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Shen J, Zhou L, Ye K, Gong J, Wu F, Mo K, Zhu Y, Chen C, Zhan R. The role of SPI1/VSIG4/THBS1 on glioblastoma progression through modulation of the PI3K/AKT pathway. J Adv Res 2024:S2090-1232(24)00260-1. [PMID: 38960279 DOI: 10.1016/j.jare.2024.06.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024] Open
Abstract
INTRODUCTION Glioblastoma multiforme (GBM) poses a significant challenge in terms of treatment due to its high malignancy, necessitating the identification of additional molecular targets. VSIG4, an oncogenic gene participates in tumor growth and migration in various cancer types. Nevertheless, the precise process through which VSIG4 facilitates the malignant progression of glioma remains to be elucidated. OBJECTIVES This research aims to explore the function and molecular mechanism involving VSIG4 in the malignant progression of glioma. METHODS The amount of VSIG4 was measured using qPCR, western blotting, and immunohistochemistry. Lentivirus infections were applied for upregulating or downregulating molecules within glioma cells. The incorporation of 5-ethynyl-20-deoxyuridine, Transwell, cell counting kit-8, and clone formation experiments, were applied to assess the biological functions of molecules on glioma cells. Dual luciferase reporter gene, RNA immunoprecipitation, and chromatin immunoprecipitation assays were used to explore the functional relationship among relevant molecules. RESULTS The upregulation of VSIG4 was observed in GBM tissues, indicating an adverse prognosis. Silencing VSIG4 in glioma cells resulted in a decrease in cell viability, invasion, proliferation, and tumorigenesis, an increase in cell apoptosis, and a stagnation in the cell cycle progression at the G0/G1 phase. Mechanistically, SPI1-mediated upregulation of VSIG4 expression led to binding between VSIG4 and THBS1 protein, ultimately facilitating the malignant progression of glioma cells through the activation of the PI3K/AKT pathway. The inhibited proliferative and invasive capabilities of glioma cells were reversed by overexpressing THBS1 following the knockdown of VSIG4. CONCLUSION Our findings provide evidence for the role of VSIG4 as an oncogene and reveal the previously unidentified contribution of the SPI1/VSIG4/THBS1 axis in the malignant progression of glioma. This signaling cascade enhances tumor growth and invasion by modulating the PI3K/AKT pathway. VSIG4 as a potential biomarker may be a viable strategy in the development of tailored molecular therapies for GBM.
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Affiliation(s)
- Jie Shen
- Department of Head and Neck Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China; College of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, PR China.
| | - Lihui Zhou
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, PR China; College of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, PR China.
| | - Ke Ye
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, PR China; College of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, PR China.
| | - Jiangbiao Gong
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, PR China.
| | - Fan Wu
- Department of Head and Neck Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China.
| | - Kangnan Mo
- Department of Head and Neck Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China.
| | - Yu Zhu
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, PR China.
| | - Chao Chen
- Department of Head and Neck Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, PR China.
| | - Renya Zhan
- Department of Neurosurgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, PR China; College of Medicine, Zhejiang University, Hangzhou 310003, Zhejiang, PR China.
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2
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Zhang LY, Tan Y, Luo XJ, Wu JF, Ni YR. The roles of ETS transcription factors in liver fibrosis. Hum Cell 2023; 36:528-539. [PMID: 36547849 DOI: 10.1007/s13577-022-00848-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
E26 transformation specific or E twenty-six (ETS) protein family consists of 28 transcription factors, five of which, named ETS1/2, PU.1, ERG and EHF, are known to involve in the development of liver fibrosis, and are expected to become diagnostic markers or therapeutic targets of liver fibrosis. In recent years, some small molecule inhibitors of ETS protein family have been discovered, which might open up a new path for the liver fibrosis therapy targeting ETS. This article reviews the research progress of ETS family members in the development liver fibrosis as well as their prospect of clinical application.
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Affiliation(s)
- Li-Ye Zhang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, China
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China
| | - Yong Tan
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, China
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China
| | - Xiao-Jie Luo
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, China
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China
| | - Jiang-Feng Wu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China.
- College of Basic Medical Science, China Three Gorges University, Yichang, China.
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China.
| | - Yi-Ran Ni
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China.
- College of Basic Medical Science, China Three Gorges University, Yichang, China.
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China.
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Tokarsky EJ, Crow JC, Guenther LM, Sherman J, Taslim C, Alexe G, Pishas KI, Rask G, Justis BS, Kasumova A, Stegmaier K, Lessnick SL, Theisen ER. Mitochondrial Dysfunction Is a Driver of SP-2509 Drug Resistance in Ewing Sarcoma. Mol Cancer Res 2022; 20:1035-1046. [PMID: 35298000 PMCID: PMC9284474 DOI: 10.1158/1541-7786.mcr-22-0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 01/07/2023]
Abstract
Expression of the fusion oncoprotein EWS/FLI causes Ewing sarcoma, an aggressive pediatric tumor characterized by widespread epigenetic deregulation. These epigenetic changes are targeted by novel lysine-specific demethylase-1 (LSD1) inhibitors, which are currently in early-phase clinical trials. Single-agent-targeted therapy often induces resistance, and successful clinical development requires knowledge of resistance mechanisms, enabling the design of effective combination strategies. Here, we used a genome-scale CRISPR-Cas9 loss-of-function screen to identify genes whose knockout (KO) conferred resistance to the LSD1 inhibitor SP-2509 in Ewing sarcoma cell lines. Multiple genes required for mitochondrial electron transport chain (ETC) complexes III and IV function were hits in our screen. We validated this finding using genetic and chemical approaches, including CRISPR KO, ETC inhibitors, and mitochondrial depletion. Further global transcriptional profiling revealed that altered complex III/IV function disrupted the oncogenic program mediated by EWS/FLI and LSD1 and blunted the transcriptomic response to SP-2509. IMPLICATIONS These findings demonstrate that mitochondrial dysfunction modulates SP-2509 efficacy and suggest that new therapeutic strategies combining LSD1 with agents that prevent mitochondrial dysfunction may benefit patients with this aggressive malignancy.
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Affiliation(s)
- E. John Tokarsky
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Jesse C. Crow
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Lillian M. Guenther
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - John Sherman
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Cenny Taslim
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Galen Rask
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Blake S. Justis
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Ana Kasumova
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Stephen L. Lessnick
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio.,Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Emily R. Theisen
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio.,Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, Ohio.,Corresponding Author: Emily R. Theisen, Abigail Wexner Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205. Phone: 614-355-2927; E-mail:
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Du B, Gao W, Qin Y, Zhong J, Zhang Z. Study on the role of transcription factor SPI1 in the development of glioma. Chin Neurosurg J 2022; 8:7. [PMID: 35361282 PMCID: PMC8973577 DOI: 10.1186/s41016-022-00276-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 03/04/2022] [Indexed: 12/19/2022] Open
Abstract
Background Glioma is a common malignant brain tumor. The purpose of this study was to investigate the role of the transcription factor SPI1 in glioma. Methods SPI1 expression in glioma was identified using qRT-PCR and Western blotting. Cell proliferation was assessed using the CCK8 assay. Transwell and wound healing assays were utilized to evaluate cell migration. Additionally, cell cycle and apoptosis were detected using flow cytometry. Results We observed that the expression level of SPI1 was up-regulated in glioma tissues, compared to normal tissues. Furthermore, we found that SPI1 is able to promote proliferation and migration of glioma cells in vitro. Flow cytometry results demonstrate that, compared to si-NC cells, si-SPI1 cells stagnated in the G1 phase, and down-regulation of SPI1 expression is able to increase rates of apoptosis. Double luciferase activity and chromatin immunoprecipitation assay results indicated that SPI1 can bind to the promoter sites and promote the proliferation and migration of glioma cells by regulating the expression of oncogenic PAICS. Conclusions Our results suggest that SPI1 can promote proliferation and migration of glioma. Furthermore, SPI1 can be utilized as a potential diagnostic marker and therapeutic target for glioma. Supplementary Information The online version contains supplementary material available at 10.1186/s41016-022-00276-2.
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Neveu B, Richer C, Cassart P, Caron M, Jimenez-Cortes C, St-Onge P, Fuchs C, Garnier N, Gobeil S, Sinnett D. Identification of new ETV6 modulators through a high-throughput functional screening. iScience 2022; 25:103858. [PMID: 35198911 PMCID: PMC8851229 DOI: 10.1016/j.isci.2022.103858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 01/01/2022] [Accepted: 01/28/2022] [Indexed: 12/02/2022] Open
Abstract
ETV6 transcriptional activity is critical for proper blood cell development in the bone marrow. Despite the accumulating body of evidence linking ETV6 malfunction to hematological malignancies, its regulatory network remains unclear. To uncover genes that modulate ETV6 repressive transcriptional activity, we performed a specifically designed, unbiased genome-wide shRNA screen in pre-B acute lymphoblastic leukemia cells. Following an extensive validation process, we identified 13 shRNAs inducing overexpression of ETV6 transcriptional target genes. We showed that the silencing of AKIRIN1, COMMD9, DYRK4, JUNB, and SRP72 led to an abrogation of ETV6 repressive activity. We identified critical modulators of the ETV6 function which could participate in cellular transformation through the ETV6 transcriptional network. We develop a genome-wide shRNAs screen for ETV6 modulators The screen uncovered 13 novel putative ETV6 modulator genes The modulators demonstrated a broad impact on the ETV6 transcriptional network T-ALL cells results suggest modulators are conserved in other cellular contexts
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Affiliation(s)
- Benjamin Neveu
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Chantal Richer
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
| | - Pauline Cassart
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
| | - Maxime Caron
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
| | - Camille Jimenez-Cortes
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Molecular Biology Program, Faculty of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Pascal St-Onge
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
| | - Claire Fuchs
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Nicolas Garnier
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
| | - Stéphane Gobeil
- CHU de Québec-Université Laval Research Center, Quebec City, QC G1V 4G2, Canada
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Corresponding author
| | - Daniel Sinnett
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
- Corresponding author
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6
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Haybaeck J, Roessner A. [Malignant round cell tumors : The Ewing sarcoma and beyond]. DER PATHOLOGE 2020; 41:116-122. [PMID: 32060684 DOI: 10.1007/s00292-020-00759-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Ewing sarcomas are highly malignant tumors that are mainly found in children and adolescents. In addition to early clinical diagnosis, correct histopathological and molecular genetic classification is the most important step. Although EWSR1-FLI1 fusion is by far the most common detectable change, there are also other representatives of the Ewing sarcoma family that cannot be distinguished histopathologically and immunohistochemically from classical Ewing sarcomas and that have different molecular genetic profiles. Although a precise molecular genetic differentiation of the various representatives of small round blue cell tumors does not yet lead to any change in the standard chemotherapy and surgical treatment applied, it does allow an estimation of the prognosis and will probably contribute in the future to an even more individualized treatment of Ewing sarcomas within the framework of personalized medicine.
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Affiliation(s)
- Johannes Haybaeck
- Institut für Pathologie, Univ.-Klinikum Magdeburg A.ö.R., Medizinische Fakultät, Otto-von-Guericke-Universität Magdeburg, Leipziger Straße 44, 39120, Magdeburg, Deutschland. .,Institut für Pathologie, Neuropathologie und Molekuarpathologie, Medizinische Universität Innsbruck, Müllerstraße 44, 6020, Innsbruck, Österreich. .,Diagnostik und Forschungsinstitut für Pathologie, Medizinische Universität Graz, Neue Stiftingtalstraße 6, 8010, Graz, Österreich.
| | - Albert Roessner
- Institut für Pathologie, Univ.-Klinikum Magdeburg A.ö.R., Medizinische Fakultät, Otto-von-Guericke-Universität Magdeburg, Leipziger Straße 44, 39120, Magdeburg, Deutschland
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7
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Albrecht AV, Kim HM, Poon GMK. Mapping interfacial hydration in ETS-family transcription factor complexes with DNA: a chimeric approach. Nucleic Acids Res 2019; 46:10577-10588. [PMID: 30295801 PMCID: PMC6237740 DOI: 10.1093/nar/gky894] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/21/2018] [Indexed: 11/12/2022] Open
Abstract
Hydration of interfaces is a major determinant of target specificity in protein/DNA interactions. Interfacial hydration is a highly variable feature in DNA recognition by ETS transcription factors and functionally relates to cellular responses to osmotic stress. To understand how hydration is mediated in the conserved ETS/DNA binding interface, secondary structures comprising the DNA contact surface of the strongly hydrated ETS member PU.1 were substituted, one at a time, with corresponding elements from its sparsely hydrated relative Ets-1. The resultant PU.1/Ets-1 chimeras exhibited variably reduced sensitivity to osmotic pressure, indicative of a distributed pattern of interfacial hydration in wildt-ype PU.1. With the exception of the recognition helix H3, the chimeras retained substantially high affinities. Ets-1 residues could therefore offset the loss of favorable hydration contributions in PU.1 via low-water interactions, but at the cost of decreased selectivity at base positions flanking the 5'-GGA-3' core consensus. Substitutions within H3 alone, which contacts the core consensus, impaired binding affinity and PU.1 transactivation in accordance with the evolutionary separation of the chimeric residues involved. The combined biophysical, bioinformatics and functional data therefore supports hydration as an evolved specificity determinant that endows PU.1 with more stringent sequence selection over its ancestral relative Ets-1.
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Affiliation(s)
- Amanda V Albrecht
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Hye Mi Kim
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
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Huang K, Xhani S, Albrecht AV, Ha VLT, Esaki S, Poon GMK. Mechanism of cognate sequence discrimination by the ETS-family transcription factor ETS-1. J Biol Chem 2019; 294:9666-9678. [PMID: 31048376 DOI: 10.1074/jbc.ra119.007866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/01/2019] [Indexed: 12/19/2022] Open
Abstract
Functional evidence increasingly implicates low-affinity DNA recognition by transcription factors as a general mechanism for the spatiotemporal control of developmental genes. Although the DNA sequence requirements for affinity are well-defined, the dynamic mechanisms that execute cognate recognition are much less resolved. To address this gap, here we examined ETS1, a paradigm developmental transcription factor, as a model for which cognate discrimination remains enigmatic. Using molecular dynamics simulations, we interrogated the DNA-binding domain of murine ETS1 alone and when bound to high-and low-affinity cognate sites or to nonspecific DNA. The results of our analyses revealed collective backbone and side-chain motions that distinguished cognate versus nonspecific as well as high- versus low-affinity cognate DNA binding. Combined with binding experiments with site-directed ETS1 mutants, the molecular dynamics data disclosed a triad of residues that respond specifically to low-affinity cognate DNA. We found that a DNA-contacting residue (Gln-336) specifically recognizes low-affinity DNA and triggers the loss of a distal salt bridge (Glu-343/Arg-378) via a large side-chain motion that compromises the hydrophobic packing of two core helices. As an intact Glu-343/Arg-378 bridge is the default state in unbound ETS1 and maintained in high-affinity and nonspecific complexes, the low-affinity complex represents a unique conformational adaptation to the suboptimization of developmental enhancers.
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Affiliation(s)
| | | | | | | | | | - Gregory M K Poon
- From the Department of Chemistry and .,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303
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9
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Yalim‐Camci I, Balcik‐Ercin P, Cetin M, Odabas G, Tokay N, Sayan AE, Yagci T. ETS1 is coexpressed with ZEB2 and mediates ZEB2‐induced epithelial‐mesenchymal transition in human tumors. Mol Carcinog 2019; 58:1068-1081. [DOI: 10.1002/mc.22994] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/06/2019] [Accepted: 02/11/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Irem Yalim‐Camci
- Department of Molecular Biology and Genetics, Laboratory of Molecular OncologyGebze Technical UniversityGebze/Kocaeli Turkey
| | - Pelin Balcik‐Ercin
- Department of Molecular Biology and Genetics, Laboratory of Molecular OncologyGebze Technical UniversityGebze/Kocaeli Turkey
| | - Metin Cetin
- Department of Molecular Biology and Genetics, Laboratory of Molecular OncologyGebze Technical UniversityGebze/Kocaeli Turkey
| | - Gorkem Odabas
- Department of Molecular Biology and Genetics, Laboratory of Molecular OncologyGebze Technical UniversityGebze/Kocaeli Turkey
| | - Nurettin Tokay
- Department of Molecular Biology and Genetics, Laboratory of Molecular OncologyGebze Technical UniversityGebze/Kocaeli Turkey
| | - A. Emre Sayan
- Cancer Sciences Unit and Cancer Research UK CentreUniversity of Southampton, Southampton General HospitalSouthampton UK
| | - Tamer Yagci
- Department of Molecular Biology and Genetics, Laboratory of Molecular OncologyGebze Technical UniversityGebze/Kocaeli Turkey
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10
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Mao P, Brown AJ, Esaki S, Lockwood S, Poon GMK, Smerdon MJ, Roberts SA, Wyrick JJ. ETS transcription factors induce a unique UV damage signature that drives recurrent mutagenesis in melanoma. Nat Commun 2018; 9:2626. [PMID: 29980679 PMCID: PMC6035183 DOI: 10.1038/s41467-018-05064-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 06/07/2018] [Indexed: 11/12/2022] Open
Abstract
Recurrent mutations are frequently associated with transcription factor (TF) binding sites (TFBS) in melanoma, but the mechanism driving mutagenesis at TFBS is unclear. Here, we use a method called CPD-seq to map the distribution of UV-induced cyclobutane pyrimidine dimers (CPDs) across the human genome at single nucleotide resolution. Our results indicate that CPD lesions are elevated at active TFBS, an effect that is primarily due to E26 transformation-specific (ETS) TFs. We show that ETS TFs induce a unique signature of CPD hotspots that are highly correlated with recurrent mutations in melanomas, despite high repair activity at these sites. ETS1 protein renders its DNA binding targets extremely susceptible to UV damage in vitro, due to binding-induced perturbations in the DNA structure that favor CPD formation. These findings define a mechanism responsible for recurrent mutations in melanoma and reveal that DNA binding by ETS TFs is inherently mutagenic in UV-exposed cells. Many factors contribute to mutation hotspots in cancer cells. Here the authors map UV damage at single-nucleotide resolution across the human genome and find that binding sites of ETS transcription factors are especially prone to forming UV lesions, leading to mutation hotspots in melanoma.
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Affiliation(s)
- Peng Mao
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA
| | - Alexander J Brown
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA
| | - Shingo Esaki
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Svetlana Lockwood
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, 99164, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303, USA
| | - Michael J Smerdon
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA
| | - Steven A Roberts
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA. .,Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA.
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA. .,Center for Reproductive Biology, Washington State University, Pullman, WA, 99164, USA.
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Stiewe T, Haran TE. How mutations shape p53 interactions with the genome to promote tumorigenesis and drug resistance. Drug Resist Updat 2018; 38:27-43. [PMID: 29857816 DOI: 10.1016/j.drup.2018.05.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/27/2018] [Accepted: 05/03/2018] [Indexed: 12/31/2022]
Abstract
The tumor suppressive transcription factor p53 regulates a wide array of cellular processes that confer upon cells an essential protection against cancer development. Wild-type p53 regulates gene expression by directly binding to DNA in a sequence-specific manner. p53 missense mutations are the most common mutations in malignant cells and can be regarded as synonymous with anticancer drug resistance and poor prognosis. The current review provides an overview of how the extraordinary variety of more than 2000 different mutant p53 proteins, known as the p53 mutome, affect the interaction of p53 with DNA. We discuss how the classification of p53 mutations to loss of function (LOF), gain of function (GOF), and dominant-negative (DN) inhibition of a remaining wild-type allele, hides a complex p53 mutation spectrum that depends on the distinctive nature of each mutant protein, requiring different therapeutic strategies for each mutant p53 protein. We propose to regard the different mutant p53 categories as continuous variables, that may not be independent of each other. In particular, we suggest here to consider GOF mutations as a special subset of LOF mutations, especially when mutant p53 binds to DNA through cooperation with other transcription factors, and we present a model for GOF mechanism that consolidates many observations on the GOF phenomenon. We review how novel mutant p53 targeting approaches aim to restore a wild-type-like DNA interaction and to overcome resistance to cancer therapy.
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Affiliation(s)
- Thorsten Stiewe
- Institute of Molecular Oncology, Philipps-University, 35037 Marburg, Germany.
| | - Tali E Haran
- Department of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel.
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12
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Johnson KM, Taslim C, Saund RS, Lessnick SL. Identification of two types of GGAA-microsatellites and their roles in EWS/FLI binding and gene regulation in Ewing sarcoma. PLoS One 2017; 12:e0186275. [PMID: 29091716 PMCID: PMC5665490 DOI: 10.1371/journal.pone.0186275] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 09/28/2017] [Indexed: 01/23/2023] Open
Abstract
Ewing sarcoma is a bone malignancy of children and young adults, frequently harboring the EWS/FLI chromosomal translocation. The resulting fusion protein is an aberrant transcription factor that uses highly repetitive GGAA-containing elements (microsatellites) to activate and repress thousands of target genes mediating oncogenesis. However, the mechanisms of EWS/FLI interaction with microsatellites and regulation of target gene expression is not clearly understood. Here, we profile genome-wide protein binding and gene expression. Using a combination of unbiased genome-wide computational and experimental analysis, we define GGAA-microsatellites in a Ewing sarcoma context. We identify two distinct classes of GGAA-microsatellites and demonstrate that EWS/FLI responsiveness is dependent on microsatellite length. At close range “promoter-like” microsatellites, EWS/FLI binding and subsequent target gene activation is highly dependent on number of GGAA-motifs. “Enhancer-like” microsatellites demonstrate length-dependent EWS/FLI binding, but minimal correlation for activated and none for repressed targets. Our data suggest EWS/FLI binds to “promoter-like” and “enhancer-like” microsatellites to mediate activation and repression of target genes through different regulatory mechanisms. Such characterization contributes valuable insight to EWS/FLI transcription factor biology and clarifies the role of GGAA-microsatellites on a global genomic scale. This may provide unique perspective on the role of non-coding DNA in cancer susceptibility and therapeutic development.
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Affiliation(s)
- Kirsten M. Johnson
- The Medical Scientist Training Program and the Biomedical Sciences Graduate Program, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
- Center for Childhood Cancer and Blood Diseases, Nationwide Children’s Hospital Research Institute, Columbus, Ohio, United States of America
| | - Cenny Taslim
- Center for Childhood Cancer and Blood Diseases, Nationwide Children’s Hospital Research Institute, Columbus, Ohio, United States of America
| | - Ranajeet S. Saund
- Center for Childhood Cancer and Blood Diseases, Nationwide Children’s Hospital Research Institute, Columbus, Ohio, United States of America
| | - Stephen L. Lessnick
- The Medical Scientist Training Program and the Biomedical Sciences Graduate Program, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
- Center for Childhood Cancer and Blood Diseases, Nationwide Children’s Hospital Research Institute, Columbus, Ohio, United States of America
- Division of Pediatric Hematology/Oncology/BMT, The Ohio State University College of Medicine, Columbus, Ohio, United States of America
- * E-mail:
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13
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Antony-Debré I, Paul A, Leite J, Mitchell K, Kim HM, Carvajal LA, Todorova TI, Huang K, Kumar A, Farahat AA, Bartholdy B, Narayanagari SR, Chen J, Ambesi-Impiombato A, Ferrando AA, Mantzaris I, Gavathiotis E, Verma A, Will B, Boykin DW, Wilson WD, Poon GM, Steidl U. Pharmacological inhibition of the transcription factor PU.1 in leukemia. J Clin Invest 2017; 127:4297-4313. [PMID: 29083320 DOI: 10.1172/jci92504] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 09/21/2017] [Indexed: 11/17/2022] Open
Abstract
The transcription factor PU.1 is often impaired in patients with acute myeloid leukemia (AML). Here, we used AML cells that already had low PU.1 levels and further inhibited PU.1 using either RNA interference or, to our knowledge, first-in-class small-molecule inhibitors of PU.1 that we developed specifically to allosterically interfere with PU.1-chromatin binding through interaction with the DNA minor groove that flanks PU.1-binding motifs. These small molecules of the heterocyclic diamidine family disrupted the interaction of PU.1 with target gene promoters and led to downregulation of canonical PU.1 transcriptional targets. shRNA or small-molecule inhibition of PU.1 in AML cells from either PU.1lo mutant mice or human patients with AML-inhibited cell growth and clonogenicity and induced apoptosis. In murine and human AML (xeno)transplantation models, treatment with our PU.1 inhibitors decreased tumor burden and resulted in increased survival. Thus, our study provides proof of concept that PU.1 inhibition has potential as a therapeutic strategy for the treatment of AML and for the development of small-molecule inhibitors of PU.1.
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Affiliation(s)
- Iléana Antony-Debré
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Ananya Paul
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Joana Leite
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Kelly Mitchell
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Hye Mi Kim
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Luis A Carvajal
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Tihomira I Todorova
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Kenneth Huang
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Abdelbasset A Farahat
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA.,Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Boris Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | | | - Jiahao Chen
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | | | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | - Ioannis Mantzaris
- Department of Medicine (Oncology), Division of Hemato-Oncology, Albert Einstein College of Medicine-Montefiore Medical Center, New York, New York, USA
| | - Evripidis Gavathiotis
- Department of Biochemistry.,Albert Einstein Cancer Center, and.,Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, New York, New York, USA
| | - Amit Verma
- Department of Medicine (Oncology), Division of Hemato-Oncology, Albert Einstein College of Medicine-Montefiore Medical Center, New York, New York, USA.,Albert Einstein Cancer Center, and.,Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, New York, New York, USA
| | - Britta Will
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA.,Albert Einstein Cancer Center, and.,Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, New York, New York, USA
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Gregory Mk Poon
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Ulrich Steidl
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA.,Department of Medicine (Oncology), Division of Hemato-Oncology, Albert Einstein College of Medicine-Montefiore Medical Center, New York, New York, USA.,Albert Einstein Cancer Center, and.,Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, New York, New York, USA
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14
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Role for the EWS domain of EWS/FLI in binding GGAA-microsatellites required for Ewing sarcoma anchorage independent growth. Proc Natl Acad Sci U S A 2017; 114:9870-9875. [PMID: 28847958 DOI: 10.1073/pnas.1701872114] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ewing sarcoma usually expresses the EWS/FLI fusion transcription factor oncoprotein. EWS/FLI regulates myriad genes required for Ewing sarcoma development. EWS/FLI binds GGAA-microsatellite sequences in vivo and in vitro. These sequences provide EWS/FLI-mediated activation to reporter constructs, suggesting that they function as EWS/FLI-response elements. We now demonstrate the critical role of an EWS/FLI-bound GGAA-microsatellite in regulation of the NR0B1 gene as well as for Ewing sarcoma proliferation and anchorage-independent growth. Clinically, genomic GGAA-microsatellites are highly variable and polymorphic. Current data suggest that there is an optimal "sweet-spot" GGAA-microsatellite length (of 18-26 GGAA repeats) that confers maximal EWS/FLI-responsiveness to target genes, but the mechanistic basis for this remains unknown. Our biochemical studies, using recombinant Δ22 (a version of EWS/FLI containing only the FLI portion), demonstrate a stoichiometry of one Δ22-monomer binding to every two consecutive GGAA-repeats on shorter microsatellite sequences. Surprisingly, the affinity for Δ22 binding to GGAA-microsatellites significantly decreased, and ultimately became unmeasureable, when the size of the microsatellite was increased to the sweet-spot length. In contrast, a fully functional EWS/FLI mutant (Mut9, which retains approximately half of the EWS portion of the fusion) showed low affinity for smaller GGAA-microsatellites but instead significantly increased its affinity at sweet-spot microsatellite lengths. Single-gene ChIP and genome-wide ChIP-sequencing (ChIP-seq) and RNA-seq studies extended these findings to the in vivo setting. Together, these data demonstrate the critical requirement of GGAA-microsatellites as EWS/FLI activating response elements in vivo and reveal an unexpected role for the EWS portion of the EWS/FLI fusion in binding to sweet-spot GGAA-microsatellites.
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15
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Guan FHX, Bailey CG, Metierre C, O'Young P, Gao D, Khoo TL, Holst J, Rasko JEJ. The antiproliferative ELF2 isoform, ELF2B, induces apoptosis in vitro and perturbs early lymphocytic development in vivo. J Hematol Oncol 2017; 10:75. [PMID: 28351373 PMCID: PMC5371273 DOI: 10.1186/s13045-017-0446-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/20/2017] [Indexed: 01/08/2023] Open
Abstract
Background ELF2 (E74-like factor 2) also known as NERF (new Ets-related factor), a member of the Ets family of transcription factors, regulates genes important in B and T cell development, cell cycle progression, and angiogenesis. Conserved ELF2 isoforms, ELF2A, and ELF2B, arising from alternative promoter usage can exert opposing effects on target gene expression. ELF2A activates, whilst ELF2B represses, gene expression, and the balance of expression between these isoforms may be important in maintaining normal cellular function. Methods We compared the function of ELF2 isoforms ELF2A and ELF2B with other ELF subfamily proteins ELF1 and ELF4 in primary and cancer cell lines using proliferation, colony-forming, cell cycle, and apoptosis assays. We further examined the role of ELF2 isoforms in haemopoietic development using a Rag1-/-murine bone marrow reconstitution model. Results ELF2B overexpression significantly reduced cell proliferation and clonogenic capacity, minimally disrupted cell cycle kinetics, and induced apoptosis. In contrast, ELF2A overexpression only marginally reduced clonogenic capacity with little effect on proliferation, cell cycle progression, or apoptosis. Deletion of the N-terminal 19 amino acids unique to ELF2B abrogated the antiproliferative and proapoptotic functions of ELF2B thereby confirming its crucial role. Mice expressing Elf2a or Elf2b in haemopoietic cells variously displayed perturbations in the pre-B cell stage and multiple stages of T cell development. Mature B cells, T cells, and myeloid cells in steady state were unaffected, suggesting that the main role of ELF2 is restricted to the early development of B and T cells and that compensatory mechanisms exist. No differences in B and T cell development were observed between ELF2 isoforms. Conclusions We conclude that ELF2 isoforms are important regulators of cellular proliferation, cell cycle progression, and apoptosis. In respect to this, ELF2B acts in a dominant negative fashion compared to ELF2A and as a putative tumour suppressor gene. Given that these cellular processes are critical during haemopoiesis, we propose that the regulatory interplay between ELF2 isoforms contributes substantially to early B and T cell development. Electronic supplementary material The online version of this article (doi:10.1186/s13045-017-0446-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fiona H X Guan
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Charles G Bailey
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Cynthia Metierre
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Patrick O'Young
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Dadi Gao
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Teh Liane Khoo
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia.,Sydney Medical School, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Jeff Holst
- Sydney Medical School, University of Sydney, Camperdown, NSW, 2006, Australia.,Origins of Cancer Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Camperdown, NSW, 2050, Australia. .,Sydney Medical School, University of Sydney, Camperdown, NSW, 2006, Australia. .,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia.
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16
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Abstract
The ETS family of transcription factors is a functionally heterogeneous group of gene regulators that share a structurally conserved, eponymous DNA-binding domain. DNA target specificity derives from combinatorial interactions with other proteins as well as intrinsic heterogeneity among ETS domains. Emerging evidence suggests molecular hydration as a fundamental feature that defines the intrinsic heterogeneity in DNA target selection and susceptibility to epigenetic DNA modification. This perspective invokes novel hypotheses in the regulation of ETS proteins in physiologic osmotic stress, their pioneering potential in heterochromatin, and the effects of passive and pharmacologic DNA demethylation on ETS regulation.
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Affiliation(s)
- Gregory M K Poon
- a Department of Chemistry , Georgia State University , Atlanta , GA , USA.,b Center for Diagnostics and Therapeutics, Georgia State University , Atlanta , GA , USA
| | - Hye Mi Kim
- a Department of Chemistry , Georgia State University , Atlanta , GA , USA
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17
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Stephens DC, Poon GMK. Differential sensitivity to methylated DNA by ETS-family transcription factors is intrinsically encoded in their DNA-binding domains. Nucleic Acids Res 2016; 44:8671-8681. [PMID: 27270080 PMCID: PMC5062964 DOI: 10.1093/nar/gkw528] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 05/30/2016] [Indexed: 01/25/2023] Open
Abstract
Transactivation by the ETS family of transcription factors, whose members share structurally conserved DNA-binding domains, is variably sensitive to methylation of their target genes. The mechanism by which DNA methylation controls ETS proteins remains poorly understood. Uncertainly also pervades the effects of hemi-methylated DNA, which occurs following DNA replication and in response to hypomethylating agents, on site recognition by ETS proteins. To address these questions, we measured the affinities of two sequence-divergent ETS homologs, PU.1 and Ets-1, to DNA sites harboring a hemi- and fully methylated CpG dinucleotide. While the two proteins bound unmethylated DNA with indistinguishable affinity, their affinities to methylated DNA are markedly heterogeneous and exhibit major energetic coupling between the two CpG methylcytosines. Analysis of simulated DNA and existing co-crystal structures revealed that hemi-methylation induced non-local backbone and groove geometries that were not conserved in the fully methylated state. Indirect readout of these perturbations was differentially achieved by the two ETS homologs, with the distinctive interfacial hydration in PU.1/DNA binding moderating the inhibitory effects of DNA methylation on binding. This data established a biophysical basis for the pioneering properties associated with PU.1, which robustly bound fully methylated DNA, but not Ets-1, which was substantially inhibited.
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Affiliation(s)
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
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18
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Gao P, Yuan M, Ma X, Jiang W, Zhu L, Wen M, Xu J, Liu Q, An H. Transcription factor Fli-1 positively regulates lipopolysaccharide-induced interleukin-27 production in macrophages. Mol Immunol 2016; 71:184-191. [PMID: 26900987 DOI: 10.1016/j.molimm.2016.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/06/2016] [Accepted: 02/09/2016] [Indexed: 11/19/2022]
Abstract
IL-27 is an important regulator of TLR4-activated innate immune. The mechanism by which IL-27 production is regulated in TLR4-activated innate immune remains largely unclear. Here we show that expression of transcription factor Fli-1 at protein level is increased in macrophages following LPS stimulation. Fli-1 overexpression increases LPS-activated IL-27 production in macrophages. Consistently, Fli-1 knockdown inhibits LPS-induced IL-27 production in macrophages. Chromatin immunoprecipitation (ChIP) assay reveals that Fli-1 binds the promoter of IL-27 p28 subunit. Further experiments manifest that Fli-1 binds the region between -250 and -150 bp upstream of the transcriptional start site of p28 gene and increases p28 gene promoter-controlled transcription. These results demonstrate that Fli-1 positively regulates IL-27 production in TLR4-activated immune response by promoting transcription of IL-27 p28 gene.
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Affiliation(s)
- Peng Gao
- Cancer Institute, Institute of Translational Medicine, Second Military Medical University, Shanghai 200433, China
| | - Ming Yuan
- National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai 200433, China
| | - Xianwei Ma
- Cancer Institute, Institute of Translational Medicine, Second Military Medical University, Shanghai 200433, China
| | - Wei Jiang
- Cancer Institute, Institute of Translational Medicine, Second Military Medical University, Shanghai 200433, China
| | - Lingxi Zhu
- Cancer Institute, Institute of Translational Medicine, Second Military Medical University, Shanghai 200433, China
| | - Mingyue Wen
- National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai 200433, China
| | - Jing Xu
- Cancer Institute, Institute of Translational Medicine, Second Military Medical University, Shanghai 200433, China
| | - Qiuyan Liu
- National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai 200433, China.
| | - Huazhang An
- Cancer Institute, Institute of Translational Medicine, Second Military Medical University, Shanghai 200433, China.
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19
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Dutta S, Agrawal Y, Mishra A, Dhanjal JK, Sundar D. A theoretical investigation of DNA dynamics and desolvation kinetics for zinc finger proteinZif268. BMC Genomics 2015; 16 Suppl 12:S5. [PMID: 26677774 PMCID: PMC4682422 DOI: 10.1186/1471-2164-16-s12-s5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background Transcription factors, regulating the expression inventory of a cell, interact with its respective DNA subjugated by a specific recognition pattern, which if well exploited may ensure targeted genome engineering. The mostly widely studied transcription factors are zinc finger proteins that bind to its target DNA via direct and indirect recognition levels at the interaction interface. Exploiting the binding specificity and affinity of the interaction between the zinc fingers and the respective DNA can help in generating engineered zinc fingers for therapeutic applications. Experimental evidences lucidly substantiate the effect of indirect interaction like DNA deformation and desolvation kinetics, in empowering ZFPs to accomplish partial sequence specificity functioning around structural properties of DNA. Exploring the structure-function relationships of the existing zinc finger-DNA complexes at the indirect recognition level can aid in predicting the probable zinc fingers that could bind to any target DNA. Deformation energy, which defines the energy required to bend DNA from its native shape to its shape when bound to the ZFP, is an effect of indirect recognition mechanism. Water is treated as a co-reactant for unfurling the affinity studies in ZFP-DNA binding equilibria that takes into account the unavoidable change in hydration that occurs when these two solvated surfaces come into contact. Results Aspects like desolvation and DNA deformation have been theoretically investigated based on simulations and free energy perturbation data revealing a consensus in correlating affinity and specificity as well as stability for ZFP-DNA interactions. Greater loss of water at the interaction interface of the DNA calls for binding with higher affinity, eventually distorting the DNA to a greater extent accounted by the change in major groove width and DNA tilt, stretch and rise. Conclusion Most prediction algorithms for ZFPs do not account for water loss at the interface. The above findings may significantly affect these algorithms. Further the sequence dependent deformation in the DNA upon complexation with our prototype as well as preference of bases at the 2nd and 3rd position of the repeating triplet provide an absolutely new insight about the indirect interactions undergoing a change that have not been probed yet.
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20
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Dittmer J. The role of the transcription factor Ets1 in carcinoma. Semin Cancer Biol 2015; 35:20-38. [PMID: 26392377 DOI: 10.1016/j.semcancer.2015.09.010] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/16/2015] [Accepted: 09/16/2015] [Indexed: 12/12/2022]
Abstract
Ets1 belongs to the large family of the ETS domain family of transcription factors and is involved in cancer progression. In most carcinomas, Ets1 expression is linked to poor survival. In breast cancer, Ets1 is primarily expressed in the triple-negative subtype, which is associated with unfavorable prognosis. Ets1 contributes to the acquisition of cancer cell invasiveness, to EMT (epithelial-to-mesenchymal transition), to the development of drug resistance and neo-angiogenesis. The aim of this review is to summarize the current knowledge on the functions of Ets1 in carcinoma progression and on the mechanisms that regulate Ets1 activity in cancer.
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Affiliation(s)
- Jürgen Dittmer
- Clinic for Gynecology, Martin Luther University Halle-Wittenberg, Germany.
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21
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Cooper CDO, Newman JA, Aitkenhead H, Allerston CK, Gileadi O. Structures of the Ets Protein DNA-binding Domains of Transcription Factors Etv1, Etv4, Etv5, and Fev: DETERMINANTS OF DNA BINDING AND REDOX REGULATION BY DISULFIDE BOND FORMATION. J Biol Chem 2015; 290:13692-709. [PMID: 25866208 PMCID: PMC4447949 DOI: 10.1074/jbc.m115.646737] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Indexed: 12/31/2022] Open
Abstract
Ets transcription factors, which share the conserved Ets DNA-binding domain, number nearly 30 members in humans and are particularly involved in developmental processes. Their deregulation following changes in expression, transcriptional activity, or by chromosomal translocation plays a critical role in carcinogenesis. Ets DNA binding, selectivity, and regulation have been extensively studied; however, questions still arise regarding binding specificity outside the core GGA recognition sequence and the mode of action of Ets post-translational modifications. Here, we report the crystal structures of Etv1, Etv4, Etv5, and Fev, alone and in complex with DNA. We identify previously unrecognized features of the protein-DNA interface. Interactions with the DNA backbone account for most of the binding affinity. We describe a highly coordinated network of water molecules acting in base selection upstream of the GGAA core and the structural features that may account for discrimination against methylated cytidine residues. Unexpectedly, all proteins crystallized as disulfide-linked dimers, exhibiting a novel interface (distant to the DNA recognition helix). Homodimers of Etv1, Etv4, and Etv5 could be reduced to monomers, leading to a 40–200-fold increase in DNA binding affinity. Hence, we present the first indication of a redox-dependent regulatory mechanism that may control the activity of this subset of oncogenic Ets transcription factors.
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Affiliation(s)
- Christopher D O Cooper
- From the Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Joseph A Newman
- From the Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Hazel Aitkenhead
- From the Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Charles K Allerston
- From the Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Opher Gileadi
- From the Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
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22
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He G, Tolic A, Bashkin JK, Poon GMK. Heterogeneous dynamics in DNA site discrimination by the structurally homologous DNA-binding domains of ETS-family transcription factors. Nucleic Acids Res 2015; 43:4322-31. [PMID: 25824951 PMCID: PMC4417174 DOI: 10.1093/nar/gkv267] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 01/09/2023] Open
Abstract
The ETS family of transcription factors exemplifies current uncertainty in how eukaryotic genetic regulators with overlapping DNA sequence preferences achieve target site specificity. PU.1 and Ets-1 represent archetypes for studying site discrimination by ETS proteins because their DNA-binding domains are the most divergent in sequence, yet they share remarkably superimposable DNA-bound structures. To gain insight into the contrasting thermodynamics and kinetics of DNA recognition by these two proteins, we investigated the structure and dynamics of site discrimination by their DNA-binding domains. Electrophoretic mobilities of complexes formed by the two homologs with circularly permuted binding sites showed significant dynamic differences only for DNA complexes of PU.1. Free solution measurements by dynamic light scattering showed PU.1 to be more dynamic than Ets-1; moreover, dynamic changes are strongly coupled to site discrimination by PU.1, but not Ets-1. Interrogation of the protein/DNA interface by DNA footprinting showed similar accessibility to dimethyl sulfate for PU.1/DNA and Ets-1/DNA complexes, indicating that the dynamics of PU.1/DNA complexes reside primarily outside that interface. An information-based analysis of the two homologs’ binding motifs suggests a role for dynamic coupling in PU.1's ability to enforce a more stringent sequence preference than Ets-1 and its proximal sequence homologs.
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Affiliation(s)
- Gaofei He
- Department of Chemistry and Biochemistry and Center for Nanoscience, University of Missouri - St. Louis, St. Louis, MO 63121, USA
| | - Ana Tolic
- College of Pharmacy, Washington State University, Spokane, WA 99210, USA
| | - James K Bashkin
- Department of Chemistry and Biochemistry and Center for Nanoscience, University of Missouri - St. Louis, St. Louis, MO 63121, USA
| | - Gregory M K Poon
- College of Pharmacy, Washington State University, Spokane, WA 99210, USA
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23
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Recent advances in the structural molecular biology of Ets transcription factors: interactions, interfaces and inhibition. Biochem Soc Trans 2014; 42:130-8. [PMID: 24450640 PMCID: PMC3901394 DOI: 10.1042/bst20130227] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The Ets family of eukaryotic transcription factors is based around the conserved Ets DNA-binding domain. Although their DNA-binding selectivity is biochemically and structurally well characterized, structures of homodimeric and ternary complexes point to Ets domains functioning as versatile protein-interaction modules. In the present paper, we review the progress made over the last decade to elucidate the structural mechanisms involved in modulation of DNA binding and protein partner selection during dimerization. We see that Ets domains, although conserved around a core architecture, have evolved to utilize a variety of interaction surfaces and binding mechanisms, reflecting Ets domains as dynamic interfaces for both DNA and protein interaction. Furthermore, we discuss recent advances in drug development for inhibition of Ets factors, and the roles structural biology can play in their future.
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24
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Mariño-Enríquez A, Fletcher CD. Round cell sarcomas – Biologically important refinements in subclassification. Int J Biochem Cell Biol 2014; 53:493-504. [DOI: 10.1016/j.biocel.2014.04.022] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/23/2014] [Accepted: 04/26/2014] [Indexed: 12/19/2022]
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25
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Wang S, Linde MH, Munde M, Carvalho VD, Wilson WD, Poon GMK. Mechanistic heterogeneity in site recognition by the structurally homologous DNA-binding domains of the ETS family transcription factors Ets-1 and PU.1. J Biol Chem 2014; 289:21605-16. [PMID: 24952944 DOI: 10.1074/jbc.m114.575340] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
ETS family transcription factors regulate diverse genes through binding at cognate DNA sites that overlap substantially in sequence. The DNA-binding domains of ETS proteins (ETS domains) are highly conserved structurally yet share limited amino acid homology. To define the mechanistic implications of sequence diversity within the ETS family, we characterized the thermodynamics and kinetics of DNA site recognition by the ETS domains of Ets-1 and PU.1, which represent the extremes in amino acid divergence among ETS proteins. Even though the two ETS domains bind their optimal sites with similar affinities under physiologic conditions, their nature of site recognition differs strikingly in terms of the role of hydration and counter ion release. The data suggest two distinct mechanisms wherein Ets-1 follows a "dry" mechanism that rapidly parses sites through electrostatic interactions and direct protein-DNA contacts, whereas PU.1 utilizes hydration to interrogate sequence-specific sites and form a long-lived complex relative to the Ets-1 counterpart. The kinetic persistence of the high affinity PU.1 · DNA complex may be relevant to an emerging role of PU.1, but not Ets-1, as a pioneer transcription factor in vivo. In addition, PU.1 activity is critical to the development and function of macrophages and lymphocytes, which present osmotically variable environments, and hydration-dependent specificity may represent an important regulatory mechanism in vivo, a hypothesis that finds support in gene expression profiles of primary murine macrophages.
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Affiliation(s)
- Shuo Wang
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and
| | - Miles H Linde
- the Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington 99210-1495
| | - Manoj Munde
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and
| | - Victor D Carvalho
- the Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington 99210-1495
| | - W David Wilson
- From the Department of Chemistry, Georgia State University, Atlanta, Georgia 30303 and
| | - Gregory M K Poon
- the Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington 99210-1495
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De S, Chan ACK, Coyne HJ, Bhachech N, Hermsdorf U, Okon M, Murphy MEP, Graves BJ, McIntosh LP. Steric mechanism of auto-inhibitory regulation of specific and non-specific DNA binding by the ETS transcriptional repressor ETV6. J Mol Biol 2014; 426:1390-406. [PMID: 24333486 PMCID: PMC4278593 DOI: 10.1016/j.jmb.2013.11.031] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/05/2013] [Accepted: 11/09/2013] [Indexed: 11/29/2022]
Abstract
DNA binding by the ETS transcriptional repressor ETV6 (or TEL) is auto-inhibited ~50-fold due to an α-helix that sterically blocks its ETS domain binding interface. Using NMR spectroscopy, we demonstrate that this marginally stable helix is unfolded, and not displaced to a non-inhibitory position, when ETV6 is bound to DNA containing a consensus (5')GGAA(3') recognition site. Although significantly lower in affinity, binding to non-specific DNA is auto-inhibited ~5-fold and is also accompanied by helix unfolding. Based on NMR chemical shift perturbations, both specific and non-specific DNA are bound via the same canonical ETS domain interface. However, spectral perturbations are smaller for the non-specific complex, suggesting weaker and less well-defined interactions than in the specific complex. In parallel, the crystal structure of ETV6 bound to a specific DNA duplex was determined. The structure of this complex reveals that a non-conserved histidine residue in the ETS domain recognition helix helps establish the specificity of ETV6 for DNA-binding sites containing (5')GGAA(3')versus(5')GGAT(3'). These studies provide a unified steric mechanism for attenuating ETV6 binding to both specific and non-specific DNA and expand the repertoire of characterized auto-inhibitory strategies utilized to regulate ETS factors.
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Affiliation(s)
- Soumya De
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Anson C K Chan
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - H Jerome Coyne
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Niraja Bhachech
- Department of Oncological Sciences, University of Utah School of Medicine, and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112-5550, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
| | - Ulrike Hermsdorf
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Michael E P Murphy
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Barbara J Graves
- Department of Oncological Sciences, University of Utah School of Medicine, and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112-5550, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA
| | - Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z3.
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Munde M, Wang S, Kumar A, Stephens CE, Farahat AA, Boykin DW, Wilson WD, Poon GMK. Structure-dependent inhibition of the ETS-family transcription factor PU.1 by novel heterocyclic diamidines. Nucleic Acids Res 2013; 42:1379-90. [PMID: 24157839 PMCID: PMC3902942 DOI: 10.1093/nar/gkt955] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
ETS transcription factors mediate a wide array of cellular functions and are attractive targets for pharmacological control of gene regulation. We report the inhibition of the ETS-family member PU.1 with a panel of novel heterocyclic diamidines. These diamidines are derivatives of furamidine (DB75) in which the central furan has been replaced with selenophene and/or one or both of the bridging phenyl has been replaced with benzimidazole. Like all ETS proteins, PU.1 binds sequence specifically to 10-bp sites by inserting a recognition helix into the major groove of a 5′-GGAA-3′ consensus, accompanied by contacts with the flanking minor groove. We showed that diamidines target the minor groove of AT-rich sequences on one or both sides of the consensus and disrupt PU.1 binding. Although all of the diamidines bind to one or both of the expected sequences within the binding site, considerable heterogeneity exists in terms of stoichiometry, site–site interactions and induced DNA conformation. We also showed that these compounds accumulate in live cell nuclei and inhibit PU.1-dependent gene transactivation. This study demonstrates that heterocyclic diamidines are capable of inhibiting PU.1 by targeting the flanking sequences and supports future efforts to develop agents for inhibiting specific members of the ETS family.
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Affiliation(s)
- Manoj Munde
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA and Department of Pharmaceutical Sciences, Washington State University, Pullman, WA 99164-6534, USA
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Kar A, Gutierrez-Hartmann A. Molecular mechanisms of ETS transcription factor-mediated tumorigenesis. Crit Rev Biochem Mol Biol 2013; 48:522-43. [PMID: 24066765 DOI: 10.3109/10409238.2013.838202] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The E26 transformation-specific (ETS) family of transcription factors is critical for development, differentiation, proliferation and also has a role in apoptosis and tissue remodeling. Changes in expression of ETS proteins therefore have a significant impact on normal physiology of the cell. Transcriptional consequences of ETS protein deregulation by overexpression, gene fusion, and modulation by RAS/MAPK signaling are linked to alterations in normal cell functions, and lead to unlimited increased proliferation, sustained angiogenesis, invasion and metastasis. Existing data show that ETS proteins control pathways in epithelial cells as well as stromal compartments, and the crosstalk between the two is essential for normal development and cancer. In this review, we have focused on ETS factors with a known contribution in cancer development. Instead of focusing on a prototype, we address cancer associated ETS proteins and have highlighted the diverse mechanisms by which they affect carcinogenesis. Finally, we discuss strategies for ETS factor targeting as a potential means for cancer therapeutics.
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29
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Structural and dynamic studies of the transcription factor ERG reveal DNA binding is allosterically autoinhibited. Proc Natl Acad Sci U S A 2013; 110:13374-9. [PMID: 23898196 DOI: 10.1073/pnas.1301726110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The Ets-Related Gene (ERG) belongs to the Ets family of transcription factors and is critically important for maintenance of the hematopoietic stem cell population. A chromosomal translocation observed in the majority of human prostate cancers leads to the aberrant overexpression of ERG. We have identified regions flanking the ERG Ets domain responsible for autoinhibition of DNA binding and solved crystal structures of uninhibited, autoinhibited, and DNA-bound ERG. NMR-based measurements of backbone dynamics show that uninhibited ERG undergoes substantial dynamics on the millisecond-to-microsecond timescale but autoinhibited and DNA-bound ERG do not. We propose a mechanism whereby the allosteric basis of ERG autoinhibition is mediated predominantly by the regulation of Ets-domain dynamics with only modest structural changes.
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30
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Tanaka S, Nakao K, Sekimoto T, Oka M, Yoneda Y. Cell density-dependent nuclear accumulation of ELK3 is involved in suppression of PAI-1 expression. Cell Struct Funct 2013; 38:145-54. [PMID: 23708702 DOI: 10.1247/csf.13007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Cell-cell contact regulates the proliferation and differentiation of non-transformed cells, e.g., NIH/3T3 cells show growth arrest at high cell density. However, only a few reports described the dynamic behavior of transcription factors involved in this process. In this study, we showed that the mRNA levels of plasminogen activator inhibitor type 1 (PAI-1) decreased drastically at high cell density, and that ELK3, a member of the Ets transcription factor family, repressed PAI-1 expression. We also demonstrated that while ELK3 was distributed evenly throughout the cell at low cell density, it accumulated in the nucleus at high cell density, and that binding of DNA by ELK3 at the A domain facilitated its nuclear accumulation. Furthermore, we found that ETS1, a PAI-1 activator, occupied the ELK3-binding site within the PAI-1 promoter at low cell density, while it was released at high cell density. These results suggest that at high cell density, the switching of binding of transcription factors from ETS1 to ELK3 occurs at a specific binding site of the PAI-1 promoter, leading to the cell-density dependent suppression of PAI-1 expression.
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Affiliation(s)
- Shu Tanaka
- Department of Frontier Biosciences, Graduate School of Frontier Biosciences, Osaka University, Yamada-oka, Suita, Osaka, Japan
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31
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Munde M, Poon GMK, Wilson WD. Probing the electrostatics and pharmacological modulation of sequence-specific binding by the DNA-binding domain of the ETS family transcription factor PU.1: a binding affinity and kinetics investigation. J Mol Biol 2013; 425:1655-69. [PMID: 23416556 DOI: 10.1016/j.jmb.2013.02.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 02/07/2013] [Indexed: 10/27/2022]
Abstract
Members of the ETS family of transcription factors regulate a functionally diverse array of genes. All ETS proteins share a structurally conserved but sequence-divergent DNA-binding domain, known as the ETS domain. Although the structure and thermodynamics of the ETS-DNA complexes are well known, little is known about the kinetics of sequence recognition, a facet that offers potential insight into its molecular mechanism. We have characterized DNA binding by the ETS domain of PU.1 by biosensor-surface plasmon resonance (SPR). SPR analysis revealed a striking kinetic profile for DNA binding by the PU.1 ETS domain. At low salt concentrations, it binds high-affinity cognate DNA with a very slow association rate constant (≤10(5)M(-)(1)s(-)(1)), compensated by a correspondingly small dissociation rate constant. The kinetics are strongly salt dependent but mutually balance to produce a relatively weak dependence in the equilibrium constant. This profile contrasts sharply with reported data for other ETS domains (e.g., Ets-1, TEL) for which high-affinity binding is driven by rapid association (>10(7)M(-)(1)s(-)(1)). We interpret this difference in terms of the hydration properties of ETS-DNA binding and propose that at least two mechanisms of sequence recognition are employed by this family of DNA-binding domain. Additionally, we use SPR to demonstrate the potential for pharmacological inhibition of sequence-specific ETS-DNA binding, using the minor groove-binding distamycin as a model compound. Our work establishes SPR as a valuable technique for extending our understanding of the molecular mechanisms of ETS-DNA interactions as well as developing potential small-molecule agents for biotechnological and therapeutic purposes.
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Affiliation(s)
- Manoj Munde
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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32
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Nhili R, Peixoto P, Depauw S, Flajollet S, Dezitter X, Munde MM, Ismail MA, Kumar A, Farahat AA, Stephens CE, Duterque-Coquillaud M, David Wilson W, Boykin DW, David-Cordonnier MH. Targeting the DNA-binding activity of the human ERG transcription factor using new heterocyclic dithiophene diamidines. Nucleic Acids Res 2013; 41:125-38. [PMID: 23093599 PMCID: PMC3592449 DOI: 10.1093/nar/gks971] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Revised: 09/24/2012] [Accepted: 09/25/2012] [Indexed: 12/04/2022] Open
Abstract
Direct modulation of gene expression by targeting oncogenic transcription factors is a new area of research for cancer treatment. ERG, an ETS-family transcription factor, is commonly over-expressed or translocated in leukaemia and prostate carcinoma. In this work, we selected the di-(thiophene-phenyl-amidine) compound DB1255 as an ERG/DNA binding inhibitor using a screening test of synthetic inhibitors of the ERG/DNA interaction followed by electrophoretic mobility shift assays (EMSA) validation. Spectrometry, footprint and biosensor-surface plasmon resonance analyses of the DB1255/DNA interaction evidenced sequence selectivity and groove binding as dimer. Additional EMSA evidenced the precise DNA-binding sequence required for optimal DB1255/DNA binding and thus for an efficient ERG/DNA complex inhibition. We further highlighted the structure activity relationships from comparison with derivatives. In cellulo luciferase assay confirmed this modulation both with the constructed optimal sequences and the Osteopontin promoter known to be regulated by ERG and which ERG-binding site was protected from DNaseI digestion on binding of DB1255. These data showed for the first time the ERG/DNA complex modulation, both in vitro and in cells, by a heterocyclic diamidine that specifically targets a portion of the ERG DNA recognition site.
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Affiliation(s)
- Raja Nhili
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Paul Peixoto
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Sabine Depauw
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Sébastien Flajollet
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Xavier Dezitter
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Manoj M. Munde
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Mohamed A. Ismail
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Arvind Kumar
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Abdelbasset A. Farahat
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Chad E. Stephens
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Martine Duterque-Coquillaud
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - W. David Wilson
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - David W. Boykin
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Marie-Hélène David-Cordonnier
- INSERM UMR837-JPARC, Team 4, Molecular and Cellular Targeting for Cancer Treatment, University of Lille North of France, IMPRT-IFR114, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, Lille F-59045, France, CNRS UMR 8161, Institut de Biologie de Lille, University of Lille North of France, Institut Pasteur de Lille IFR 142, Lille F-59021, France and Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
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Gromiha MM, Nagarajan R. Computational approaches for predicting the binding sites and understanding the recognition mechanism of protein-DNA complexes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 91:65-99. [PMID: 23790211 DOI: 10.1016/b978-0-12-411637-5.00003-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein-DNA recognition plays an important role in the regulation of gene expression. Understanding the influence of specific residues for protein-DNA interactions and the recognition mechanism of protein-DNA complexes is a challenging task in molecular and computational biology. Several computational approaches have been put forward to tackle these problems from different perspectives: (i) development of databases for the interactions between protein and DNA and binding specificity of protein-DNA complexes, (ii) structural analysis of protein-DNA complexes, (iii) discriminating DNA-binding proteins from amino acid sequence, (iv) prediction of DNA-binding sites and protein-DNA binding specificity using sequence and/or structural information, and (v) understanding the recognition mechanism of protein-DNA complexes. In this review, we focus on all these issues and extensively discuss the advancements on the development of comprehensive bioinformatics databases for protein-DNA interactions, efficient tools for identifying the binding sites, and plausible mechanisms for understanding the recognition of protein-DNA complexes. Further, the available online resources for understanding protein-DNA interactions are collectively listed, which will serve as ready-to-use information for the research community.
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Affiliation(s)
- M Michael Gromiha
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India.
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34
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Monument MJ, Johnson KM, Grossmann AH, Schiffman JD, Randall RL, Lessnick SL. Microsatellites with macro-influence in ewing sarcoma. Genes (Basel) 2012; 3:444-60. [PMID: 24704979 PMCID: PMC3899989 DOI: 10.3390/genes3030444] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 07/04/2012] [Accepted: 07/05/2012] [Indexed: 01/02/2023] Open
Abstract
Numerous molecular abnormalities contribute to the genetic derangements involved in tumorigenesis. Chromosomal translocations are a frequent source of these derangements, producing unique fusion proteins with novel oncogenic properties. EWS/ETS fusions in Ewing sarcoma are a prime example of this, resulting in potent chimeric oncoproteins with novel biological properties and a unique transcriptional signature essential for oncogenesis. Recent evidence demonstrates that EWS/FLI, the most common EWS/ETS fusion in Ewing sarcoma, upregulates gene expression using a GGAA microsatellite response element dispersed throughout the human genome. These GGAA microsatellites function as enhancer elements, are sites of epigenetic regulation and are necessary for EWS/FLI DNA binding and upregulation of principal oncogenic targets. An increasing number of GGAA motifs appear to substantially enhance EWS/FLI-mediated gene expression, which has compelling biological implications as these GGAA microsatellites are highly polymorphic within and between ethnically distinct populations. Historically regarded as junk DNA, this emerging evidence clearly demonstrates that microsatellite DNA plays an instrumental role in EWS/FLI-mediated transcriptional regulation and oncogenesis in Ewing sarcoma. This unprecedented role of GGAA microsatellite DNA in Ewing sarcoma provides a unique opportunity to expand our mechanistic understanding of how EWS/ETS fusions influence cancer susceptibility, prognosis and transcriptional regulation.
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Affiliation(s)
- Michael J Monument
- Center for Children's Cancer Research, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA.
| | - Kirsten M Johnson
- Center for Children's Cancer Research, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA.
| | - Allie H Grossmann
- Department of Pathology and Program in Molecular Medicine, University of Utah, Salt Lake City, UT 84112, USA.
| | - Joshua D Schiffman
- Center for Children's Cancer Research, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA.
| | - R Lor Randall
- Center for Children's Cancer Research, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA.
| | - Stephen L Lessnick
- Center for Children's Cancer Research, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA.
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35
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Yamasaki S, Terada T, Kono H, Shimizu K, Sarai A. A new method for evaluating the specificity of indirect readout in protein-DNA recognition. Nucleic Acids Res 2012; 40:e129. [PMID: 22618872 PMCID: PMC3458528 DOI: 10.1093/nar/gks462] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Proteins recognize a specific DNA sequence not only through direct contact (direct readout) with base pairs but also through sequence-dependent conformation and/or flexibility of DNA (indirect readout). However, it is difficult to assess the contribution of indirect readout to the sequence specificity. What is needed is a straightforward method for quantifying its contributions to specificity. Using Bayesian statistics, we derived the probability of a particular sequence for a given DNA structure from the trajectories of molecular dynamics (MD) simulations of DNAs containing all possible tetramer sequences. Then, we quantified the specificity of indirect readout based on the information entropy associated with the probability. We tested this method with known structures of protein–DNA complexes. This method enabled us to correctly predict those regions where experiments suggested the involvement of indirect readout. The results also indicated new regions where the indirect readout mechanism makes major contributions to the recognition. The present method can be used to estimate the contribution of indirect readout without approximations to the distributions in the conformational ensembles of DNA, and would serve as a powerful tool to study the mechanism of protein–DNA recognition.
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Affiliation(s)
- Satoshi Yamasaki
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.
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36
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Poon GMK. DNA Binding Regulates the Self-Association of the ETS Domain of PU.1 in a Sequence-Dependent Manner. Biochemistry 2012; 51:4096-107. [DOI: 10.1021/bi300331v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Gregory M. K. Poon
- Department of Pharmaceutical
Sciences, Washington State University,
Pullman, Washington 99164-6534, United States
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37
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Poon GMK. Sequence discrimination by DNA-binding domain of ETS family transcription factor PU.1 is linked to specific hydration of protein-DNA interface. J Biol Chem 2012; 287:18297-307. [PMID: 22474303 DOI: 10.1074/jbc.m112.342345] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
PU.1 is an essential transcription factor in normal hematopoietic lineage development. It recognizes a large number of promoter sites differing only in bases flanking a core consensus of 5'-GGAA-3'. DNA binding is mediated by its ETS domain, whose sequence selectivity directly corresponds to the transactivational activity and frequency of binding sites for full-length PU.1 in vivo. To better understand the basis of sequence discrimination, we characterized its binding properties to a high affinity and low affinity site. Despite sharing a homologous structural framework as confirmed by DNase I and hydroxyl radical footprinting, the two complexes exhibit striking heterogeneity in terms of hydration properties. High affinity binding is destabilized by osmotic stress, whereas low affinity binding is insensitive. Dimethyl sulfate footprinting showed that the major groove at the core consensus is protected in the high affinity complex but accessible in the low affinity one. Finally, destabilization of low affinity binding by salt is in quantitative agreement with the number of phosphate contacts but is substantially attenuated in high affinity binding. These observations support a mechanism of sequence discrimination wherein specifically bound water molecules couple flanking backbone contacts with base-specific interactions in a sequestered cavity at the core consensus. The implications of this model with respect to other ETS paralogs are discussed.
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Affiliation(s)
- Gregory M K Poon
- Department of Pharmaceutical Sciences, Washington State University, Pullman, Washington 99164-6534, USA.
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38
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Hussain A, Shaw PE, Hirst JD. Molecular dynamics simulations and in silico peptide ligand screening of the Elk-1 ETS domain. J Cheminform 2011; 3:49. [PMID: 22044511 PMCID: PMC3227621 DOI: 10.1186/1758-2946-3-49] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 11/01/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Elk-1 transcription factor is a member of a group of proteins called ternary complex factors, which serve as a paradigm for gene regulation in response to extracellular signals. Its deregulation has been linked to multiple human diseases including the development of tumours. The work herein aims to inform the design of potential peptidomimetic compounds that can inhibit the formation of the Elk-1 dimer, which is key to Elk-1 stability. We have conducted molecular dynamics simulations of the Elk-1 ETS domain followed by virtual screening. RESULTS We show the ETS dimerisation site undergoes conformational reorganisation at the α1β1 loop. Through exhaustive screening of di- and tri-peptide libraries against a collection of ETS domain conformations representing the dynamics of the loop, we identified a series of potential binders for the Elk-1 dimer interface. The di-peptides showed no particular preference toward the binding site; however, the tri-peptides made specific interactions with residues: Glu17, Gln18 and Arg49 that are pivotal to the dimer interface. CONCLUSIONS We have shown molecular dynamics simulations can be combined with virtual peptide screening to obtain an exhaustive docking protocol that incorporates dynamic fluctuations in a receptor. Based on our findings, we suggest experimental binding studies to be performed on the 12 SILE ranked tri-peptides as possible compounds for the design of inhibitors of Elk-1 dimerisation. It would also be reasonable to consider the score-ranked tri-peptides as a comparative test to establish whether peptide size is a determinant factor of binding to the ETS domain.
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Affiliation(s)
- Abrar Hussain
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Peter E Shaw
- School of Biomedical Sciences, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
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39
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Hollenhorst PC, McIntosh LP, Graves BJ. Genomic and biochemical insights into the specificity of ETS transcription factors. Annu Rev Biochem 2011; 80:437-71. [PMID: 21548782 DOI: 10.1146/annurev.biochem.79.081507.103945] [Citation(s) in RCA: 373] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
ETS proteins are a group of evolutionarily related, DNA-binding transcriptional factors. These proteins direct gene expression in diverse normal and disease states by binding to specific promoters and enhancers and facilitating assembly of other components of the transcriptional machinery. The highly conserved DNA-binding ETS domain defines the family and is responsible for specific recognition of a common sequence motif, 5'-GGA(A/T)-3'. Attaining specificity for biological regulation in such a family is thus a conundrum. We present the current knowledge of routes to functional diversity and DNA binding specificity, including divergent properties of the conserved ETS and PNT domains, the involvement of flanking structured and unstructured regions appended to these dynamic domains, posttranslational modifications, and protein partnerships with other DNA-binding proteins and coregulators. The review emphasizes recent advances from biochemical and biophysical approaches, as well as insights from genomic studies that detect ETS-factor occupancy in living cells.
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Affiliation(s)
- Peter C Hollenhorst
- Medical Sciences, Indiana University School of Medicine, Bloomington, Indiana 47405, USA.
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40
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Toomey EC, Schiffman JD, Lessnick SL. Recent advances in the molecular pathogenesis of Ewing's sarcoma. Oncogene 2010; 29:4504-16. [PMID: 20543858 PMCID: PMC3555143 DOI: 10.1038/onc.2010.205] [Citation(s) in RCA: 157] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Revised: 04/23/2010] [Accepted: 04/25/2010] [Indexed: 12/17/2022]
Abstract
Tumor development is a complex process resulting from interplay between mutations in oncogenes and tumor suppressors, host susceptibility factors, and cellular context. Great advances have been made by studying rare tumors with unique clinical, genetic, or molecular features. Ewing's sarcoma serves as an excellent paradigm for understanding tumorigenesis because it exhibits some very useful and important characteristics. For example, nearly all cases of Ewing's sarcoma contain the (11;22)(q24;q12) chromosomal translocation that encodes the EWS/FLI oncoprotein. Besides the t(11;22), however, many cases have otherwise simple karyotypes with no other demonstrable abnormalities. Furthermore, it seems that an underlying genetic susceptibility to Ewing's sarcoma, if it exists, must be rare. These two features suggest that EWS/FLI is the primary mutation that drives the development of this tumor. Finally, Ewing's sarcoma is an aggressive tumor that requires aggressive treatment. Thus, improved understanding of the pathogenesis of this tumor will not only be of academic interest, but may also lead to new therapeutic approaches for individuals afflicted with this disease. The purpose of this review is to highlight recent advances in understanding the molecular pathogenesis of Ewing's sarcoma, while considering the questions surrounding this disease that still remain and how this knowledge may be applied to developing new treatments for patients with this highly aggressive disease.
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Affiliation(s)
- Elizabeth C. Toomey
- Department of Oncological Sciences and Center for Children's Cancer Research at Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT
| | - Joshua D. Schiffman
- Department of Oncological Sciences and Center for Children's Cancer Research at Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT
- Division of Pediatric Hematology/Oncology, University of Utah School of Medicine, Salt Lake City, UT
| | - Stephen L. Lessnick
- Department of Oncological Sciences and Center for Children's Cancer Research at Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT
- Division of Pediatric Hematology/Oncology, University of Utah School of Medicine, Salt Lake City, UT
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41
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Green SM, Coyne HJ, McIntosh LP, Graves BJ. DNA binding by the ETS protein TEL (ETV6) is regulated by autoinhibition and self-association. J Biol Chem 2010; 285:18496-504. [PMID: 20400516 PMCID: PMC2881775 DOI: 10.1074/jbc.m109.096958] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Revised: 04/08/2010] [Indexed: 01/19/2023] Open
Abstract
The ETS protein TEL, a transcriptional repressor, contains a PNT domain that, as an isolated fragment in vitro, self-associates to form a head-to-tail polymer. How such polymerization might affect the DNA-binding properties of full-length TEL is unclear. Here we report that monomeric TEL binds to a consensus ETS site with unusually low affinity (K(d) = 2.8 x 10(-8) M). A deletion analysis demonstrated that the low affinity was caused by a C-terminal inhibitory domain (CID) that attenuates DNA binding by approximately 10-fold. An NMR spectroscopically derived structure of a TEL fragment, deposited in the Protein Data Bank, revealed that the CID consists of two alpha-helices, one of which appears to block the DNA binding surface of the TEL ETS domain. Based on this structure, we substituted two conserved glutamic acids (Glu-431 and Glu-434) with alanines and found that this activated DNA binding and enhanced trypsin sensitivity in the CID. We propose that TEL displays a conformational equilibrium between inhibited and activated states and that electrostatic interactions involving these negatively charged residues play a role in stabilizing the inhibited conformation. Using a TEL dimer as a model polymer, we show that self-association facilitates cooperative binding to DNA. Cooperativity was observed on DNA duplexes containing tandem consensus ETS sites at variable spacing and orientations, suggesting flexibility in the region of TEL linking its self-associating PNT domain and DNA-binding ETS domain. We speculate that TEL compensates for the low affinity, which is caused by autoinhibition, by binding to DNA as a cooperative polymer.
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Affiliation(s)
- Sean M. Green
- From the
Department of Oncological Sciences, University of Utah School of Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112-5550 and
| | - H. Jerome Coyne
- the
Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Lawrence P. McIntosh
- the
Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Barbara J. Graves
- From the
Department of Oncological Sciences, University of Utah School of Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112-5550 and
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42
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Gangwal K, Close D, Enriquez CA, Hill CP, Lessnick SL. Emergent Properties of EWS/FLI Regulation via GGAA Microsatellites in Ewing's Sarcoma. Genes Cancer 2010; 1:177-187. [PMID: 20827386 DOI: 10.1177/1947601910361495] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
ETS proteins are a family of transcription factors that play important roles in the development of cancer. The Ewing's sarcoma EWS/ETS fusion oncoproteins control a number of cancer-relevant phenotypes in that disease. We recently demonstrated that EWS/FLI, the most common EWS/ETS fusion in Ewing's sarcoma, regulates a portion of its target genes, including the critical target NR0B1, via GGAA-containing microsatellites in their promoters. Given the unusual nature of microsatellites as EWS/FLI response elements, we sought to elucidate the mechanism of EWS/FLI activity at these sites. We found that the ability to bind GGAA microsatellites is shared by multiple ETS family members from distinct phylogenetic subfamilies. Importantly, however, only EWS/ETS-containing fusions are capable of mediating transcriptional activation via these elements, highlighting a neomorphic function of the Ewing's sarcoma fusion proteins. Additional analysis revealed that the GGAA microsatellite binds EWS/FLI with an affinity that is 2 to 3 orders of magnitude lower than previously identified high-affinity consensus/redundant binding sites. The stoichiometry of this interaction is 2 protein molecules for each DNA molecule, suggesting that EWS/FLI binds these elements as a homodimer. The isolated FLI ETS domain bound microsatellite sequences in a nearly identical fashion to full-length EWS/FLI, thus indicating that residues required for homodimeric binding are localized to the ETS domain. These data suggest a new paradigm for an ETS family member binding to DNA at cancer-relevant genetic loci and highlight emergent properties of EWS/FLI that are required for the development of Ewing's sarcoma.
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Affiliation(s)
- Kunal Gangwal
- Department of Oncological Sciences, University of Utah School of Medicine, and Center for Children's Cancer Research, Huntsman Cancer Institute, Salt Lake City, Utah
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43
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Wu T, Zhao Y, Hao Z, Zhao H, Wang W. Involvement of PU.1 in mouse adar-1 gene transcription induced by high-dose esiRNA. Int J Biol Macromol 2009; 45:157-62. [PMID: 19422845 DOI: 10.1016/j.ijbiomac.2009.04.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 04/24/2009] [Accepted: 04/24/2009] [Indexed: 11/16/2022]
Abstract
Adar-1 gene plays an important role in the negative regulation of RNA interference. We previously showed that increased adar-1 mRNA level was associated with the rebound of gene expression after RNAi suppression. In this study, we identified a PU.1 binding site upstream from transcription start point of adar-1 gene and is essential for the promoter activity. Knockdown and over-expression of the PU.1 gene resulted in decreased and increased activity of adar-1 promoter, respectively. Our results suggest that transcription factor PU.1, could bind to the adar-1 promoter and play a key role in activating transcription of gene induced by high-dose esiRNAs.
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Affiliation(s)
- Tongde Wu
- Department of Biochemistry, School of Life Sciences, Fudan University, No. 220 Handan Road, Liren Building 106, Shanghai 200433, PR China
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44
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The oncogenic EWS-FLI1 protein binds in vivo GGAA microsatellite sequences with potential transcriptional activation function. PLoS One 2009; 4:e4932. [PMID: 19305498 PMCID: PMC2654724 DOI: 10.1371/journal.pone.0004932] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Accepted: 02/21/2009] [Indexed: 12/21/2022] Open
Abstract
The fusion between EWS and ETS family members is a key oncogenic event in Ewing tumors and important EWS-FLI1 target genes have been identified. However, until now, the search for EWS-FLI1 targets has been limited to promoter regions and no genome-wide comprehensive analysis of in vivo EWS-FLI1 binding sites has been undertaken. Using a ChIP-Seq approach to investigate EWS-FLI1-bound DNA sequences in two Ewing cell lines, we show that this chimeric transcription factor preferentially binds two types of sequences including consensus ETS motifs and microsatellite sequences. Most bound sites are found outside promoter regions. Microsatellites containing more than 9 GGAA repeats are very significantly enriched in EWS-FLI1 immunoprecipitates. Moreover, in reporter gene experiments, the transcription activation is highly dependent upon the number of repeats that are included in the construct. Importantly, in vivo EWS-FLI1-bound microsatellites are significantly associated with EWS-FLI1-driven gene activation. Put together, these results point out the likely contribution of microsatellite elements to long-distance transcription regulation and to oncogenesis.
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45
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Rangannan V, Bansal M. Relative stability of DNA as a generic criterion for promoter prediction: whole genome annotation of microbial genomes with varying nucleotide base composition. MOLECULAR BIOSYSTEMS 2009; 5:1758-69. [DOI: 10.1039/b906535k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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46
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Dang X, Raffler NA, Ley K. Transcriptional regulation of mouse L-selectin. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1789:146-52. [PMID: 19041738 DOI: 10.1016/j.bbagrm.2008.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 10/14/2008] [Accepted: 10/23/2008] [Indexed: 01/20/2023]
Abstract
L-selectin mediates the initial tethering and rolling of lymphocytes in high endothelial venules. To study the transcriptional regulation of mouse L-selectin, we cloned 4.5 kb 5'-flanking sequences of the mouse sell. Luciferase analysis of serial 5'-deletion mutants showed that the first 285 bp was sufficient to drive high promoter activity in EL4 cells, but not in Sell-negative HeLa cells, suggesting that this fragment harbors the minimal mouse sell promoter and contains cis-elements for lymphocyte-specific expression. Site-directed mutagenesis and chromatin immunoprecipitation showed that Mzf1, Klf2, Sp1, Ets1, and Irf1 bind to and activate the mouse sell promoter. Over expression of these transcription factors in EL4 cells increased expression of sell mRNA. Silencing the expression of Sp1 by siRNA significantly decreased sell promoter activity in EL4 cells. We conclude that sell transcription is regulated by Mzf1, Klf2, Sp1, Ets1, and Irf1.
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Affiliation(s)
- Xitong Dang
- Division of Inflammation Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
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47
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Chin KL, Aerbajinai W, Zhu J, Drew L, Chen L, Liu W, Rodgers GP. The regulation of OLFM4 expression in myeloid precursor cells relies on NF-kappaB transcription factor. Br J Haematol 2008; 143:421-32. [PMID: 18764868 DOI: 10.1111/j.1365-2141.2008.07368.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The human olfactomedin 4 gene (OLFM4, also known as hGC-1, GW112) is thought to be a useful marker for early myeloid development. To understand the molecular mechanisms underlying granulocyte colony-stimulating factor (G-CSF)-stimulated OLFM4 expression, we characterized the promoter region of OLFM4. The 35-bp region (-101 to -66) of the proximal promoter regulated reporter gene expression, and mutation of the nuclear factor (NF)-kappaB binding site within the promoter abolished the binding of the transcription factor and the ability to regulate OLFM4 expression. G-CSF increased reactive oxygen species (ROS) production in human CD34(+) cells, which was abrogated by inhibition of phosphatidylinositol 3-kinase (PI3K) or NADPH oxidase. Phosphorylation of ERK1/2 mitogen-activated protein kinase (MAPK) induced by G-CSF inhibited by the antioxidant N-acetyl-L-cysteine (NAC), ERK1/2 inhibitor PD98059, or U0126. However, phosphorylation of signal transducer and activator of transcription (STAT)3 was only partially inhibited by NAC, but not by PD98059 or U0126. Inhibition of the ERK pathway remarkably decreased OLFM4 expression and this inhibition required NF-kappaB transcription factor. Inhibition of ROS or the ERK pathway remarkably decreased G-CSF-induced OLFM4 expression. Our results suggest that G-CSF-induced expression of OLFM4 is regulated by the transcription factor NF-kappaB, and that this induction is mediated by the ERK1/2 MAPK signaling pathway through PI3K-driven ROS production.
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Affiliation(s)
- Kyung L Chin
- Molecular and Clinical Hematology Branch, National Institute of Diabetes, Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
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48
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Abstract
The ETS gene family is frequently involved in chromosome translocations that cause human cancer, including prostate cancer, leukemia, and sarcoma. However, the mechanisms by which oncogenic ETS proteins, which are DNA-binding transcription factors, target genes necessary for tumorigenesis is not well understood. Ewing's sarcoma serves as a paradigm for the entire class of ETS-associated tumors because nearly all cases harbor recurrent chromosomal translocations involving ETS genes. The most common translocation in Ewing's sarcoma encodes the EWS/FLI oncogenic transcription factor. We used whole genome localization (ChIP-chip) to identify target genes that are directly bound by EWS/FLI. Analysis of the promoters of these genes demonstrated a significant over-representation of highly repetitive GGAA-containing elements (microsatellites). In a parallel approach, we found that EWS/FLI uses GGAA microsatellites to regulate the expression of some of its target genes including NR0B1, a gene required for Ewing's sarcoma oncogenesis. The microsatellite in the NR0B1 promoter bound EWS/FLI in vitro and in vivo and was both necessary and sufficient to confer EWS/FLI regulation to a reporter gene. Genome wide computational studies demonstrated that GGAA microsatellites were enriched close to EWS/FLI-up-regulated genes but not down-regulated genes. Mechanistic studies demonstrated that the ability of EWS/FLI to bind DNA and modulate gene expression through these repetitive elements depended on the number of consecutive GGAA motifs. These findings illustrate an unprecedented route to specificity for ETS proteins and use of microsatellites in tumorigenesis.
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49
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Fazio G, Palmi C, Rolink A, Biondi A, Cazzaniga G. PAX5/TEL Acts as a Transcriptional Repressor Causing Down-modulation of CD19, Enhances Migration to CXCL12, and Confers Survival Advantage in pre-BI Cells. Cancer Res 2008; 68:181-9. [DOI: 10.1158/0008-5472.can-07-2778] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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50
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Knosp WM, Saneyoshi C, Shou S, Bächinger HP, Stadler HS. Elucidation, Quantitative Refinement, and in Vivo Utilization of the HOXA13 DNA Binding Site. J Biol Chem 2007; 282:6843-53. [PMID: 17200107 DOI: 10.1074/jbc.m610775200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Mutations in Hoxa13 cause malformations of the appendicular skeleton and genitourinary tract, including digit loss, syndactyly, and hypospadias. To determine the molecular basis for these defects, the DNA sequences bound by HOXA13 were empirically determined, revealing a novel high affinity binding site. Correlating the utilization of this high affinity binding site with genes exhibiting perturbed expression in Hoxa13 mutant limbs, we identified that HOXA13 suppresses the expression of the BMP antagonist, Sostdc1. In the absence of HOXA13 function, Sostdc1 is ectopically expressed in the distal limb, causing reduced expression of BMP-activated genes and decreased SMAD phosphorylation. Limb chromatin immunoprecipitation revealed HOXA13 binding at its high affinity site in two conserved Sostdc1 regulatory sites in vivo. In vitro, HOXA13 represses gene expression through the Sostdc1 high affinity binding sites in a dosage-dependent manner. Together, these findings confirm that the high affinity HOXA13 binding site deduced by quantitative analyses is used in vivo to facilitate HOXA13 target gene regulation, providing a critical advance toward understanding the molecular basis for defects associated with the loss of HOXA13 function.
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Affiliation(s)
- Wendy M Knosp
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA
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