DOCSLIB.ORG

The Role of the Oncogene Prostate Tumor Overexpressed-1 and the Regulation of Mrna Translation in Prostate Cancer Progression and Chemoresistance

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Role of the Oncogene Prostate Tumor Overexpressed-1 and the Regulation of Mrna Translation in Prostate Cancer Progression and Chemoresistance ADVERTIMENT. Lʼaccés als continguts dʼaquesta tesi queda condicionat a lʼacceptació de les condicions dʼús establertes per la següent llicència Creative Commons: http://cat.creativecommons.org/?page_id=184 ADVERTENCIA. El acceso a los contenidos de esta tesis queda condicionado a la aceptación de las condiciones de uso establecidas por la siguiente licencia Creative Commons: http://es.creativecommons.org/blog/licencias/ WARNING. The access to the contents of this doctoral thesis it is limited to the acceptance of the use conditions set by the following Creative Commons license: https://creativecommons.org/licenses/?lang=en UNIVERSITAT AUTÒNOMA DE BARCELONA DEPARTAMENTO DE BIOQUÍMICA Y BIOLOGÍA MOLECULAR PROGRAMA DE DOCTORADO EN BIOQUÍMICA, BIOLOGÍA MOLECULAR Y BIOMEDICINA The role of the oncogene Prostate Tumor Overexpressed-1 and the regulation of mRNA translation in Prostate Cancer progression and chemoresistance Tesis presentada por Verónica Cánovas Hernández para optar al grado de Doctor por la Universitat Autònoma de Barcelona. Trabajo realizado en el Grupo de Investigación Biomédica en Urología del Institut de Recerca del Hospital Vall d’Hebron, bajo la dirección de la Dra. Rosanna Paciucci. Tesis doctoral adscrita al Departamento de Bioquímica y Biología Molecular de la Universitat Autònoma de Barcelona, bajo la tutoría de la Dra. Anna Meseguer. La doctoranda, Verónica Cánovas Hernández La directora, La tutora, Dra. Rosanna Paciucci Dra. Anna Meseguer Agradecimientos Gracias a mi familia Collserola. A mis buenas compañeras de laboratorio y amigas (Yolanda, Valentina), de pasillo (Luz, Laia, Aroa, Ana, Carla, Elena, Irene, Blanca, Laura, Lucía, Tati, Mireia, Gabriel, Alfonso, Yoelsis, Marta, Maria José, Pedro, Kim, Eva, Ana, Paula …. ) a todos los estudiantes que han pasado por el laboratorio (Marga, Adriana, Blanca, Vicente, Enric, Sandra, Lidia, Estela, Daniele, Laura, Marc), y especialmente a Rosanna. Gracias por vuestras enseñanzas, consejos, por crear un entorno de trabajo agradable y en ocasiones muy divertido y contribuir a que vuestras experiencias sean parte hoy de mis experiencias. Gracias también al resto de investigadores, sobre todo a Miguel Segura por su enorme paciencia, grandes consejos y críticas constructivas. No me olvido de los celadores (Ray, Pilar, Tao, Xavi), coordinación (Eulalia, Rosa), mantenimiento y técnicos (Rashida, Nuria), gracias por el soporte y cariño recibido durante estos años, porque sin vuestro trabajo el nuestro no sería posible. Gracias al Dr. Sonenberg por brindarme la oportunidad de realizar una estancia en su laboratorio y especialmente, gracias al Dr. Mehdi por su ayuda en el día a día del laboratorio, su paciencia y por mantener y transmitir en todo momento una actitud calmada y positiva, a pesar del más horrible de los días, cuando piensas que tu trabajo ha sido en balde. A mi tesoro más preciado: amigos, los encontrados por el camino durante mi paso por Barcelona (entre ellos Gabi ☺) y a mis Biofriends murcianos y adoptados (Blanca, Joni, Juanjo, Rafa, Miriam, Pablo, Santi, Mari Paz, Javi, Gloria, Antonio) por acompañarme durante todos estos años y hacer los momentos más simples inolvidables. OS ADORO FAMILIA BIOFRIENDS. A mis padres por su educación, consejos y paciencia, porque sin vuestro esfuerzo y apoyo nada de esto hubiera sido posible. A toda mi familia, también a los Guijarro Carrillo, por apoyarme y ayudarme en este nuevo reto. A la memoria de mi abuelo Antonio, por endulzarme la vida con sus “solano” e inculcarme el valor del esfuerzo y la perseverancia. Y sobre todo a mi compañero de vida, Pedro, por haber creído siempre en mí, aconsejarme y apoyarme en todas las decisiones importantes durante estos más de 10 años. Gracias por tus mejores sonrisas y por acompañarme durante esta etapa permitiendo descubrir junto a ti esta hermosa Cataluña. A todos y cada uno de vosotros, un millón de gracias. A mi tierra… “En Murcia hablan el más bello catalán del mundo” http://www.laverdad.es/murcia/ciudad-murcia/201609/04/murcia-hablanbello-catalan-20160904012144-v.html “Dadme un punto de apoyo y moveré el mundo” Arquímedes Index Index INDEX OF FIGURES ...................................................................................................... 13 ABBREVIATIONS .......................................................................................................... 17 Chapter 1: .......................................................................................................................... 21 INTRODUCTION ............................................................................................................ 21 1. Natural history, genetic alterations and current treatments of primary and metastatic prostate cancer ............................................................................................................... 23 1.1 Anatomy and histology of the normal prostate ................................................... 23 1.2 Prostate Cancer ................................................................................................... 25 1.2.1 General concepts and risk factors ................................................................ 25 1.2.2 Natural history of prostate cancer ................................................................ 26 1.2.3 Genetic and epigenetic alterations in prostate cancer .................................. 27 1.2.4 Early detection, prognosis and risk stratification of prostate cancer ........... 29 1.2.4.1 Biomarkers for early diagnosis of prostate cancer ................................. 32 1.2.4.2 Biomarkers for disease progression and post-treatment risk stratification ............................................................................................................................ 35 1.2.5 Treatment options for prostate cancer ......................................................... 36 1.2.6 Mechanisms of therapeutic resistance to docetaxel treatment in CRPC ...... 38 2. Prostate Tumor Overexpressed1 (PTOV1) ............................................................ 39 2.1 The gene structure ............................................................................................... 39 2.3 The protein structure ........................................................................................... 42 2.4 PTOV1 expression in cancer tissues ................................................................... 44 2.5 PTOV1 transcriptional regulatory functions ....................................................... 45 2.5.1 The Retinoic Acid Receptor promoter ......................................................... 46 2.5.2 The HES1 and HEY1 promoters.................................................................. 46 2.5.3 The Dickkopf-1 promoter ............................................................................ 47 Index Index Index 2.6 PTOV1 interactions and regulation of other cellular functions .......................... 48 2.6.1 BUZ/Znf-Ubp domains of the histone deacetylase 6, HDAC6 ................... 49 2.6.1 Flotillin1 ..................................................................................................... 50 2.6.3 Receptor of Activated protein C Kinase, RACK1 ....................................... 50 3. mRNA translation regulation in prostate cancer ................................................... 52 3.1 Regulation of mRNA translation ........................................................................ 52 3.2 Translation deregulation in cancer ...................................................................... 54 3.3 From transcriptome to proteome: focusing on the translatome .......................... 55 3.3.1 Polysome profiling ....................................................................................... 56 3.3.2 Ribosome profiling ...................................................................................... 57 Chapter 2: .......................................................................................................................... 59 HYPOTHESIS .................................................................................................................. 59 Chapter 3: .......................................................................................................................... 63 OBJECTIVES ................................................................................................................... 63 Chapter 4: .......................................................................................................................... 67 MATERIAL AND METHODS ........................................................................................ 67 1. Cellular cultures ........................................................................................................ 69 1.1 Cell lines ............................................................................................................. 69 1.2 Cell culture methods and reagents ...................................................................... 70 1.3 Production of lentiviral vectors and cellular transduction .................................. 71 1.4 Cell transfections ................................................................................................ 73 2. Functional assays....................................................................................................... 74 2.1 Proliferation assay ............................................................................................... 74 2.2 Cytotoxicity
Load more

Recommended publications
  • Depleting PTOV1 Sensitizes Non-Small Cell Lung Cancer Cells to Chemotherapy Through Attenuating Cancer Stem Cell Traits
    Wu et al. Journal of Experimental & Clinical Cancer Research (2019) 38:341 https://doi.org/10.1186/s13046-019-1349-y RESEARCH Open Access Depleting PTOV1 sensitizes non-small cell lung cancer cells to chemotherapy through attenuating cancer stem cell traits Zhiqiang Wu1*† , Zhuang Liu1†, Xiangli Jiang2†, Zeyun Mi3, Maobin Meng1, Hui Wang1, Jinlin Zhao1, Boyu Zheng1 and Zhiyong Yuan1* Abstract Background: Prostate tumor over expressed gene 1 (PTOV1) has been reported as an oncogene in several human cancers. However, the clinical significance and biological role of PTOV1 remain elusive in non-small cell lung cancer (NSCLC). Methods: The Cancer Genome Atlas (TCGA) data and NCBI/GEO data mining, western blotting analysis and immunohistochemistry were employed to characterize the expression of PTOV1 in NSCLC cell lines and tissues. The clinical significance of PTOV1 in NSCLC was studied by immunohistochemistry statistical analysis and Kaplan–Meier Plotter database mining. A series of in-vivo and in-vitro assays, including colony formation, CCK-8 assays, flow cytometry, wound healing, trans-well assay, tumor sphere formation, quantitative PCR, gene set enrichment analysis (GSEA), immunostaining and xenografts tumor model, were performed to demonstrate the effects of PTOV1 on chemosensitivity of NSCLC cells and the underlying mechanisms. Results: PTOV1 is overexpressed in NSCLC cell lines and tissues. High PTOV1 level indicates a short survival time and poor response to chemotherapy of NSCLC patients. Depleting PTOV1 increased sensitivity to chemotherapy drugs cisplatin and docetaxel by increasing cell apoptosis, inhibiting cell migration and invasion. Our study verified that depleting PTOV1 attenuated cancer stem cell traits through impairing DKK1/β-catenin signaling to enhance chemosensitivity of NSCLC cells.
    [Show full text]
  • Upregulation of 15 Antisense Long Non-Coding Rnas in Osteosarcoma
    G C A T T A C G G C A T genes Article Upregulation of 15 Antisense Long Non-Coding RNAs in Osteosarcoma Emel Rothzerg 1,2 , Xuan Dung Ho 3 , Jiake Xu 1 , David Wood 1, Aare Märtson 4 and Sulev Kõks 2,5,* 1 School of Biomedical Sciences, The University of Western Australia, Perth, WA 6009, Australia; [email protected] (E.R.); [email protected] (J.X.); [email protected] (D.W.) 2 Perron Institute for Neurological and Translational Science, QEII Medical Centre, Nedlands, WA 6009, Australia 3 Department of Oncology, College of Medicine and Pharmacy, Hue University, Hue 53000, Vietnam; [email protected] 4 Department of Traumatology and Orthopaedics, University of Tartu, Tartu University Hospital, 50411 Tartu, Estonia; [email protected] 5 Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia * Correspondence: [email protected]; Tel.: +61-(0)-8-6457-0313 Abstract: The human genome encodes thousands of natural antisense long noncoding RNAs (lncR- NAs); they play the essential role in regulation of gene expression at multiple levels, including replication, transcription and translation. Dysregulation of antisense lncRNAs plays indispensable roles in numerous biological progress, such as tumour progression, metastasis and resistance to therapeutic agents. To date, there have been several studies analysing antisense lncRNAs expression profiles in cancer, but not enough to highlight the complexity of the disease. In this study, we investi- gated the expression patterns of antisense lncRNAs from osteosarcoma and healthy bone samples (24 tumour-16 bone samples) using RNA sequencing.
    [Show full text]
  • The Role of Prostate Tumor Overexpressed 1 in Cancer Progression
    www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 7), pp: 12451-12471 Review The role of prostate tumor overexpressed 1 in cancer progression Verónica Cánovas1,4, Matilde Lleonart2,4, Juan Morote1,3,4, Rosanna Paciucci1,4 1Biomedical Research Group of Urology, Vall d’Hebron Research Institute, Pg. Vall d’Hebron 119-129, 08035 Barcelona, Spain 2Biomedical Research in Cancer Stem Cells, Vall d’Hebron Research Institute, Pg. Vall d’Hebron 119-129, 08035 Barcelona, Spain 3Deparment of Urology, Vall d’Hebron Hospital, Pg. Vall d’Hebron 119-129, 08035 Barcelona, Spain 4Universitat Autònoma de Barcelona, Spain Correspondence to: Rosanna Paciucci, email: [email protected] Keywords: PTOV1, cancer progression, prostate cancer, cancer stem cells, transcription Received: August 26, 2016 Accepted: November 14, 2016 Published: December 22, 2016 SUMMARY Prostate-Tumor-Overexpressed-1 (PTOV1) is a conserved adaptor protein discovered as overexpressed in prostate cancer. Since its discovery, the number of binding partners and associated cellular functions has increased and helped to identify PTOV1 as regulator of gene expression at transcription and translation levels. Its overexpression is associated with increased tumor grade and proliferation in prostate cancer and other neoplasms, including breast, ovarian, nasopharyngeal, squamous laryngeal, hepatocellular and urothelial carcinomas. An important contribution to higher levels of PTOV1 in prostate tumors is given by the frequent rate of gene amplifications, also found in other tumor types. The recent resolution of the structure by NMR of the PTOV domain in PTOV2, also identified as Arc92/ACID1/MED25, has helped to shed light on the functions of PTOV1 as a transcription factor.
    [Show full text]
  • New Insights Into the Interplay Between Non-Coding Rnas and RNA-Binding Protein Hnrnpk in Regulating Cellular Functions
    cells Review New Insights into the Interplay between Non-Coding RNAs and RNA-Binding Protein HnRNPK in Regulating Cellular Functions Yongjie Xu, Wei Wu, Qiu Han, Yaling Wang, Cencen Li, Pengpeng Zhang * and Haixia Xu * College of Life Science, Xinyang Normal University, Xinyang 464000, China; [email protected] (Y.X.); [email protected] (W.W.); [email protected] (Q.H.); [email protected] (Y.W.); [email protected] (C.L.) * Correspondence: [email protected] (P.Z.); [email protected] (H.X.); Tel.: +86-376-6391380 (H.X.) Received: 19 December 2018; Accepted: 15 January 2019; Published: 17 January 2019 Abstract: The emerging data indicates that non-coding RNAs (ncRNAs) epresent more than the “junk sequences” of the genome. Both miRNAs and long non-coding RNAs (lncRNAs) are involved in fundamental biological processes, and their deregulation may lead to oncogenesis and other diseases. As an important RNA-binding protein (RBP), heterogeneous nuclear ribonucleoprotein K (hnRNPK) is known to regulate gene expression through the RNA-binding domain involved in various pathways, such as transcription, splicing, and translation. HnRNPK is a highly conserved gene that is abundantly expressed in mammalian cells. The interaction of hnRNPK and ncRNAs defines the novel way through which ncRNAs affect the expression of protein-coding genes and form autoregulatory feedback loops. This review summarizes the interactions of hnRNPK and ncRNAs in regulating gene expression at transcriptional and post-transcriptional levels or by changing the genomic structure, highlighting their involvement in carcinogenesis, glucose metabolism, stem cell differentiation, virus infection and other cellular functions. Drawing connections between such discoveries might provide novel targets to control the biological outputs of cells in response to different stimuli.
    [Show full text]
  • Content Based Search in Gene Expression Databases and a Meta-Analysis of Host Responses to Infection
    Content Based Search in Gene Expression Databases and a Meta-analysis of Host Responses to Infection A Thesis Submitted to the Faculty of Drexel University by Francis X. Bell in partial fulfillment of the requirements for the degree of Doctor of Philosophy November 2015 c Copyright 2015 Francis X. Bell. All Rights Reserved. ii Acknowledgments I would like to acknowledge and thank my advisor, Dr. Ahmet Sacan. Without his advice, support, and patience I would not have been able to accomplish all that I have. I would also like to thank my committee members and the Biomed Faculty that have guided me. I would like to give a special thanks for the members of the bioinformatics lab, in particular the members of the Sacan lab: Rehman Qureshi, Daisy Heng Yang, April Chunyu Zhao, and Yiqian Zhou. Thank you for creating a pleasant and friendly environment in the lab. I give the members of my family my sincerest gratitude for all that they have done for me. I cannot begin to repay my parents for their sacrifices. I am eternally grateful for everything they have done. The support of my sisters and their encouragement gave me the strength to persevere to the end. iii Table of Contents LIST OF TABLES.......................................................................... vii LIST OF FIGURES ........................................................................ xiv ABSTRACT ................................................................................ xvii 1. A BRIEF INTRODUCTION TO GENE EXPRESSION............................. 1 1.1 Central Dogma of Molecular Biology........................................... 1 1.1.1 Basic Transfers .......................................................... 1 1.1.2 Uncommon Transfers ................................................... 3 1.2 Gene Expression ................................................................. 4 1.2.1 Estimating Gene Expression ............................................ 4 1.2.2 DNA Microarrays ......................................................
    [Show full text]
  • Methods and Models for the Analysis of Biological Signifïcance Based on High-Throughput Data
    Methods and Models for the Analysis of Biological Signifïcance Based on High-Throughput Data Jose Luis Mosquera Mayo Aquesta tesi doctoral està subjecta a la llicència Reconeixement- NoComercial – CompartirIgual 3.0. Espanya de Creative Commons. Esta tesis doctoral está sujeta a la licencia Reconocimiento - NoComercial – CompartirIgual 3.0. España de Creative Commons. This doctoral thesis is licensed under the Creative Commons Attribution-NonCommercial- ShareAlike 3.0. Spain License. Methods and Models for the Analysis of Biological Significance Based on High Throughput Data Jose Luis Mosquera Mayo 2 Methods and Models for the Analysis of Biological Significance Based on High Throughput Data M`etodes i Models per a l’An`aliside la Significaci´oBiol`ogicaBasada en Dades d'Alt Rendiment Mem`oriapresentada per en Jose Luis Mosquera Mayo per optar al grau de doctor per la Universitat de Barcelona SIGNATURES El Doctorand: Jose Luis Mosquera Mayo El Director de la Tesi: Dr. Alexandre Sanchez´ Pla El Tutor de la Tesi: Dr. Josep Mar´ıa Oller Sala Programa de doctorat en estad´ıstica Departament d'Estad´ıstica,Facultat de Biologia Universitat de Barcelona 4 Acknowledgements \A teacher affects eternity, he can never tell where his influence stops." Henry Brooks Adams \Mathematicians do not study objects, but relations between objects." Jules Henri Poincar´e It is truly an honor for me to address these words of gratitude to everyone who has contributed, to a greater or lesser extent by supporting me during this exciting program of studies, to help make my lifelong dream come true: to complete my doctoral dissertation. First and foremost, I would like (and feel compelled) to mention a special debt of gratitude to Prof.
    [Show full text]
  • Investigating the Effects of Chronic Perinatal Alcohol and Combined
    www.nature.com/scientificreports OPEN Investigating the efects of chronic perinatal alcohol and combined nicotine and alcohol exposure on dopaminergic and non‑dopaminergic neurons in the VTA Tina Kazemi, Shuyan Huang, Naze G. Avci, Yasemin M. Akay & Metin Akay* The ventral tegmental area (VTA) is the origin of dopaminergic neurons and the dopamine (DA) reward pathway. This pathway has been widely studied in addiction and drug reinforcement studies and is believed to be the central processing component of the reward circuit. In this study, we used a well‑ established rat model to expose mother dams to alcohol, nicotine‑alcohol, and saline perinatally. DA and non‑DA neurons collected from the VTA of the rat pups were used to study expression profles of miRNAs and mRNAs. miRNA pathway interactions, putative miRNA‑mRNA target pairs, and downstream modulated biological pathways were analyzed. In the DA neurons, 4607 genes were diferentially upregulated and 4682 were diferentially downregulated following nicotine‑alcohol exposure. However, in the non‑DA neurons, only 543 genes were diferentially upregulated and 506 were diferentially downregulated. Cell proliferation, diferentiation, and survival pathways were enriched after the treatments. Specifcally, in the PI3K/AKT signaling pathway, there were 41 miRNAs and 136 mRNAs diferentially expressed in the DA neurons while only 16 miRNAs and 20 mRNAs were diferentially expressed in the non‑DA neurons after the nicotine‑alcohol exposure. These results depicted that chronic nicotine and alcohol exposures during pregnancy diferentially afect both miRNA and gene expression profles more in DA than the non‑DA neurons in the VTA. Understanding how the expression signatures representing specifc neuronal subpopulations become enriched in the VTA after addictive substance administration helps us to identify how neuronal functions may be altered in the brain.
    [Show full text]
  • Identification and Mechanistic Investigation of Recurrent Functional Genomic and Transcriptional Alterations in Advanced Prostat
    Identification and Mechanistic Investigation of Recurrent Functional Genomic and Transcriptional Alterations in Advanced Prostate Cancer Thomas A. White A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2013 Reading Committee: Peter S. Nelson, Chair Janet L. Stanford Raymond J. Monnat Jay A. Shendure Program Authorized to Offer Degree: Molecular and Cellular Biology ©Copyright 2013 Thomas A. White University of Washington Abstract Identification and Mechanistic Investigation of Recurrent Functional Genomic and Transcriptional Alterations in Advanced Prostate Cancer Thomas A. White Chair of the Supervisory Committee: Peter S. Nelson, MD Novel functionally altered transcripts may be recurrent in prostate cancer (PCa) and may underlie lethal and advanced disease and the neuroendocrine small cell carcinoma (SCC) phenotype. We conducted an RNASeq survey of the LuCaP series of 24 PCa xenograft tumors from 19 men, and validated observations on metastatic tumors and PCa cell lines. Key findings include discovery and validation of 40 novel fusion transcripts including one recurrent chimera, many SCC-specific and castration resistance (CR) -specific novel splice isoforms, new observations on SCC-specific and TMPRSS2-ERG specific differential expression, the allele-specific expression of certain recurrent non- synonymous somatic single nucleotide variants (nsSNVs) previously discovered via exome sequencing of the same tumors, rgw ubiquitous A-to-I RNA editing of base excision repair (BER) gene NEIL1 as well as CDK13, a kinase involved in RNA splicing, and the SCC expression of a previously unannotated long noncoding RNA (lncRNA) at Chr6p22.2. Mechanistic investigation of the novel lncRNA indicates expression is regulated by derepression by master neuroendocrine regulator RE1-silencing transcription factor (REST), and may regulate some genes of axonogenesis and angiogenesis.
    [Show full text]
  • Ep 2270226 B1
    (19) TZZ Z _T (11) EP 2 270 226 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12Q 1/68 (2006.01) G01N 33/569 (2006.01) 18.05.2016 Bulletin 2016/20 G01N 33/68 (2006.01) (21) Application number: 10013575.5 (22) Date of filing: 30.03.2006 (54) Method for distinguishing mesenchymal stem cell using molecular marker and use thereof Verfahren zur Unterscheidung mesenchymaler Stammzellen mittels molekularem Marker und Nutzung dieses Marker Procédé de distinction d’une cellule souche mésenchymateuse en utilisant un marqueur moléculaire et son usage (84) Designated Contracting States: (74) Representative: Müller Hoffmann & Partner AT BE BG CH CY CZ DE DK EE ES FI FR GB GR Patentanwälte mbB HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI St.-Martin-Strasse 58 SK TR 81541 München (DE) (30) Priority: 31.03.2005 JP 2005104563 (56) References cited: EP-A1- 1 475 438 WO-A1-02/46373 (43) Date of publication of application: WO-A1-03/016916 WO-A1-03/106492 05.01.2011 Bulletin 2011/01 WO-A2-2004/025293 WO-A2-2004/044142 JP-A- 2004 290 189 US-A1- 2003 161 817 (62) Document number(s) of the earlier application(s) in accordance with Art. 76 EPC: • DESCHASEAUX FREDERIC ET AL: "Direct 06730606.8 / 1 870 455 selection of human bone marrow mesenchymal stem cells using an anti-CD49a antibody reveals (73) Proprietor: Two Cells Co., Ltd their CD45med,low phenotype", BRITISH Minami-ku JOURNAL OF HAEMATOLOGY, Hiroshima City WILEY-BLACKWELL PUBLISHING LTD, GB, vol.
    [Show full text]
  • Sirna-Mediated Gene Silencing: a Global Genome View Dimitri Semizarov*, Paul Kroeger and Stephen Fesik
    Published online July 22, 2004 3836–3845 Nucleic Acids Research, 2004, Vol. 32, No. 13 doi:10.1093/nar/gkh714 siRNA-mediated gene silencing: a global genome view Dimitri Semizarov*, Paul Kroeger and Stephen Fesik Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60064, USA Received March 23, 2004; Revised June 4, 2004; Accepted July 1, 2004 ABSTRACT validating new drug targets, and treating disease (3–8). Downloaded from https://academic.oup.com/nar/article/32/13/3836/2375704 by guest on 30 September 2021 siRNA may also prove to be a useful tool for dissecting The task of specific gene knockdown in vitro has been cellular pathways, if siRNA-mediated gene knockdown is facilitated through the use of short interfering RNA followed by a systematic analysis of downstream effects. (siRNA), which is now widely used for studying gene Here, we combined the use of siRNA, microarray techno- function, as well as for identifying and validating new logies and quantitative pathway analysis to determine the drug targets. We explored the possibility of using effects of a gene knockdown on the cell. The combination siRNA for dissecting cellular pathways by siRNA- of the siRNA and microarray technologies is a powerful mediated gene silencing followed by gene expression tool in large-scale genomics experiments, particularly if the profiling and systematic pathway analysis. We used vast amount of gene expression data is systematically analyzed siRNA to eliminate the Rb1 gene in human cells and in the context of the biological pathways. We have previously determined the effects of Rb1 knockdown on the cell used DNA microarrays to assess the consequences of gene silencing on a genome-wide scale (9).
    [Show full text]
  • Bioinformatic Identification of Disease Driver Networks Using Functional Profiling Data
    Institute for Molecular Medicine Finland, FIMM University of Helsinki, Helsinki, Finland Doctoral Programme in Biomedicine (DPBM) BIOINFORMATIC IDENTIFICATION OF DISEASE DRIVER NETWORKS USING FUNCTIONAL PROFILING DATA Agnieszka Szwajda ACADEMIC DISSERTATION To be presented, with the permission of the Faculty of Medicine, University of Helsinki, for public examination in lecture hall 3, Biomedicum Helsinki, Haartmaninkatu 8, on Friday 2nd of February 2018, at 12 noon. Helsinki, 2018 Supervised by: Professor Tero Aittokallio, Ph.D. Institute for Molecular Medicine Finland, FIMM University of Helsinki Helsinki, Finland Krister Wennerberg, Ph.D. Institute for Molecular Medicine Finland, FIMM University of Helsinki Helsinki, Finland Reviewed by: Associate Professor Harri Lähdesmäki, D.Sc. Department of Computer Science Aalto University School of Science Espoo, Finland Associate Professor Henri Xhaard, Ph.D. Division of Pharmaceutical Chemistry and Technology University of Helsinki Helsinki, Finland Opponent: Professor Matti Nykter, Ph.D. Institute of Biosciences and Medical Technology University of Tampere Tampere, Finland Custos: Professor Samuli Ripatti, Ph.D. Institute for Molecular Medicine Finland, FIMM University of Helsinki Helsinki, Finland © Agnieszka Szwajda Cover layout by Anita Tienhaara ISBN 978-951-51-3959-7 (paperback) ISBN 978-951-51-3960-3 (PDF) ISSN 2342-3161 (print) ISSN 2342-317X (online) Unigrafia Oy, Helsinki 2018 2 Table of contents ABBREVIATIONS ......................................................................................................................................
    [Show full text]
  • Original Article High Expression of Prostate Tumor Overexpressed 1 (PTOV1) Is a Potential Prognostic Biomarker for Cervical Cancer
    Int J Clin Exp Pathol 2017;10(11):11044-11050 www.ijcep.com /ISSN:1936-2625/IJCEP0056434 Original Article High expression of prostate tumor overexpressed 1 (PTOV1) is a potential prognostic biomarker for cervical cancer Yongwei Chen1, Zongyi Hu2, Dan Chai1 1Division of Obstetrics and Gynecology, Shenzhen Hospital, Southern Medical University, Shenzhen, China; 2Divi- sion of Anesthesiology, Shenzhen Nanshan District Maternity and Child Health Care Hospital, Shenzhen, China Received April 28, 2017; Accepted June 27, 2017; Epub November 1, 2017; Published November 15, 2017 Abstract: Background: To investigate the role of prostate tumor overexpressed 1 (PTOV1) in the development and progression of human cervical cancer. Methods: Real-time quantitative PCR, Western blot, and immunohistochem- istry were used to explore PTOV1 expression in cervical cancer tissues and cell lines. Cell proliferation capability was examined by MTT assay. Statistical analyzes were applied to evaluate the correlation of PTOV1 expression with clinical parameters and prognosis. Results: The expression level of PTOV1 was markedly higher in cervical cancer tissues and cell lines than that in adjacent noncancerous tissues and the normal cervical epithelial cells. PTOV1 overexpression was correlated with higher tumor stage (P = 0.001), larger tumor size (P = 0.004), and lymph node involvement (P = 0.036). Moreover, patients with high PTOV1 expression showed shorter overall and recurrence- free survival time (P = 0.013 and P = 0.010, respectively). PTOV1 knockdown by short hairpin RNAi inhibited cancer cell growth in vitro. Conclusion: PTOV1 may be an important factor associated with proliferation of cervical cancer. Keywords: PTOV1, cervical cancer, proliferation Introduction coded protein with two similar, tandemly- arranged domains [5].
    [Show full text]