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Kenny HA, Hart PC, Kordylewicz K, Lal M, Shen M, Kara B, Chen YJ, Grassl N, Alharbi Y, Pattnaik BR, Watters KM, Patankar MS, Ferrer M, Lengyel E. The Natural Product β-Escin Targets Cancer and Stromal Cells of the Tumor Microenvironment to Inhibit Ovarian Cancer Metastasis. Cancers (Basel) 2021; 13:cancers13163931. [PMID: 34439084 PMCID: PMC8394501 DOI: 10.3390/cancers13163931] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/30/2021] [Accepted: 07/31/2021] [Indexed: 01/11/2023] Open
Abstract
Simple Summary β-escin, a component of horse chestnut seed extract, was first identified as an inhibitor of ovarian cancer (OvCa) adhesion/invasion in our high-throughput screening program using a three-dimensional organotypic model assembled from primary human cells and extracellular matrix. The goal of the study presented here is to determine if β-escin and structurally-similar compounds have a therapeutic potential against OvCa metastasis. β-escin and cardiac glycosides inhibit ovarian cancer adhesion/invasion to the omental microenvironment in vivo, and β-escin inhibits ovarian cancer metastasis in the prevention and intervention setting. Additionally, β-escin was found to decrease the stemness of ovarian cancer cells, inhibit extracellular matrix production in the tumor microenvironment, and inhibit HIF1α stability in ovarian cancer cells and the tumor microenvironment. This study reveals that the natural compound β-escin has therapeutic potential because of its ability to prevent OvCa dissemination by targeting both cancer and stromal cells in the OvCa tumor microenvironment. Abstract The high mortality of OvCa is caused by the wide dissemination of cancer within the abdominal cavity. OvCa cells metastasize to the peritoneum, which is covered by mesothelial cells, and invade into the underlying stroma, composed of extracellular matrices (ECM) and stromal cells. In a study using a three-dimensional quantitative high-throughput screening platform (3D-qHTS), we found that β-escin, a component of horse chestnut seed extract, inhibited OvCa adhesion/invasion. Here, we determine whether β-escin and structurally similar compounds have a therapeutic potential against OvCa metastasis. Different sources of β-escin and horse chestnut seed extract inhibited OvCa cell adhesion/invasion, both in vitro and in vivo. From a collection of 160 structurally similar compounds to β-escin, we found that cardiac glycosides inhibited OvCa cell adhesion/invasion and proliferation in vitro, and inhibited adhesion/invasion and metastasis in vivo. Mechanistically, β-escin and the cardiac glycosides inhibited ECM production in mesothelial cells and fibroblasts. The oral administration of β-escin inhibited metastasis in both OvCa prevention and intervention mouse models. Specifically, β-escin inhibited ECM production in the omental tumors. Additionally, the production of HIF1α-targeted proteins, lactate dehydrogenase A, and hexokinase 2 in omental tumors was blocked by β-escin. This study reveals that the natural compound β-escin has a therapeutic potential because of its ability to prevent OvCa dissemination by targeting both cancer and stromal cells in the OvCa tumor microenvironment.
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Affiliation(s)
- Hilary A. Kenny
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA; (P.C.H.); (K.K.); (B.K.); (Y.-J.C.); (K.M.W.); (E.L.)
- Correspondence:
| | - Peter C. Hart
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA; (P.C.H.); (K.K.); (B.K.); (Y.-J.C.); (K.M.W.); (E.L.)
| | - Kasjusz Kordylewicz
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA; (P.C.H.); (K.K.); (B.K.); (Y.-J.C.); (K.M.W.); (E.L.)
| | - Madhu Lal
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), NIH, Rockville, MD 20852, USA; (M.L.); (M.S.); (M.F.)
| | - Min Shen
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), NIH, Rockville, MD 20852, USA; (M.L.); (M.S.); (M.F.)
| | - Betul Kara
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA; (P.C.H.); (K.K.); (B.K.); (Y.-J.C.); (K.M.W.); (E.L.)
| | - Yen-Ju Chen
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA; (P.C.H.); (K.K.); (B.K.); (Y.-J.C.); (K.M.W.); (E.L.)
| | - Niklas Grassl
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Yousef Alharbi
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI 53792, USA; (Y.A.); (M.S.P.)
| | - Bikash R. Pattnaik
- Department of Pediatrics and Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Karen M. Watters
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA; (P.C.H.); (K.K.); (B.K.); (Y.-J.C.); (K.M.W.); (E.L.)
| | - Manish S. Patankar
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI 53792, USA; (Y.A.); (M.S.P.)
| | - Marc Ferrer
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), NIH, Rockville, MD 20852, USA; (M.L.); (M.S.); (M.F.)
| | - Ernst Lengyel
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA; (P.C.H.); (K.K.); (B.K.); (Y.-J.C.); (K.M.W.); (E.L.)
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Hart PC, Kenny HA, Grassl N, Watters KM, Litchfield LM, Coscia F, Blaženović I, Ploetzky L, Fiehn O, Mann M, Lengyel E, Romero IL. Mesothelial Cell HIF1α Expression Is Metabolically Downregulated by Metformin to Prevent Oncogenic Tumor-Stromal Crosstalk. Cell Rep 2020; 29:4086-4098.e6. [PMID: 31851935 DOI: 10.1016/j.celrep.2019.11.079] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 10/04/2019] [Accepted: 11/19/2019] [Indexed: 01/04/2023] Open
Abstract
The tumor microenvironment (TME) plays a pivotal role in cancer progression, and, in ovarian cancer (OvCa), the primary TME is the omentum. Here, we show that the diabetes drug metformin alters mesothelial cells in the omental microenvironment. Metformin interrupts bidirectional signaling between tumor and mesothelial cells by blocking OvCa cell TGF-β signaling and mesothelial cell production of CCL2 and IL-8. Inhibition of tumor-stromal crosstalk by metformin is caused by the reduced expression of the tricarboxylic acid (TCA) enzyme succinyl CoA ligase (SUCLG2). Through repressing this TCA enzyme and its metabolite, succinate, metformin activated prolyl hydroxylases (PHDs), resulting in the degradation of hypoxia-inducible factor 1α (HIF1α) in mesothelial cells. Disruption of HIF1α-driven IL-8 signaling in mesothelial cells by metformin results in reduced OvCa invasion in an organotypic 3D model. These findings indicate that tumor-promoting signaling between mesothelial and OvCa cells in the TME can be targeted using metformin.
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Affiliation(s)
- Peter C Hart
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Hilary A Kenny
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Niklas Grassl
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Karen M Watters
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Lacey M Litchfield
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Fabian Coscia
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Ivana Blaženović
- West Coast Metabolomics Center, University of California, Davis Genome Center, Davis, CA, USA
| | - Lisa Ploetzky
- West Coast Metabolomics Center, University of California, Davis Genome Center, Davis, CA, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis Genome Center, Davis, CA, USA
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Ernst Lengyel
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA.
| | - Iris L Romero
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA.
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Coscia F, Watters KM, Curtis M, Eckert MA, Chiang CY, Tyanova S, Montag A, Lastra RR, Lengyel E, Mann M. Integrative proteomic profiling of ovarian cancer cell lines reveals precursor cell associated proteins and functional status. Nat Commun 2016; 7:12645. [PMID: 27561551 PMCID: PMC5007461 DOI: 10.1038/ncomms12645] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 07/19/2016] [Indexed: 12/11/2022] Open
Abstract
A cell line representative of human high-grade serous ovarian cancer (HGSOC) should not only resemble its tumour of origin at the molecular level, but also demonstrate functional utility in pre-clinical investigations. Here, we report the integrated proteomic analysis of 26 ovarian cancer cell lines, HGSOC tumours, immortalized ovarian surface epithelial cells and fallopian tube epithelial cells via a single-run mass spectrometric workflow. The in-depth quantification of >10,000 proteins results in three distinct cell line categories: epithelial (group I), clear cell (group II) and mesenchymal (group III). We identify a 67-protein cell line signature, which separates our entire proteomic data set, as well as a confirmatory publicly available CPTAC/TCGA tumour proteome data set, into a predominantly epithelial and mesenchymal HGSOC tumour cluster. This proteomics-based epithelial/mesenchymal stratification of cell lines and human tumours indicates a possible origin of HGSOC either from the fallopian tube or from the ovarian surface epithelium. High-grade serous ovarian cancer is the most common and aggressive ovarian cancer, with uncertain cell of origin. Here, the authors undertake a mass spectrometric analysis of 26 cancer cell lines and identify a protein signature that classifies ovarian cancer tissues into epithelial and mesenchymal groups.
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Affiliation(s)
- F Coscia
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - K M Watters
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, Illinois 60637, USA
| | - M Curtis
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, Illinois 60637, USA
| | - M A Eckert
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, Illinois 60637, USA
| | - C Y Chiang
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, Illinois 60637, USA
| | - S Tyanova
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - A Montag
- Department of Pathology, University of Chicago Medicine, Chicago, Illinois 60637, USA
| | - R R Lastra
- Department of Pathology, University of Chicago Medicine, Chicago, Illinois 60637, USA
| | - E Lengyel
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, Illinois 60637, USA
| | - M Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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Mitra AK, Chiang CY, Tiwari P, Tomar S, Watters KM, Peter ME, Lengyel E. Microenvironment-induced downregulation of miR-193b drives ovarian cancer metastasis. Oncogene 2015; 34:5923-32. [PMID: 25798837 PMCID: PMC4580483 DOI: 10.1038/onc.2015.43] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 11/24/2014] [Accepted: 12/01/2014] [Indexed: 12/14/2022]
Abstract
The cross-talk between ovarian cancer (OvCa) cells and the metastatic microenvironment is an essential determinant of successful colonization. Micro(mi)RNAs play several critical roles during metastasis; however, the role of microenvironmental cues in the regulation of miRNAs in metastasizing cancer cells has not been studied. Using a 3D culture model that mimics the human omentum, one of the principal sites of OvCa metastasis, we identified and characterized the microenvironment-induced downregulation of a tumor suppressor miRNA, miR-193b, in metastasizing OvCa cells. The direct interaction of the OvCa cells with mesothelial cells, which cover the surface of the omentum, caused a DNA methyltransferase 1 (DNMT1) mediated decrease in the expression of miR-193b. The reduction in miR-193b enabled the metastasizing cancer cells to invade and proliferate into human omental pieces ex vivo and into the omentum of a mouse xenograft model of OvCa metastasis. The functional effects of miR-193b were mediated, in large part, by the concomitant increased expression of its target, urokinase-type plasminogen activator (uPA), a known tumor-associated protease. These findings link paracrine signals from the microenvironment with the regulation of a key miRNA that is essential for the initial steps of OvCa metastatic colonization. Targeting miR-193b could prove effective in the treatment of OvCa metastasis.
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Affiliation(s)
- A K Mitra
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology - Center for Integrative Science, University of Chicago, Chicago, IL, USA.,Medical Sciences Program, Indiana University School of Medicine, Indiana University, Bloomington, IN, USA
| | - C Y Chiang
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology - Center for Integrative Science, University of Chicago, Chicago, IL, USA
| | - P Tiwari
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology - Center for Integrative Science, University of Chicago, Chicago, IL, USA
| | - S Tomar
- Medical Sciences Program, Indiana University School of Medicine, Indiana University, Bloomington, IN, USA
| | - K M Watters
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology - Center for Integrative Science, University of Chicago, Chicago, IL, USA
| | - M E Peter
- Division of Hematology/Oncology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - E Lengyel
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology - Center for Integrative Science, University of Chicago, Chicago, IL, USA
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McCoy RJ, Widaa A, Watters KM, Wuerstle M, Stallings RL, Duffy GP, O'Brien FJ. Orchestrating osteogenic differentiation of mesenchymal stem cells--identification of placental growth factor as a mechanosensitive gene with a pro-osteogenic role. Stem Cells 2014; 31:2420-31. [PMID: 23897668 DOI: 10.1002/stem.1482] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 06/17/2013] [Accepted: 07/01/2013] [Indexed: 01/09/2023]
Abstract
Skeletogenesis is initiated during fetal development and persists through adult life as either a remodeling process in response to homeostatic regulation or as a regenerative process in response to physical injury. Mesenchymal stem cells (MSCs) play a crucial role providing progenitor cells from which osteoblasts, bone matrix forming cells are differentiated. The mechanical environment plays an important role in regulating stem cell differentiation into osteoblasts, however, the mechanisms by which MSCs respond to mechanical stimuli are yet to be fully elucidated. To increase understanding of MSC mechanotransuction and osteogenic differentiation, this study aimed to identify novel, mechanically augmented genes and pathways with pro-osteogenic functionality. Using collagen glycoaminoglycan scaffolds as mimics of native extracellular matrix, to create a 3D environment more representative of that found in bone, MSC-seeded constructs were mechanically stimulated in a flow-perfusion bioreactor. Global gene expression profiling techniques were used to identify potential candidates warranting further investigation. Of these, placental growth factor (PGF) was selected and expression levels were shown to strongly correlate to both the magnitude and duration of mechanical stimulation. We demonstrated that PGF gene expression was modulated through an actin polymerization-mediated mechanism. The functional role of PGF in modulating MSC osteogenic differentiation was interrogated, and we showed a concentration-dependent response whereby low concentrations exhibited the strongest pro-osteogenic effect. Furthermore, pre-osteoclast migration and differentiation, as well as endothelial cell tubule formation also maintained concentration-dependent responses to PGF, suggesting a potential role for PGF in bone resorption and angiogenesis, processes key to bone remodeling and fracture repair.
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Affiliation(s)
- Ryan J McCoy
- Tissue Engineering Research Group, Dept. of Anatomy, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland; Trinity Centre for Bioengineering, Trinity College Dublin (TCD), Dublin 2, Ireland; Advanced Materials and Bioengineering Research (AMBER) Centre, RCSI & TCD, Ireland
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Bryan K, Terrile M, Bray IM, Domingo-Fernandéz R, Watters KM, Koster J, Versteeg R, Stallings RL. Discovery and visualization of miRNA-mRNA functional modules within integrated data using bicluster analysis. Nucleic Acids Res 2013; 42:e17. [PMID: 24357407 PMCID: PMC3919560 DOI: 10.1093/nar/gkt1318] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression at a post-transcriptional level. An miRNA may target many messenger RNA (mRNA) transcripts, and each transcript may be targeted by multiple miRNAs. Our understanding of miRNA regulation is evolving to consider modules of miRNAs that regulate groups of functionally related mRNAs. Here we expand the model of miRNA functional modules and use it to guide the integration of miRNA and mRNA expression and target prediction data. We present evidence of cooperativity between miRNA classes within this integrated miRNA–mRNA association matrix. We then apply bicluster analysis to uncover miRNA functional modules within this integrated data set and develop a novel application to visualize and query these results. We show that this wholly unsupervised approach can discover a network of miRNA–mRNA modules that are enriched for both biological processes and miRNA classes. We apply this method to investigate the interplay of miRNAs and mRNAs in integrated data sets derived from neuroblastoma and human immune cells. This study is the first to apply the technique of biclustering to model functional modules within an integrated miRNA–mRNA association matrix. Results provide evidence of an extensive modular miRNA functional network and enable characterization of miRNA function and dysregulation in disease.
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Affiliation(s)
- Kenneth Bryan
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland, National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland and Department of Oncogenomics, Academic Medical Center, University of Amsterdam, 1100 DE Amsterdam, The Netherlands
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Watters KM, Bryan K, Foley NH, Meehan M, Stallings RL. Expressional alterations in functional ultra-conserved non-coding RNAs in response to all-trans retinoic acid--induced differentiation in neuroblastoma cells. BMC Cancer 2013; 13:184. [PMID: 23565812 PMCID: PMC3626850 DOI: 10.1186/1471-2407-13-184] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 03/20/2013] [Indexed: 12/02/2022] Open
Abstract
Background Ultra-conserved regions (UCRs) are segments of the genome (≥ 200 bp) that exhibit 100% DNA sequence conservation between human, mouse and rat. Transcribed UCRs (T-UCRs) have been shown to be differentially expressed in cancers versus normal tissue, indicating a possible role in carcinogenesis. All-trans-retinoic acid (ATRA) causes some neuroblastoma (NB) cell lines to undergo differentiation and leads to a significant decrease in the oncogenic transcription factor MYCN. Here, we examine the impact of ATRA treatment on T-UCR expression and investigate the biological significance of these changes. Methods We designed a custom tiling microarray to profile the expression of 481 T-UCRs in sense and anti-sense orientation (962 potential transcripts) in untreated and ATRA-treated neuroblastoma cell lines (SH-SY5Y, SK-N-BE, LAN-5). Following identification of significantly differentially expressed T-UCRs, we carried out siRNA knockdown and gene expression microarray analysis to investigate putative functional roles for selected T-UCRs. Results Following ATRA-induced differentiation, 32 T-UCRs were differentially expressed (16 up-regulated, 16 down-regulated) across all three cell lines. Further insight into the possible role of T-UC.300A, an independent transcript whose expression is down-regulated following ATRA was achieved by siRNA knockdown, resulting in the decreased viability and invasiveness of ATRA-responsive cell lines. Gene expression microarray analysis following knockdown of T-UC.300A revealed a number of genes whose expression was altered by changing T-UC.300A levels and that might play a role in the increased proliferation and invasion of NB cells prior to ATRA-treatment. Conclusions Our results indicate that significant numbers of T-UCRs have altered expression levels in response to ATRA. While the precise roles that T-UCRs might play in cancer or in normal development are largely unknown and an important area for future study, our findings strongly indicate that the function of non-coding RNA T-UC.300A is connected with proliferation, invasion and the inhibition of differentiation of neuroblastoma cell lines prior to ATRA treatment.
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Affiliation(s)
- Karen M Watters
- Cancer Genetics, Department of Molecular & Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland.
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Watters KM, Bryan KR, Foley NH, Stallings RL. Abstract 202: Expressional alterations in functional ultra-conserved non-coding RNAs in response to ATRA-induced differentiation and changes in MYCN levels in neuroblastoma cells. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Neuroblastoma (NB) is a childhood cancer arising from precursor cells of the sympathetic nervous system with highly heterogeneous clinical behaviour, ranging from spontaneous regression to rapid progression and death due to disease. Amplification and over-expression of the MYCN transcription factor in NB tumors is highly correlated with poor survival. Children with high risk NB are given the synthetic retinoic acid, 13-cis-retinoic acid to reduce minimal residual disease, and exposure of a number of NB cell lines to the compound all-trans-retinoic acid (ATRA) induces neural differentiation along with the down-regulation of MYCN. Thus, identification of targets regulated by either ATRA or MYCN is of potential interest for the development of novel therapeutics. Ultra-conserved regions (UCRs) are sequences ≥200bp in length that are 100% conserved between human, mouse and rat genomes. In NB, transcribed UCRs (T-UCRs) exhibit specific profiles in MYCN-amplified (MNA) compared to non-MNA tumors (Mestdagh et al., Oncogene 2010 29:3583), and in high risk versus low risk tumors (Scaruffi et al., BMC Cancer 2009 9;441). Here we identify T-UCRs that are responsive to ATRA as well as T-UCRs that are directly or indirectly regulated by MYCN, and evaluate the biological significance of selected T-UCRs in functional studies of NB cell lines. We designed a custom tiling microarray to profile the expression of 481 UCRs in sense and antisense orientation (962 potential T-UCRs) in three ATRA-sensitive NB cell lines, and in SHEP-21N cells which contain a MYCN trans-gene controlled by a tetracycline responsive repressor element. Thirty-two T-UCRs were differentially expressed following ATRA treatment across all three ATRA sensitive cell lines (p<0.05), while analysis of doxycyclin-treated SHEP-21N cells (to deplete MYCN levels) indicated that 42 T-UCRs were altered by changing MYCN levels. In addition we identified a small number of T-UCRs, including T-UC.396 (intergenic) and T-UC.324 (antisense to host gene), whose expression was altered in both systems. These T-UCRs may represent independent ncRNAs directly or indirectly regulated by MYCN. Functionality of T-UC.300A and T-UC.324 was assessed by siRNA knockdown. While knockdown of T-UC.324 had no effect on cell viability or invasion, depletion of T-UC.300A resulted in a significant decrease in both cell viability and invasion. Our results indicate that significant numbers of T-UCRs have altered expression levels in response to changing MYCN levels and ATRA-induced differentiation. While the precise roles that these ncRNAs might play in cancer or in normal development are largely unknown, we have identified a T-UCR, T-UC.300A, whose down-regulation results in the decreased viability and invasiveness of ATRA-responsive cell lines and may play a functional role in ATRA-induced differentiation.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 202. doi:1538-7445.AM2012-202
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Affiliation(s)
| | | | - Nimah H. Foley
- 1The Royal College of Surgeons in Ireland, Dublin, Ireland
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Lynch J, Fay J, Meehan M, Bryan K, Watters KM, Murphy DM, Stallings RL. MiRNA-335 suppresses neuroblastoma cell invasiveness by direct targeting of multiple genes from the non-canonical TGF-β signalling pathway. Carcinogenesis 2012; 33:976-85. [PMID: 22382496 DOI: 10.1093/carcin/bgs114] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Transforming growth factor-β (TGF-β) signaling regulates many diverse cellular activities through both canonical (SMAD-dependent) and non-canonical branches, which includes the mitogen-activated protein kinase (MAPK), Rho-like guanosine triphosphatase and phosphatidylinositol-3-kinase/AKT pathways. Here, we demonstrate that miR-335 directly targets and downregulates genes in the TGF-β non-canonical pathways, including the Rho-associated coiled-coil containing protein (ROCK1) and MAPK1, resulting in reduced phosphorylation of downstream pathway members. Specifically, inhibition of ROCK1 and MAPK1 reduces phosphorylation levels of the motor protein myosin light chain (MLC) leading to a significant inhibition of the invasive and migratory potential of neuroblastoma cells. Additionally, miR-335 targets the leucine-rich alpha-2-glycoprotein 1 (LRG1) messenger RNA, which similarly results in a significant reduction in the phosphorylation status of MLC and a decrease in neuroblastoma cell migration and invasion. Thus, we link LRG1 to the migratory machinery of the cell, altering its activity presumably by exerting its effect within the non-canonical TGF-β pathway. Moreover, we demonstrate that the MYCN transcription factor, whose coding sequence is highly amplified in a particularly clinically aggressive neuroblastoma tumor subtype, directly binds to a region immediately upstream of the miR-335 transcriptional start site, resulting in transcriptional repression. We conclude that MYCN contributes to neuroblastoma cell migration and invasion, by directly downregulating miR-335, resulting in the upregulation of the TGF-β signaling pathway members ROCK1, MAPK1 and putative member LRG1, which positively promote this process. Our results provide novel insight into the direct regulation of TGF-β non-canonical signaling by miR-335, which in turn is downregulated by MYCN.
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Affiliation(s)
- Jennifer Lynch
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland
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Murphy DM, Buckley PG, Das S, Watters KM, Bryan K, Stallings RL. Co-localization of the oncogenic transcription factor MYCN and the DNA methyl binding protein MeCP2 at genomic sites in neuroblastoma. PLoS One 2011; 6:e21436. [PMID: 21731748 PMCID: PMC3120883 DOI: 10.1371/journal.pone.0021436] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 06/01/2011] [Indexed: 12/20/2022] Open
Abstract
Background MYCN is a transcription factor that is expressed during the development of the neural crest and its dysregulation plays a major role in the pathogenesis of pediatric cancers such as neuroblastoma, medulloblastoma and rhabdomyosarcoma. MeCP2 is a CpG methyl binding protein which has been associated with a number of cancers and developmental disorders, particularly Rett syndrome. Methods and Findings Using an integrative global genomics approach involving chromatin immunoprecipitation applied to microarrays, we have determined that MYCN and MeCP2 co-localize to gene promoter regions, as well as inter/intragenic sites, within the neuroblastoma genome (MYCN amplified Kelly cells) at high frequency (70.2% of MYCN sites were also positive for MeCP2). Intriguingly, the frequency of co-localization was significantly less at promoter regions exhibiting substantial hypermethylation (8.7%), as determined by methylated DNA immunoprecipitation (MeDIP) applied to the same microarrays. Co-immunoprecipitation of MYCN using an anti-MeCP2 antibody indicated that a MYCN/MeCP2 interaction occurs at protein level. mRNA expression profiling revealed that the median expression of genes with promoters bound by MYCN was significantly higher than for genes bound by MeCP2, and that genes bound by both proteins had intermediate expression. Pathway analysis was carried out for genes bound by MYCN, MeCP2 or MYCN/MeCP2, revealing higher order functions. Conclusions Our results indicate that MYCN and MeCP2 protein interact and co-localize to similar genomic sites at very high frequency, and that the patterns of binding of these proteins can be associated with significant differences in transcriptional activity. Although it is not yet known if this interaction contributes to neuroblastoma disease pathogenesis, it is intriguing that the interaction occurs at the promoter regions of several genes important for the development of neuroblastoma, including ALK, AURKA and BDNF.
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Affiliation(s)
- Derek M. Murphy
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Patrick G. Buckley
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
- Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sudipto Das
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Karen M. Watters
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Kenneth Bryan
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
| | - Raymond L. Stallings
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland
- * E-mail:
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11
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Bray I, Tivnan A, Bryan K, Foley NH, Watters KM, Tracey L, Davidoff AM, Stallings RL. MicroRNA-542-5p as a novel tumor suppressor in neuroblastoma. Cancer Lett 2011; 303:56-64. [PMID: 21310526 DOI: 10.1016/j.canlet.2011.01.016] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 01/05/2011] [Accepted: 01/19/2011] [Indexed: 01/31/2023]
Abstract
Several studies have implicated the dysregulation of microRNAs in neuroblastoma pathogenesis, an often fatal paediatric cancer arising from precursor cells of the sympathetic nervous system. Our group and others have demonstrated that lower expression of miR-542-5p is highly associated with poor patient survival, indicating a potential tumor suppressive function. Here, we demonstrate that ectopic over-expression of this miRNA decreases the invasive potential of neuroblastoma cell lines in vitro, along with primary tumor growth and metastases in an orthotopic mouse xenograft model, providing the first functional evidence for the involvement of miR-542-5p as a tumor suppressor in any type of cancer.
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Affiliation(s)
- Isabella Bray
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland
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Buckley PG, Das S, Bryan K, Watters KM, Alcock L, Koster J, Versteeg R, Stallings RL. Genome-wide DNA methylation analysis of neuroblastic tumors reveals clinically relevant epigenetic events and large-scale epigenomic alterations localized to telomeric regions. Int J Cancer 2011; 128:2296-305. [PMID: 20669225 DOI: 10.1002/ijc.25584] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The downregulation of specific genes through DNA hypermethylation is a major hallmark of cancer, although the extent and genomic distribution of hypermethylation occurring within cancer genomes is poorly understood. We report on the first genome-wide analysis of DNA methylation alterations in different neuroblastic tumor subtypes and cell lines, revealing higher order organization and clinically relevant alterations of the epigenome. The methylation status of 33,485 discrete loci representing all annotated CpG islands and RefSeq gene promoters was assessed in primary neuroblastic tumors and cell lines. A comparison of genes that were hypermethylated exclusively in the clinically favorable ganglioneuroma/ganglioneuroblastoma tumors revealed that nine genes were associated with poor clinical outcome when overexpressed in the unfavorable neuroblastoma (NB) tumors. Moreover, an integrated DNA methylation and copy number analysis identified 80 genes that were recurrently concomitantly deleted and hypermethylated in NB, with 37 reactivated by 5-aza-deoxycytidine. Lower expression of four of these genes was correlated with poor clinical outcome, further implicating their inactivation in aggressive disease pathogenesis. Analysis of genome-wide hypermethylation patterns revealed 70 recurrent large-scale blocks of contiguously hypermethylated promoters/CpG islands, up to 590 kb in length, with a distribution bias toward telomeric regions. Genome-wide hypermethylation events in neuroblastic tumors are extensive and frequently occur in large-scale blocks with a significant bias toward telomeric regions, indicating that some methylation alterations have occurred in a coordinated manner. Our results indicate that methylation contributes toward the clinicopathological features of neuroblastic tumors, revealing numerous genes associated with poor patient survival in NB.
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Affiliation(s)
- Patrick G Buckley
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
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Foley NH, Bray I, Watters KM, Das S, Bryan K, Bernas T, Prehn JHM, Stallings RL. MicroRNAs 10a and 10b are potent inducers of neuroblastoma cell differentiation through targeting of nuclear receptor corepressor 2. Cell Death Differ 2011; 18:1089-98. [PMID: 21212796 DOI: 10.1038/cdd.2010.172] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs function as negative regulators of posttranscriptional gene expression, having major roles in cellular differentiation. Several neuroblastoma cell lines can be induced to undergo differentiation by all-trans-retinoic acid (ATRA) and are used for modeling signaling pathways involved in this process. To identify miRNAs contributing to differentiation, we profiled 364 loci following ATRA treatment of neuroblastoma cell lines and found miR-10a and miR-10b to be highly overexpressed in SK-N-BE, LAN5 and SHSY-5Y. Ectopic overexpression of these miRNAs led to a major reprogramming of the transcriptome and a differentiated phenotype that was similar to that induced by ATRA in each of these cell lines. One of the predicted downregulated miR-10a/b targets was nuclear receptor corepressor 2 (NCOR2), a corepressor of gene transcription, which is known to suppress neurite outgrowth. NCOR2 was experimentally validated as a direct target of miR-10a/b, and siRNA-mediated inhibition of this mRNA alone resulted in neural cell differentiation. Moreover, induction of differentiation could be blocked by ectopic upregulation of NCOR2 using an expression construct lacking the miR-10a/b 3' untranslated region target site. We conclude that miR-10a/b has major roles in the process of neural cell differentiation through direct targeting of NCOR2, which in turn induces a cascade of primary and secondary transcriptional alterations, including the downregulation of MYCN.
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Affiliation(s)
- N H Foley
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
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14
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Murphy DM, Buckley PG, Bryan K, Watters KM, Koster J, van Sluis P, Molenaar J, Versteeg R, Stallings RL. Dissection of the oncogenic MYCN transcriptional network reveals a large set of clinically relevant cell cycle genes as drivers of neuroblastoma tumorigenesis. Mol Carcinog 2010; 50:403-11. [PMID: 21557326 DOI: 10.1002/mc.20722] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 11/19/2010] [Indexed: 01/11/2023]
Abstract
Amplification of the oncogenic transcription factor MYCN plays a major role in the pathogenesis of several pediatric cancers, including neuroblastoma, medulloblastoma, and rhabodomyosarcoma. For neuroblastoma, MYCN amplification is the most powerful genetic predictor of poor patient survival, yet the mechanism by which MYCN drives tumorigenesis is only partially understood. To gain an insight into the distribution of MYCN binding and to identify clinically relevant MYCN target genes, we performed an integrated analysis of MYCN ChIP-chip and mRNA expression using the MYCN repressible SHEP-21N neuroblastoma cell line. We hypothesized that genes exclusively MYCN bound in SHEP-21N cells over-expressing MYCN would be enriched for direct targets which contribute to the process of disease progression. Integrated analysis revealed that MYCN drives tumorigenesis predominantly as a positive regulator of target gene transcription. A high proportion of genes (24%) that are MYCN bound and up-regulated in the SHEP-21N model are significantly associated with poor overall patient survival (OS) in a set of 88 tumors. In contrast, the proportion of genes down-regulated when bound by MYCN in the SHEP-21N model and which are significantly associated with poor overall patient survival when under-expressed in primary tumors was significantly lower (5%). Gene ontology analysis determined a highly statistically significant enrichment for cell cycle related genes within the over-expressed MYCN target group which were also associated with poor OS. We conclude that the over-expression of MYCN leads to aberrant binding and over-expression of genes associated with cell cycle regulation which are significantly correlated with poor OS and MYCN amplification.
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Affiliation(s)
- Derek M Murphy
- Departments of Cancer Genetics, Royal College of Surgeons in Ireland, York House, Dublin, Ireland
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Das S, Foley N, Bryan K, Watters KM, Bray I, Murphy DM, Buckley PG, Stallings RL. MicroRNA mediates DNA demethylation events triggered by retinoic acid during neuroblastoma cell differentiation. Cancer Res 2010; 70:7874-81. [PMID: 20841484 PMCID: PMC2955783 DOI: 10.1158/0008-5472.can-10-1534] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Neuroblastoma is an often fatal pediatric cancer arising from precursor cells of the sympathetic nervous system. 13-Cis retinoic acid is included in the treatment regimen for patients with high-risk disease, and a similar derivative, all-trans-retinoic acid (ATRA), causes neuroblastoma cell lines to undergo differentiation. The molecular signaling pathways involved with ATRA-induced differentiation are complex, and the role that DNA methylation changes might play are unknown. The purpose of this study was to evaluate the genome-wide effects of ATRA on DNA methylation using methylated DNA immunoprecipitation applied to microarrays representing all known promoter and CpG islands. Four hundred and two gene promoters became demethylated, whereas 88 were hypermethylated post-ATRA. mRNA expression microarrays revealed that 82 of the demethylated genes were overexpressed by >2-fold, whereas 13 of the hypermethylated genes were underexpressed. Gene ontology analysis indicated that demethylated and re-expressed genes were enriched for signal transduction pathways, including NOS1, which is required for neural cell differentiation. As a potential mechanism for the DNA methylation changes, we show the downregulation of methyltransferases, DNMT1 and DNMT3B, along with the upregulation of endogenous microRNAs targeting them. Ectopic overexpression of miR-152, targeting DNMT1, also negatively affected cell invasiveness and anchorage-independent growth, contributing in part to the differentiated phenotype. We conclude that functionally important, miRNA-mediated DNA demethylation changes contribute to the process of ATRA-induced differentiation resulting in the activation of NOS1, a critical determinant of neural cell differentiation. Our findings illustrate the plasticity and dynamic nature of the epigenome during cancer cell differentiation.
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Affiliation(s)
- Sudipto Das
- Departments of Cancer Genetics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland
- Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin 12, Ireland
| | - Niamh Foley
- Departments of Cancer Genetics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland
- Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin 12, Ireland
| | - Kenneth Bryan
- Departments of Cancer Genetics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland
- Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin 12, Ireland
| | - Karen M Watters
- Departments of Cancer Genetics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland
- Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin 12, Ireland
| | - Isabella Bray
- Departments of Cancer Genetics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland
- Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin 12, Ireland
| | - Derek M Murphy
- Departments of Cancer Genetics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland
- Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin 12, Ireland
| | - Patrick G Buckley
- Departments of Cancer Genetics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland
- Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin 12, Ireland
| | - Raymond L Stallings
- Departments of Cancer Genetics, Royal College of Surgeons in Ireland, York House, York Street, Dublin 2, Ireland
- Children’s Research Centre, Our Lady’s Children’s Hospital, Crumlin, Dublin 12, Ireland
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Watters KM, Dean J, Hasegawa H, Sawa H, Hall W, Sheehy N. Cytokine and growth factor expression by HTLV-1 Lck-tax transgenic cells in SCID mice. AIDS Res Hum Retroviruses 2010; 26:593-603. [PMID: 20438380 DOI: 10.1089/aid.2009.0212] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Tax protein encoded by HTLV-1 plays a key role in the development of ATL in infected individuals. Our previous studies showed that tax transgenic mice develop disease that is almost identical to human ATL, with widespread organ invasion by lymphomatous cells and the development of leukemia. The same pathology develops rapidly in SCID mice engrafted with cells from the transgenic animals. In the present study, we used this SCID model to analyze the expression levels of several cytokines, growth factors, and adhesion molecules to determine their possible involvement in the development of disease. We showed that Tax expression was undetectable at the protein level in the tax-transformed cells used to inoculate the SCID mice and that these cells displayed constitutive NF-kappaB and Akt activity. We demonstrated significant differences in the levels of circulating PDGF-BB, TNF-alpha, sICAM-1, and sVCAM-1 in inoculated animals. Cell-surface staining of the tax transgenic cells showed that they do not express receptors for any of the upregulated growth factors. Significant differences were not found in the secreted levels of bFGF, MMP9, VEGF, or E-selectin, whereas IL-2, IL-15, IL-6, IL-1beta, and IFN-gamma expression was undetectable. Even though the number of factors analyzed is limited, our study identified TNF-alpha, PDGF-BB, and the adhesion molecules sICAM-1 and sVCAM-1 as factors that may contribute to the high levels of organ infiltration by leukemic cells in this tax transgenic SCID model.
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Affiliation(s)
- Karen M. Watters
- UCD Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Jonathan Dean
- UCD Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Hideki Hasegawa
- Department of Pathology, National Institute of Infectious Diseases, Gakuen, Musashimurayama-shi, Tokyo, Japan
| | - Hirofumi Sawa
- Department of Molecular Pathobiology, Research Center for Zoonosis Control, and Global COE Program, Hokkaido University, Sapporo, Japan
| | - William Hall
- UCD Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Noreen Sheehy
- UCD Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
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Murphy DM, Buckley PG, Bryan K, Das S, Alcock L, Foley NH, Prenter S, Bray I, Watters KM, Higgins D, Stallings RL. Global MYCN transcription factor binding analysis in neuroblastoma reveals association with distinct E-box motifs and regions of DNA hypermethylation. PLoS One 2009; 4:e8154. [PMID: 19997598 PMCID: PMC2781550 DOI: 10.1371/journal.pone.0008154] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 11/09/2009] [Indexed: 01/19/2023] Open
Abstract
Background Neuroblastoma, a cancer derived from precursor cells of the sympathetic nervous system, is a major cause of childhood cancer related deaths. The single most important prognostic indicator of poor clinical outcome in this disease is genomic amplification of MYCN, a member of a family of oncogenic transcription factors. Methodology We applied MYCN chromatin immunoprecipitation to microarrays (ChIP-chip) using MYCN amplified/non-amplified cell lines as well as a conditional knockdown cell line to determine the distribution of MYCN binding sites within all annotated promoter regions. Conclusion Assessment of E-box usage within consistently positive MYCN binding sites revealed a predominance for the CATGTG motif (p<0.0016), with significant enrichment of additional motifs CATTTG, CATCTG, CAACTG in the MYCN amplified state. For cell lines over-expressing MYCN, gene ontology analysis revealed enrichment for the binding of MYCN at promoter regions of numerous molecular functional groups including DNA helicases and mRNA transcriptional regulation. In order to evaluate MYCN binding with respect to other genomic features, we determined the methylation status of all annotated CpG islands and promoter sequences using methylated DNA immunoprecipitation (MeDIP). The integration of MYCN ChIP-chip and MeDIP data revealed a highly significant positive correlation between MYCN binding and DNA hypermethylation. This association was also detected in regions of hemizygous loss, indicating that the observed association occurs on the same homologue. In summary, these findings suggest that MYCN binding occurs more commonly at CATGTG as opposed to the classic CACGTG E-box motif, and that disease associated over expression of MYCN leads to aberrant binding to additional weaker affinity E-box motifs in neuroblastoma. The co-localization of MYCN binding and DNA hypermethylation further supports the dual role of MYCN, namely that of a classical transcription factor affecting the activity of individual genes, and that of a mediator of global chromatin structure.
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Affiliation(s)
- Derek M. Murphy
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
| | - Patrick G. Buckley
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
| | - Kenneth Bryan
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
| | - Sudipto Das
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
| | - Leah Alcock
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
| | - Niamh H. Foley
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
| | - Suzanne Prenter
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
| | - Isabella Bray
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
| | - Karen M. Watters
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
| | - Desmond Higgins
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Raymond L. Stallings
- Department of Cancer Genetics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland
- * E-mail:
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