMR-S1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69008 Lyon, France; Centre Léon Bérard, F-69008 Lyon, France
| | - Aurélien Marabelle
- Université Lyon 1, F-69000 Lyon, France; INSERM UMR-S1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69008 Lyon, France; Centre Léon Bérard, F-69008 Lyon, France; Pôle des Sciences Cliniques, Lyon, F-69008, France
| | - Sandrine Valsesia-Wittmann
- Université Lyon 1, F-69000 Lyon, France; Centre Léon Bérard, F-69008 Lyon, France; Pôle des Sciences Cliniques, Lyon, F-69008, France.
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Wirth M, Stojanovic N, Christian J, Paul MC, Stauber RH, Schmid RM, Häcker G, Krämer OH, Saur D, Schneider G. MYC and EGR1 synergize to trigger tumor cell death by controlling NOXA and BIM transcription upon treatment with the proteasome inhibitor bortezomib. Nucleic Acids Res 2014; 42:10433-47. [PMID: 25147211 PMCID: PMC4176343 DOI: 10.1093/nar/gku763] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The c-MYC (MYC afterward) oncogene is well known for driving numerous oncogenic programs. However, MYC can also induce apoptosis and this function of MYC warrants further clarification. We report here that a clinically relevant proteasome inhibitor significantly increases MYC protein levels and that endogenous MYC is necessary for the induction of apoptosis. This kind of MYC-induced cell death is mediated by enhanced expression of the pro-apoptotic BCL2 family members NOXA and BIM. Quantitative promoter-scanning chromatin immunoprecipitations (qChIP) further revealed binding of MYC to the promoters of NOXA and BIM upon proteasome inhibition, correlating with increased transcription. Both promoters are further characterized by the presence of tri-methylated lysine 4 of histone H3, marking active chromatin. We provide evidence that in our apoptosis models cell death occurs independently of p53 or ARF. Furthermore, we demonstrate that recruitment of MYC to the NOXA as well as to the BIM gene promoters depends on MYC's interaction with the zinc finger transcription factor EGR1 and an EGR1-binding site in both promoters. Our study uncovers a novel molecular mechanism by showing that the functional cooperation of MYC with EGR1 is required for bortezomib-induced cell death. This observation may be important for novel therapeutic strategies engaging the inherent pro-death function of MYC.
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Affiliation(s)
- Matthias Wirth
- Medizinische Klinik, Technische Universität München, München 81675, Germany
| | - Natasa Stojanovic
- Medizinische Klinik, Technische Universität München, München 81675, Germany
| | - Jan Christian
- Departments of Medicine and of Microbiology and Immunology, The Research Institute of the McGill University Health Centre, McGill University, Montréal H3A 2B4, Canada
| | - Mariel C Paul
- Medizinische Klinik, Technische Universität München, München 81675, Germany
| | - Roland H Stauber
- Molecular and Cellular Oncology/Mainz Screening Center (MSC), University Hospital of Mainz, Mainz 55101, Germany
| | - Roland M Schmid
- Medizinische Klinik, Technische Universität München, München 81675, Germany
| | - Georg Häcker
- Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinik Freiburg, Freiburg 79104, Germany
| | - Oliver H Krämer
- Department of Toxicology, University of Mainz Medical Center, Mainz 55131, Germany
| | - Dieter Saur
- Medizinische Klinik, Technische Universität München, München 81675, Germany
| | - Günter Schneider
- Medizinische Klinik, Technische Universität München, München 81675, Germany
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Walz S, Lorenzin F, Morton J, Wiese KE, von Eyss B, Herold S, Rycak L, Dumay-Odelot H, Karim S, Bartkuhn M, Roels F, Wüstefeld T, Fischer M, Teichmann M, Zender L, Wei CL, Sansom O, Wolf E, Eilers M. Activation and repression by oncogenic MYC shape tumour-specific gene expression profiles. Nature 2014; 511:483-7. [PMID: 25043018 PMCID: PMC6879323 DOI: 10.1038/nature13473] [Citation(s) in RCA: 386] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Accepted: 05/13/2014] [Indexed: 12/26/2022]
Abstract
In mammalian cells, the MYC oncoprotein binds to thousands of promoters. During mitogenic stimulation of primary lymphocytes, MYC promotes an increase in the expression of virtually all genes. In contrast, MYC-driven tumour cells differ from normal cells in the expression of specific sets of up- and downregulated genes that have considerable prognostic value. To understand this discrepancy, we studied the consequences of inducible expression and depletion of MYC in human cells and murine tumour models. Changes in MYC levels activate and repress specific sets of direct target genes that are characteristic of MYC-transformed tumour cells. Three factors account for this specificity. First, the magnitude of response parallels the change in occupancy by MYC at each promoter. Functionally distinct classes of target genes differ in the E-box sequence bound by MYC, suggesting that different cellular responses to physiological and oncogenic MYC levels are controlled by promoter affinity. Second, MYC both positively and negatively affects transcription initiation independent of its effect on transcriptional elongation. Third, complex formation with MIZ1 (also known as ZBTB17) mediates repression of multiple target genes by MYC and the ratio of MYC and MIZ1 bound to each promoter correlates with the direction of response.
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Affiliation(s)
- Susanne Walz
- 1] Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany [2]
| | - Francesca Lorenzin
- 1] Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany [2]
| | - Jennifer Morton
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Katrin E Wiese
- Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Björn von Eyss
- Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Steffi Herold
- Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Lukas Rycak
- Institute for Molecular Biology and Tumor Research (IMT), Emil-Mannkopff-Str.2, 35033 Marburg, Germany
| | - Hélène Dumay-Odelot
- University of Bordeaux, IECB, ARNA laboratory, Equipe Labellisée Contre le Cancer, 33600 Pessac, France
| | - Saadia Karim
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Marek Bartkuhn
- Institute for Genetics, Justus-Liebig-University, Heinrich-Buff-Ring 58, 35390 Giessen, Germany
| | - Frederik Roels
- University Children's Hospital of Cologne, and Cologne Center for Molecular Medicine (CMMC), University of Cologne, Kerpener Str. 62, 50924 Cologne, Germany
| | - Torsten Wüstefeld
- University Hospital Tübingen, Division of Translational Gastrointestinal Oncology, Department of Internal Medicine I, Otfried-Mueller-Strasse 10, 72076 Tübingen, Germany
| | - Matthias Fischer
- University Children's Hospital of Cologne, and Cologne Center for Molecular Medicine (CMMC), University of Cologne, Kerpener Str. 62, 50924 Cologne, Germany
| | - Martin Teichmann
- University of Bordeaux, IECB, ARNA laboratory, Equipe Labellisée Contre le Cancer, 33600 Pessac, France
| | - Lars Zender
- 1] University Hospital Tübingen, Division of Translational Gastrointestinal Oncology, Department of Internal Medicine I, Otfried-Mueller-Strasse 10, 72076 Tübingen, Germany [2] Translational Gastrointestinal Oncology Group within the German Center for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Chia-Lin Wei
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
| | - Owen Sansom
- CRUK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Elmar Wolf
- 1] Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany [2] Rudolf Virchow Center/DFG Research Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Str.2, 97080 Würzburg, Germany [3]
| | - Martin Eilers
- 1] Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany [2] Comprehensive Cancer Center Mainfranken, University of Würzburg, Josef-Schneider-Str. 6, 97080 Würzburg, Germany [3]
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Shi Y, Xu X, Zhang Q, Fu G, Mo Z, Wang GS, Kishi S, Yang XL. tRNA synthetase counteracts c-Myc to develop functional vasculature. eLife 2014; 3:e02349. [PMID: 24940000 PMCID: PMC4057782 DOI: 10.7554/elife.02349] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Recent studies suggested an essential role for seryl-tRNA synthetase (SerRS) in vascular development. This role is specific to SerRS among all tRNA synthetases and is independent of its well-known aminoacylation function in protein synthesis. A unique nucleus-directing domain, added at the invertebrate-to-vertebrate transition, confers this novel non-translational activity of SerRS. Previous studies showed that SerRS, in some unknown way, controls VEGFA expression to prevent vascular over-expansion. Using in vitro, cell and animal experiments, we show here that SerRS intervenes by antagonizing c-Myc, the major transcription factor promoting VEGFA expression, through a tandem mechanism. First, by direct head-to-head competition, nuclear-localized SerRS blocks c-Myc from binding to the VEGFA promoter. Second, DNA-bound SerRS recruits the SIRT2 histone deacetylase to erase prior c-Myc-promoted histone acetylation. Thus, vertebrate SerRS and c-Myc is a pair of ‘Yin-Yang’ transcriptional regulator for proper development of a functional vasculature. Our results also discover an anti-angiogenic activity for SIRT2. DOI:http://dx.doi.org/10.7554/eLife.02349.001 The network of blood vessels is one of the earliest structures to develop in a vertebrate embryo. A protein called Vascular Endothelial Growth Factor A (or VEGFA for short) is needed to promote the growth of these blood vessels, but too much VEGFA can cause blood vessels to grow too much and to grow abnormally. Like most of the DNA in the nucleus, the gene for VEGFA is tightly wrapped around proteins called histones and must be unwrapped before it can be expressed as a protein. For the VEGFA gene, this unwrapping process starts when a protein called c-Myc adds chemical tags to the histones. Recent research suggested that an enzyme called seryl-tRNA synthetase (or SerRS for short) also controls the expression of VEGFA. This came as a surprise because no other tRNA synthetase has a similar role during development. And although SerRS is known to enter the cell nucleus in vertebrates, researchers did not know what SerRS did in the nucleus to control the expression of VEGFA. Now, Shi et al. have discovered that SerRS controls blood vessel development in zebrafish embryos by counteracting the activity of c-Myc. It does this in two different ways: first, it directly blocks c-Myc from binding to and unpacking the DNA; and second, SerRS works with another enzyme to remove tags that are already on the histones. Shi et al. found that if the expression of this other enzyme (called SIRT2) was reduced in zebrafish, the fish expressed more VEGFA and their blood vessels grew too much. Since blood vessel growth is important in the development of cancers, the findings of Shi et al. could also lead to a better understanding of how tumors develop, as well as how blood vessels develop normally. DOI:http://dx.doi.org/10.7554/eLife.02349.002
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Affiliation(s)
- Yi Shi
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, United States
| | - Xiaoling Xu
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, United States
| | - Qian Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, United States
| | - Guangsen Fu
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, United States
| | - Zhongying Mo
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, United States
| | - George S Wang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, United States
| | - Shuji Kishi
- Department of Metabolism and Aging, The Scripps Research Institute, Jupiter, United States
| | - Xiang-Lei Yang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, United States
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Link JM, Hurlin PJ. The activities of MYC, MNT and the MAX-interactome in lymphocyte proliferation and oncogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:554-62. [PMID: 24731854 DOI: 10.1016/j.bbagrm.2014.04.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 03/25/2014] [Accepted: 04/04/2014] [Indexed: 12/29/2022]
Abstract
The MYC family of proteins plays essential roles in embryonic development and in oncogenesis. Efforts over the past 30 years to define the transcriptional activities of MYC and how MYC functions to promote proliferation have produced evolving models of MYC function. One picture that has emerged of MYC and its partner protein MAX is of a transcription factor complex with a seemingly unique ability to stimulate the transcription of genes that are epigenetically poised for transcription and to amplify the transcription of actively transcribed genes. During lymphocyte activation, MYC is upregulated and stimulates a pro-proliferative program in part through the upregulation of a wide variety of metabolic effector genes that facilitate cell growth and cell cycle progression. MYC upregulation simultaneously sensitizes cells to apoptosis and activated lymphocytes and lymphoma cells have pro-survival attributes that allow MYC-driven proliferation to prevail. For example, the MAX-interacting protein MNT is upregulated in activated lymphocytes and was found to protect lymphocytes from MYC-dependent apoptosis. Here we review the activities of MYC, MNT and other MAX interacting proteins in the setting of T and B cell activation and oncogenesis. This article is part of a Special Issue entitled: Myc proteins in cell biology and pathology.
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Affiliation(s)
- Jason M Link
- Shriners Hospitals for Children Portland, 3101 SW Sam Jackson Park Road, Portland, OR 97239, USA; Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
| | - Peter J Hurlin
- Shriners Hospitals for Children Portland, 3101 SW Sam Jackson Park Road, Portland, OR 97239, USA; Department of Cell and Developmental Biology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Knight Cancer Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
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Abstract
Myc-family proteins are key controllers of the metabolic and proliferative status of the cell, and are subjected to a complex network of regulatory events that guarantee their efficient and fast modulation by extracellular stimuli. Hence, unbalances in regulatory mechanisms leading to altered Myc levels or activities are often reported in cancer cells. Here we show that c- and N-Myc are conjugated to SUMO proteins at conserved lysines in their C-terminal domain. No obvious effects of SUMOylation were detected on bulk N-Myc stability or activities, including the regulation of transcription, proliferation or apoptosis. N-Myc SUMOylation could be induced by cellular stresses, such as heat shock and proteasome inhibition, and in all instances concerned a small fraction of the N-Myc protein. We surmise that, as shown for other substrates, SUMOylation may be part of a quality-control mechanism acting on misfolded Myc proteins.
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Affiliation(s)
- Arianna Sabò
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, Italy
| | - Mirko Doni
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, Italy
| | - Bruno Amati
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, Italy
- * E-mail:
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ELFN1-AS1: a novel primate gene with possible microRNA function expressed predominantly in human tumors. BIOMED RESEARCH INTERNATIONAL 2014; 2014:398097. [PMID: 24707484 PMCID: PMC3953637 DOI: 10.1155/2014/398097] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 12/24/2013] [Accepted: 12/27/2013] [Indexed: 01/11/2023]
Abstract
Human gene LOC100505644 uncharacterized LOC100505644 [Homo sapiens] (Entrez Gene ID 100505644) is abundantly expressed in tumors but weakly expressed in few normal tissues. Till now the function of this gene remains unknown. Here we identified the chromosomal borders of the transcribed region and the major splice form of the LOC100505644-specific transcript. We characterised the major regulatory motifs of the gene and its splice sites. Analysis of the secondary structure of the major transcript variant revealed a hairpin-like structure characteristic for precursor microRNAs. Comparative genomic analysis of the locus showed that it originated in primates de novo. Taken together, our data indicate that human gene LOC100505644 encodes some non-protein coding RNA, likely a microRNA. It was assigned a gene symbol ELFN1-AS1 (ELFN1 antisense RNA 1 (non-protein coding)). This gene combines features of evolutionary novelty and predominant expression in tumors.
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Murakami-Tonami Y, Kishida S, Takeuchi I, Katou Y, Maris JM, Ichikawa H, Kondo Y, Sekido Y, Shirahige K, Murakami H, Kadomatsu K. Inactivation of SMC2 shows a synergistic lethal response in MYCN-amplified neuroblastoma cells. Cell Cycle 2014; 13:1115-31. [PMID: 24553121 PMCID: PMC4013162 DOI: 10.4161/cc.27983] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The condensin complex is required for chromosome condensation during mitosis; however, the role of this complex during interphase is unclear. Neuroblastoma is the most common extracranial solid tumor of childhood, and it is often lethal. In human neuroblastoma, MYCN gene amplification is correlated with poor prognosis. This study demonstrates that the gene encoding the condensin complex subunit SMC2 is transcriptionally regulated by MYCN. SMC2 also transcriptionally regulates DNA damage response genes in cooperation with MYCN. Downregulation of SMC2 induced DNA damage and showed a synergistic lethal response in MYCN-amplified/overexpression cells, leading to apoptosis in human neuroblastoma cells. Finally, this study found that patients bearing MYCN-amplified tumors showed improved survival when SMC2 expression was low. These results identify novel functions of SMC2 in DNA damage response, and we propose that SMC2 (or the condensin complex) is a novel molecular target for the treatment of MYCN-amplified neuroblastoma.
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Affiliation(s)
- Yuko Murakami-Tonami
- Department of Molecular Biology; Nagoya University Graduate School of Medicine; Nagoya, Japan
| | - Satoshi Kishida
- Department of Molecular Biology; Nagoya University Graduate School of Medicine; Nagoya, Japan
| | - Ichiro Takeuchi
- Department of Computer Science/Scientific and Engineering Simulation; Nagoya Institute of Technology; Nagoya, Japan
| | - Yuki Katou
- Laboratory of Genome Structure & Function; Institute of Molecular and Cellular Biosciences; The University of Tokyo; Tokyo, Japan
| | - John M Maris
- Department of Pediatrics and Center for Childhood Cancer Research; Children's Hospital of Philadelphia; University of Pennsylvania; Philadelphia, PA USA
| | | | - Yutaka Kondo
- Division of Molecular Oncology; Aichi Cancer Center Research Institute; Nagoya, Japan; Division of Epigenomics; Aichi Cancer Center Research Institute; Nagoya, Japan
| | - Yoshitaka Sekido
- Division of Molecular Oncology; Aichi Cancer Center Research Institute; Nagoya, Japan
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure & Function; Institute of Molecular and Cellular Biosciences; The University of Tokyo; Tokyo, Japan
| | - Hiroshi Murakami
- Department of Biological Science; Faculty of Science and Engineering; Chuo University; Tokyo, Japan
| | - Kenji Kadomatsu
- Department of Molecular Biology; Nagoya University Graduate School of Medicine; Nagoya, Japan
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Guo J, Li T, Schipper J, Nilson KA, Fordjour FK, Cooper JJ, Gordân R, Price DH. Sequence specificity incompletely defines the genome-wide occupancy of Myc. Genome Biol 2014; 15:482. [PMID: 25287278 PMCID: PMC4242493 DOI: 10.1186/s13059-014-0482-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 09/22/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The Myc-Max heterodimer is a transcription factor that regulates expression of a large number of genes. Genome occupancy of Myc-Max is thought to be driven by Enhancer box (E-box) DNA elements, CACGTG or variants, to which the heterodimer binds in vitro. RESULTS By analyzing ChIP-Seq datasets, we demonstrate that the positions occupied by Myc-Max across the human genome correlate with the RNA polymerase II, Pol II, transcription machinery significantly better than with E-boxes. Metagene analyses show that in promoter regions, Myc is uniformly positioned about 100 bp upstream of essentially all promoter proximal paused polymerases with Max about 15 bp upstream of Myc. We re-evaluate the DNA binding properties of full length Myc-Max proteins. Electrophoretic mobility shift assay results demonstrate Myc-Max heterodimers display significant sequence preference, but have high affinity for any DNA. Quantification of the relative affinities of Myc-Max for all possible 8-mers using universal protein-binding microarray assays shows that sequences surrounding core 6-mers significantly affect binding. Compared to the in vitro sequence preferences,Myc-Max genomic occupancy measured by ChIP-Seq is largely, although not completely, independent of sequence specificity. CONCLUSIONS We quantified the affinity of Myc-Max to all possible 8-mers and compared this with the sites of Myc binding across the human genome. Our results indicate that the genomic occupancy of Myc cannot be explained by its intrinsic DNA specificity and suggest that the transcription machinery and associated promoter accessibility play a predominant role in Myc recruitment.
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Affiliation(s)
- Jiannan Guo
- />Department of Biochemistry, University of Iowa, Iowa City, IA 52242 USA
| | - Tiandao Li
- />Department of Biochemistry, University of Iowa, Iowa City, IA 52242 USA
- />The Genome Institute, Washington University in St. Louis, St. Louis, MO 63108 USA
| | - Joshua Schipper
- />Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708 USA
| | - Kyle A Nilson
- />Molecular and Cellular Biology Program, University of Iowa, Iowa City, IA 52242 USA
| | - Francis K Fordjour
- />Department of Biochemistry, University of Iowa, Iowa City, IA 52242 USA
| | - Jeffrey J Cooper
- />Department of Biochemistry, University of Iowa, Iowa City, IA 52242 USA
| | - Raluca Gordân
- />Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708 USA
| | - David H Price
- />Department of Biochemistry, University of Iowa, Iowa City, IA 52242 USA
- />Molecular and Cellular Biology Program, University of Iowa, Iowa City, IA 52242 USA
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Patel N, Varghese J, Masaratana P, Latunde-Dada GO, Jacob M, Simpson RJ, McKie AT. The transcription factor ATOH8 is regulated by erythropoietic activity and regulates HAMP transcription and cellular pSMAD1,5,8 levels. Br J Haematol 2013; 164:586-96. [PMID: 24236640 PMCID: PMC4232863 DOI: 10.1111/bjh.12649] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 09/30/2013] [Indexed: 12/21/2022]
Abstract
ATOH8 has previously been shown to be an iron-regulated transcription factor, however its role in iron metabolism is not known. ATOH8 expression in HEK293 cells resulted in increased endogenous HAMP mRNA levels as well as HAMP promoter activity. Mutation of the E-box or SMAD response elements within the HAMP promoter significantly reduced the effects of ATOH8, indicating that ATOH8 activates HAMP transcription directly as well as through bone morphogenic protein (BMP) signalling. In support of the former, Chromatin immunoprecipitation assays provided evidence that ATOH8 binds to E-box regions within the HAMP promoter while the latter was supported by the finding that ATOH8 expression in HEK293 cells led to increased phosphorylated SMAD1,5,8 levels. Liver Atoh8 levels were reduced in mice under conditions associated with increased erythropoietic activity such as hypoxia, haemolytic anaemia, hypotransferrinaemia and erythropoietin treatment and increased by inhibitors of erythropoiesis. Hepatic Atoh8mRNA levels increased in mice treated with holo transferrin, suggesting that Atoh8 responds to changes in plasma iron. ATOH8 is therefore a novel transcriptional regulator of HAMP, which is responsive to changes in plasma iron and erythroid activity and could explain how changes in erythroid activity lead to regulation of HAMP.
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Affiliation(s)
- Neeta Patel
- Division of Diabetes and Nutritional Sciences, Kings College London, London, UK
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48
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Yang J, Sung E, Donlin-Asp PG, Corces VG. A subset of Drosophila Myc sites remain associated with mitotic chromosomes colocalized with insulator proteins. Nat Commun 2013; 4:1464. [PMID: 23403565 PMCID: PMC3573855 DOI: 10.1038/ncomms2469] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 01/07/2013] [Indexed: 12/31/2022] Open
Abstract
Myc has been characterized as a transcription factor that activates expression of genes involved in pluripotency and cancer, and as a component of the replication complex. Here we find that Myc is present at promoters and enhancers of D. melanogaster genes during interphase. Myc co-localizes with Orc2, which is part of the pre-replication complex, during G1. As is the case in mammals, Myc associates preferentially with paused genes, suggesting that it may also be involved in the release of RNAPII from promoter proximal pausing in Drosophila. Interestingly, about 40% of Myc sites present in interphase persists during mitosis. None of the Myc mitotic sites correspond to enhancers and only some correspond to promoters. The rest of mitotic Myc sites overlap with binding sites for multiple insulator proteins that are also maintained in mitosis. These results suggest alternative mechanisms to explain the role of Myc in pluripotency and cancer.
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Affiliation(s)
- Jingping Yang
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA
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Xiong L, Jiang W, Zhou R, Mao C, Guo Z. Identification and analysis of the regulatory network of Myc and microRNAs from high-throughput experimental data. Comput Biol Med 2013; 43:1252-60. [PMID: 23930820 DOI: 10.1016/j.compbiomed.2013.06.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Revised: 05/31/2013] [Accepted: 06/03/2013] [Indexed: 11/15/2022]
Abstract
As a transcription factor, c-Myc exerts significant influence in cancer development by regulating transcription of a large number of target genes including microRNAs. However, details of regulatory networks composed of Myc, microRNAs, and microRNA target genes are still unclear. Here, at system level, we built a comprehensive Myc-regulated miRNAs (Myc-miRNAs) regulatory network through the integration of experimentally validated high-throughput data and computational predictions. Using miRNA genomic information with ChIP-PET, we identified 30 Myc-miRNAs and found most of these Myc-miRNAs target genes were significantly enriched in cell cycle, apoptosis, cell proliferation GO terms and Myc-regulated signaling pathways, using gene sets enrichment analysis. We found most Myc-miRNAs involved in Myc-related cancer pathways expressed abnormally in Myc-associated tumors through the integration of diverse types of experimental data. Based upon Myc target genes identified by ChIP-chip assays, we identified that 1031 Myc-miRNAs feed-forward loops (FFLs) were significantly different from those obtained by chance; also, 11 high-quality FFLs were extracted from experimentally validated interactions. Finally, we built the miRNA-protein interaction network of experimentally validated Myc-miRNAs and discussed the more complex network composed of several FFLs networks. As shown in this study, we performed comprehensive analysis of the Myc-miRNAs regulatory network and provided potential Myc-miRNAs target genes which were involved in Myc pathway and cancer-related biological processes.
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Affiliation(s)
- Lili Xiong
- School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu 610031, PR China
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50
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Charlet J, Szemes M, Malik KTA, Brown KW. MYCN is recruited to the RASSF1A promoter but is not critical for DNA hypermethylation in neuroblastoma. Mol Carcinog 2012; 53:413-20. [PMID: 23280764 DOI: 10.1002/mc.21994] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 11/09/2012] [Accepted: 11/28/2012] [Indexed: 01/14/2023]
Abstract
Tumor suppressor genes such as RASSF1A are often epigenetically repressed by DNA hypermethylation in neuroblastoma, where the MYCN proto-oncogene is frequently amplified. MYC has been shown to associate with DNA methyltransferases, thereby inducing transcriptional repression of target genes, which suggested that MYCN might play a similar mechanistic role in the hypermethylation of tumor suppressor genes in neuroblastoma. This study tested that hypothesis by using co-immunoprecipitation and ChIP to investigate MYCN-DNA methyltransferase interactions, together with MYCN knock-down and over-expression systems to examine the effect of MYCN expression changes on gene methylation, employing both candidate gene and genome-wide assays. We show that MYCN interacts with DNA methyltransferases and is recruited to the promoter region of RASSF1A. However, using four model systems, we showed that long-term silencing of MYCN induces only a small loss of DNA methylation at the RASSF1A promoter in MYCN amplified neuroblastoma cell lines and over-expression of MYCN does not induce any DNA methylation, suggesting that MYCN is not critical for DNA hypermethylation in neuroblastoma.
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Affiliation(s)
- Jessica Charlet
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
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