(12) Patent Application Publication (10) Pub. No.: US 2004/0023207 A1 Polansky (43) Pub
Total Page:16
File Type:pdf, Size:1020Kb

Load more
Recommended publications
-
Enhanced Expression of Vascular Endothelial Growth Factor (VEGF) Plays a Critical Role in the Tumor Progression Potential Induced by Simian Virus 40 Large T Antigen
Oncogene (2002) 21, 2896 ± 2900 ã 2002 Nature Publishing Group All rights reserved 0950 ± 9232/02 $25.00 www.nature.com/onc Enhanced expression of vascular endothelial growth factor (VEGF) plays a critical role in the tumor progression potential induced by simian virus 40 large T antigen Alfonso Catalano1, Mario Romano*,2, Stefano Martinotti3 and Antonio Procopio*,1 1Institute of Experimental Pathology, University of Ancona, Faculty of Medicine, Via Ranieri, 60131 Ancona, Italy; 2Department of Human Pathology, University of Messina, 98125 Messina, Italy; 3Department of Oncology and Neuroscience, `G. D'Annunzio' University, Chieti, Italy Vascular endothelial growth factor (VEGF), an impor- disorders, including mesotheliomas (Kumar-Singh et tant angiogenic factor, regulates cell proliferation, al., 1999). Among these, VEGF, whose crucial role in dierentiation, and apoptosis through activation of its tumor angiogenesis is well established (Hanahan and tyrosine-kinase receptors, such as Flt-1 and Flk-1/Kdr. Folkman., 1996), acts also as a potent mitogen and Human malignant mesothelioma cells (HMC), which survival factor for human malignant mesothelioma have wild-type p53, express VEGF and exhibit cell cells (HMC). In fact, VEGF regulates HMC prolifera- growth increased by VEGF. Here, we demonstrate that tion through its tyrosine-kinase receptors activation early transforming proteins of simian virus (SV) 40, large (i.e. Flt-1 and KDR/¯k-1) (Strizzi et al., 2001). In tumor antigen (Tag) and small tumor antigen (tag), addition, VEGF is the main eector of 5-lipoxygenase which have been associated with mesotheliomas, en- action on HMC survival (Romano et al., 2001). Thus, hanced HMC proliferation by inducing VEGF expres- VEGF plays a key role by regulating multiple sion. -
Androgen Receptor Expression Predicts Breast Cancer Survival: The
Peters et al. BMC Cancer 2012, 12:132 http://www.biomedcentral.com/1471-2407/12/132 RESEARCHARTICLE Open Access Androgen receptor expression predicts breast cancer survival: the role of genetic and epigenetic events Kate M Peters1, Stacey L Edwards1, Shalima S Nair2, Juliet D French1, Peter J Bailey1, Kathryn Salkield1, Sandra Stein3, Sarah Wagner3, Glenn D Francis3, Susan J Clark2 and Melissa A Brown1* Abstract Background: Breast cancer outcome, including response to therapy, risk of metastasis and survival, is difficult to predict using currently available methods, highlighting the urgent need for more informative biomarkers. Androgen receptor (AR) has been implicated in breast carcinogenesis however its potential to be an informative biomarker has yet to be fully explored. In this study, AR protein levels were determined in a cohort of 73 Grade III invasive breast ductal adenocarcinomas. Methods: The levels of Androgen receptor protein in a cohort of breast tumour samples was determined by immunohistochemistry and the results were compared with clinical characteristics, including survival. The role of defects in the regulation of Androgen receptor gene expression were examined by mutation and methylation screening of the 5’ end of the gene, reporter assays of the 5’ and 3’ end of the AR gene, and searching for miRNAs that may regulate AR gene expression. Results: AR was expressed in 56% of tumours and expression was significantly inversely associated with 10-year survival (P = 0.004). An investigation into the mechanisms responsible for the loss of AR expression revealed that hypermethylation of the AR promoter is associated with loss of AR expression in breast cancer cells but not in primary breast tumours. -
Pnas.201413825SI.Pdf
Supporting Information Impens et al. 10.1073/pnas.1413825111 13 15 13 15 SI Methods beling) (Silantes Gmbh), or C6 N2 L-lysine HCl and C6 N4 L- Plasmids. pSG5-His6-SUMO1 plasmid encodes the N-terminal arginine HCl (heavy labeling) (Silantes Gmbh). L-Lysine HCl was His6-tagged mature Small ubiquitin modifier 1 (SUMO1) isoform added at its normal concentration in DMEM (146 mg/L), but the (kind gift of A. Dejean, Institut Pasteur, Paris). The pSG5-His6- concentration of L-arginine HCl was reduced to 25 mg/L (30% of SUMO1 T95R mutat was derived from this plasmid using PCR the normal concentration in DMEM) to prevent metabolic con- mutagenesis. pSG5-His6-SUMO2 was obtained by inserting the version of arginine to proline (4). Cells were kept for at least six cDNA corresponding to the human mature SUMO2 isoform population doublings to ensure complete incorporation of the la- with an N-terminal His6 tag in the pSG5 vector (Stratagene). beled lysine and arginine. 2 The pSG5-His6-SUMO2 T91R mutant was derived from this For transfections, cells were seeded in 75-cm flasks or in 6- or plasmid by PCR mutagenesis. N-terminally HA-tagged human 24-well plates at a density of 2.7 × 106 cells per flask or 3 × 105 or cDNA of ZBTB20 (Zinc finger and BTB domain containing 0.5 × 105 cells per well, respectively. The next day cells were 20) isoform 2 (UniProt identifier Q9HC78-2), HMBOX1 (Ho- transfected with Lipofectamine LTX reagents (Invitrogen) (20 μg meobox containing protein 1) isoform 1 (HMBOX1A) (UniProt of DNA per flask, 3.5 μg per well in the six-well plates, or 0.75 μg identifier Q6NT76-1), NACC1 (Nucleus accumbens-associated per well in the 24-well plates) for 48 h. -
A Polyoma Mutant That Encodessmall T Antigen but Not Middle T Antigen
MOLECULAR AND CELLULAR BIOLOGY, Dec. 1984, p. 2774-2783 Vol. 4, No. 12 0270-7306/84/122774-10$02.00/0 Copyright © 1984, American Society for Microbiology A Polyoma Mutant That Encodes Small T Antigen But Not Middle T Antigen Demonstrates Uncoupling of Cell Surface and Cytoskeletal Changes Associated with Cell Transformation T. JAKE LIANG, GORDON G. CARMICHAEL,t AND THOMAS L. BENJAMIN* Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115 Received 2 July 1984/Accepted 31 August 1984 The hr-t gene of polyoma virus encodes both the small and middle T (tumor) antigens and exerts pleiotropic effects on cells. By mutating the 3' splice site for middle T mRNA, we have constructed a virus mutant, Py8O8A, which fails to express middle T but encodes normal small and large T proteins. The mutant failed to induce morphological transformation or growth in soft agar, but did stimulate postconfluent growth of normal cells. Cells infected by Py8O8A became fully agglutinable by lectins while retaining normal actin cable architecture and normal levels of extracellular fibronectin. These properties of Py8O8A demonstrated the separability of structural changes at the cell surface from those in the cytoskeleton and extracellular matrix, parameters which have heretofore been linked in the action of the hr-t and other viral oncogenes. The early region of polyoma encodes three proteins de- substitution of phenylalanine for tyrosine at position 315 in tected as tumor (T) antigens. These polypeptides of 100,000 middle T has been made and studied in two laboratories, daltons (100K; large T), 56K (middle T), and 22K (small T) with different results. -
Supplementary Table 1: Adhesion Genes Data Set
Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like, -
Cellular and Molecular Signatures in the Disease Tissue of Early
Cellular and Molecular Signatures in the Disease Tissue of Early Rheumatoid Arthritis Stratify Clinical Response to csDMARD-Therapy and Predict Radiographic Progression Frances Humby1,* Myles Lewis1,* Nandhini Ramamoorthi2, Jason Hackney3, Michael Barnes1, Michele Bombardieri1, Francesca Setiadi2, Stephen Kelly1, Fabiola Bene1, Maria di Cicco1, Sudeh Riahi1, Vidalba Rocher-Ros1, Nora Ng1, Ilias Lazorou1, Rebecca E. Hands1, Desiree van der Heijde4, Robert Landewé5, Annette van der Helm-van Mil4, Alberto Cauli6, Iain B. McInnes7, Christopher D. Buckley8, Ernest Choy9, Peter Taylor10, Michael J. Townsend2 & Costantino Pitzalis1 1Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK. Departments of 2Biomarker Discovery OMNI, 3Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, California 94080 USA 4Department of Rheumatology, Leiden University Medical Center, The Netherlands 5Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands 6Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy 7Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK 8Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK 9Institute of -
Review Article Human Polyomaviruses in Skin Diseases
SAGE-Hindawi Access to Research Pathology Research International Volume 2011, Article ID 123491, 12 pages doi:10.4061/2011/123491 Review Article Human Polyomaviruses in Skin Diseases Ugo Moens,1 Maria Ludvigsen,1 and Marijke Van Ghelue2 1 Institute of Medical Biology, Faculty of Health Sciences, University of Tromsø, 9037 Tromsø, Norway 2 Department of Medical Genetics, University Hospital of Northern-Norway, 9038 Tromsø, Norway Correspondence should be addressed to Ugo Moens, [email protected] Received 28 February 2011; Accepted 29 June 2011 Academic Editor: Gerardo Ferrara Copyright © 2011 Ugo Moens et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Polyomaviruses are a family of small, nonenveloped viruses with a circular double-stranded DNA genome of ∼5,000 base pairs protected by an icosahedral protein structure. So far, members of this family have been identified in birds and mammals. Until 2006, BK virus (BKV), JC virus (JCV), and simian virus 40 (SV40) were the only polyomaviruses known to circulate in the human population. Their occurrence in individuals was mainly confirmed by PCR and the presence of virus-specific antibodies. Using the same methods, lymphotropic polyomavirus, originally isolated in monkeys, was recently shown to be present in healthy individuals although with much lower incidence than BKV, JCV, and SV40. The use of advanced high-throughput sequencing and improved rolling circle amplification techniques have identified the novel human polyomaviruses KI, WU, Merkel cell polyomavirus, HPyV6, HPyV7, trichodysplasia spinulosa-associated polyomavirus, and HPyV9. -
Tumor Antigen (Hybrid Trp-Lac Promoter/Actin Cable Effect) ILAN BIKEL*, THOMAS M
Proc. NatL Acad. Sci. USA Vol. 80, pp. 906-910, February 1983 Biochemistry Purification of biologically active simian virus 40 small tumor antigen (hybrid trp-lac promoter/actin cable effect) ILAN BIKEL*, THOMAS M. ROBERTS*, MARILUCI T. BLADON*, ROBERT GREEN*, EGON AMANNt, AND DAVID M. LIVINGSTON* *The Sidney Farber Cancer Institute and The Departments of Medicine and Pathology, Harvard Medical School, Boston, Massachusetts 02115; and tDepartment of Biochemistry and Molecular Biology, Harvard University, Cambridge, Massachusetts 02138 Communicated by Morris Friedkin, October 29, 1982 The simian virus 40 small tumor antigen (t antigen) gene has been were grown in L broth containing ampicillin (40 Ag/ml) to an cloned downstream from a hybrid Escherichia coli trp-lac pro- ODW of0.7 and then incubated for 2 hr with 5 mM isopropyl moter anda suitable ribosome binding site. Abacterial clone (865i) f3-D-thiogalactopyranoside. Radiolabeling of proteins with transformed by such a plasmid (pTR865) expresses this gene and, [3S]methionine was performed as described (31). under optimal conditions, can produce .5% ofits total protein as t Antigen and Protein Assays. t antigen was detected by Na- t antigen. Soluble extracts ofsuch a clone were relatively depleted DodSO4/polyacrylamide slab gel electrophoresis (32) using 4% in t antigen, which was found in the initial pellet fraction. The stacking and 15% separating gels. Marker proteins were bovine protein was recovered from this fraction in a significantly purified serum albumin (Mr 68,000), carbonic anhydrase (29,000), form byextraction with urea-containing buffer. After gel filtration concentrations were deter- of such t antigen-enriched solutions, highly purified protein was and myoglobin (17,000). -
PP2A-Dependent Disruption of Centrosome Replication and Cytoskeleton Organization in Drosophila by SV40 Small Tumor Antigen
Oncogene (2008) 27, 6334–6346 & 2008 Macmillan Publishers Limited All rights reserved 0950-9232/08 $32.00 www.nature.com/onc ORIGINAL ARTICLE PP2A-dependent disruption of centrosome replication and cytoskeleton organization in Drosophila by SV40 small tumor antigen S Kotadia1,LRKao1, SA Comerford2, RT Jones1, RE Hammer3 and TL Megraw1 1Department of Pharmacology, The Cecil and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA; 2Department of Molecular Genetics, The Cecil and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA and 3Department of Biochemistry, The Cecil and Ida Green Center for Reproductive Biology Sciences, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA Viruses of the DNA tumor virus family share the ability to cell-cycle and apoptosis regulation, viral oncoproteins transform vertebrate cells through the action of virus- transform cells. Investigation of DNA tumor virus encoded tumor antigens that interfere with normal cell oncoproteins has led to the identification of many physiology. They accomplish this very efficiently by fundamental mechanisms of tumor suppression (Lavia inhibiting endogenous tumor suppressor proteins that et al., 2003; Ahuja et al., 2005). By altering the activity control cell proliferation and apoptosis. Simian virus 40 of p53, retinoblastoma protein and serine/threonine (SV40) encodes two oncoproteins, large tumor antigen, protein phosphatase 2A (PP2A), three key tumor which directly inhibits the tumor suppressors p53 and Rb, suppressors, SV40 can cause tumor formation in and small tumor antigen (ST), which interferes with transgenic mouse models (Ahuja et al., 2005; Arroyo serine/threonine protein phosphatase 2A (PP2A). -
The Human Genome Project
TO KNOW OURSELVES ❖ THE U.S. DEPARTMENT OF ENERGY AND THE HUMAN GENOME PROJECT JULY 1996 TO KNOW OURSELVES ❖ THE U.S. DEPARTMENT OF ENERGY AND THE HUMAN GENOME PROJECT JULY 1996 Contents FOREWORD . 2 THE GENOME PROJECT—WHY THE DOE? . 4 A bold but logical step INTRODUCING THE HUMAN GENOME . 6 The recipe for life Some definitions . 6 A plan of action . 8 EXPLORING THE GENOMIC LANDSCAPE . 10 Mapping the terrain Two giant steps: Chromosomes 16 and 19 . 12 Getting down to details: Sequencing the genome . 16 Shotguns and transposons . 20 How good is good enough? . 26 Sidebar: Tools of the Trade . 17 Sidebar: The Mighty Mouse . 24 BEYOND BIOLOGY . 27 Instrumentation and informatics Smaller is better—And other developments . 27 Dealing with the data . 30 ETHICAL, LEGAL, AND SOCIAL IMPLICATIONS . 32 An essential dimension of genome research Foreword T THE END OF THE ROAD in Little has been rapid, and it is now generally agreed Cottonwood Canyon, near Salt that this international project will produce Lake City, Alta is a place of the complete sequence of the human genome near-mythic renown among by the year 2005. A skiers. In time it may well And what is more important, the value assume similar status among molecular of the project also appears beyond doubt. geneticists. In December 1984, a conference Genome research is revolutionizing biology there, co-sponsored by the U.S. Department and biotechnology, and providing a vital of Energy, pondered a single question: Does thrust to the increasingly broad scope of the modern DNA research offer a way of detect- biological sciences. -
Omics Knowledgebase for Mammalian Cellular Signaling Pathways Scott A
www.nature.com/scientificdata OPEN The Signaling Pathways Project, an ARTICLE integrated ‘omics knowledgebase for mammalian cellular signaling pathways Scott A. Ochsner1, David Abraham1,8, Kirt Martin1,8, Wei Ding2, Apollo McOwiti2, Wasula Kankanamge2, Zichen Wang 3, Kaitlyn Andreano4, Ross A. Hamilton1, Yue Chen1, Angelica Hamilton5, Marin L. Gantner6, Michael Dehart2, Shijing Qu2, Susan G. Hilsenbeck2, Lauren B. Becnel2, Dave Bridges7, Avi Ma’ayan 3, Janice M. Huss5, Fabio Stossi1, Charles E. Foulds1, Anastasia Kralli6, Donald P. McDonnell4 & Neil J. McKenna 1* Mining of integrated public transcriptomic and ChIP-Seq (cistromic) datasets can illuminate functions of mammalian cellular signaling pathways not yet explored in the research literature. Here, we designed a web knowledgebase, the Signaling Pathways Project (SPP), which incorporates community classifcations of signaling pathway nodes (receptors, enzymes, transcription factors and co-nodes) and their cognate bioactive small molecules. We then mapped over 10,000 public transcriptomic or cistromic experiments to their pathway node or biosample of study. To enable prediction of pathway node-gene target transcriptional regulatory relationships through SPP, we generated consensus ‘omics signatures, or consensomes, which ranked genes based on measures of their signifcant diferential expression or promoter occupancy across transcriptomic or cistromic experiments mapped to a specifc node family. Consensomes were validated using alignment with canonical literature knowledge, gene target-level integration of transcriptomic and cistromic data points, and in bench experiments confrming previously uncharacterized node-gene target regulatory relationships. To expose the SPP knowledgebase to researchers, a web browser interface was designed that accommodates numerous routine data mining strategies. SPP is freely accessible at https://www.signalingpathways.org. -
Interactions Between Polyomavirus Large T Antigen and the Viral Replication Origin Dna: How and Why
INTERACTIONS BETWEEN POLYOMAVIRUS LARGE T ANTIGEN AND THE VIRAL REPLICATION ORIGIN DNA: HOW AND WHY by Yu-Cai Peng Department of Microbiology and Immunology McGill University, Montreal April, 1999 A thesis submitted to the Faculty of Craduate Studies and Re3earch in partial fulfullmeat of the requirements of the degree of doctor of philosophy @Yu-Cai Peng, 1999 National Library Biblioth ue nationale 1+1 of Canada du Cana7 a Acquisitions and Acquisitions et Bibliographie Srvices services bibliographiques 395 Wellmgton Street 395, nie Weliingîm Ottawa ON KIA ON4 OrtawaON K1AON4 Canada Canada The author has granted a non- L'auteur a accordé une licence non exclusive Licence ailowing the exclusive permettant à la National Library of Canada to Bibliothèque nationale du Canada de reproduce, loan, distribute or sell reproduire, prêter, distribuer ou copies of this thesis in microform, vendre des copies de cette thèse sous paper or electronic formats. la forme de microfichelfilm, de reproduction sur papier ou sur format électronique. The author retains ownership of the L'auteur conserve la propriété du copyright in this thesis. Neither the droit d'auteur qui protège cette thèse. thesis nor substantial extracts fkom it Ni la thèse ni des extraits substantiels may be printed or othenvise de celle-ci ne doivent être imprimés reproduced without the author's ou autrement reproduits sans son permission. autorisation. TABLE OF CONTENTS Page Tableofcontents................................................... I Abstract .......................................................... VI Resumé........................................................... VI11 Acknowledgements ................................................. X Claim of contribution to kaowledge ................................... XI Listoffigures ...................................................... XllI Guidelines regarding doctoral thesis ................................... XV CHAPTER 1. INTRODUCTION .................................... 1 1. Overview: Life cycle of polyomavirus and simian virus 40 ..........