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Human Shrna Library Screening to Dissect Pathways Involved in Telomerase Actions

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Human Shrna Library Screening to Dissect Pathways Involved in Telomerase Actions HUMAN SHORT HAIRPIN RNA LIBRARY SCREENING TO DISSECT PATHWAYS INVOLVED IN TELOMERASE ACTIONS APPROVED BY SUPERVISORY COMMITTEE Jerry W. Shay, Ph.D. Professor of Cell Biology Woodring E. Wright, M.D, Ph.D. Professor of Cell Biology Hongtao Yu, Ph.D. Professor of Pharmacology Pier Paolo Scaglioni, M.D. Assistant Professor of Internal Medicine David J. Chen, Ph.D. Professor of Radiation Oncology DEDICATION Dedicated to my parents, Motoyasu Hoshiyama and Hiroko Hoshiyama, and relatives for support. HUMAN SHRNA LIBRARY SCREENING TO DISSECT PATHWAYS INVLOVED IN TELOMERASE ACTIONS by HIROTOSHI HOSHIYAMA DISSERTATION Presented to the Faculty of the Graduate School of Biomedical Sciences The University of Texas Southwestern Medical Center at Dallas In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY The University of Texas Southwestern Medical Center at Dallas Dallas, Texas May, 2011 Copyright by HIROTOSHI HOSHIYAMA, 2011 All Rights Reserved ACKNOWLEDGEMENTS I would like to acknowledge Woody and Jerry, who gave me many opportunities and training throughout my graduate work. My strong determination to pursue telomere biology guided me to UTSW and it was certain that I wanted to join the Shay/Wright Lab. Jerry and Woody also gave me many opportunities and challenges to satisfy my interest in cutting-edge biotechnology and its applied discovery. On every step I was moving forward in the new area of research, I encountered many obstacles to overcome, some failed but some succeeded. No matter what the consequences were, with their advices and encouragement, I was continuously making progress toward my personal goal to become a scientist with special skills and experiences. I will not forget things learned here and will make further improvement to reach higher stages. I would also like to acknowledge my favorite professors on my committees, Dr. Hongtao Yu, Dr. David Chen, Dr. Pier Paolo Scaglioni, and Dr. Matthew Porteus. Your critical suggestions and tough criticisms were really appreciated and often showed me different perspectives and temporarily released me from Woody’s mind. I would like to further acknowledge Dr. David Chen who gave me personal support. I thank to Kevin Kennon who has supported me for facilitating my work and gave me relief from lab work as well as free food. I had a lot of fun with you. I acknowledge people in the Lab who had gone through the tough times as I did, Phil, Yong, Jun, Calin, Jin-yong, Guido, Tracy, Martin, Agnel, Nuno, Ugur, Gail, Christine B, Jennifer, Jesper, Shobhana, Melissa, Greg, Chun-hong, Ying, Bill, Dojun, SB, Wallace, Masahiro, Steven, and especially to my favorite Italian-American doctor, David Minna. I wish success for all of you. Lastly, I want to acknowledge my parents, Motoyasu Hoshiyama and Hiroko Hoshiyama. I was an ordinary child with extraordinary passion but I did not know how to direct the passion to do something other than soccer. Once I found out that science was my passion when I was late teenager, my parents let me try reckless challenges in the United States, pursuing my Ph.D. They are the ultimate support for my accomplishments. Now, it’s my turn to support them by using my expertise for all human beings. v HUMAN SHRNA LIBRARY SCREENING TO DISSECT PATHWAYS INVOLVED IN TELOMERASE ACTIONS Hirotoshi Hoshiyama, Ph.D. The University of Texas Southwestern Medical Center at Dallas, 2011 Jerry W. Shay, Ph.D. and Woodring E. Wright, M.D., Ph.D. The minimal components of human telomerase are the human telomerase reverse transcriptase (hTERT) and the human telomerase template RNA (hTR). Although it is known that both components are minimally sufficient to reconstitute telomerase activity, the factors involved in any of the multiple steps of telomerase action such as telomerase assembly, telomerase recruitment to telomeres, and telomere extension/regulation are not well understood. There are a large numbers of proteins that have associations with telomerase, yet the functional roles of those in telomere maintenance and telomerase regulation are not well understood. Identifying novel proteins and pathways involved in vi any of these important telomerase-associated functions will be useful for identifying new targets for the development of novel inhibitors that block telomerase function in cancer cells. Therefore, my goal has been to develop methods to dissect these molecular pathways and identify functional factors involved in any step of telomerase actions. To accomplish this, I designed a selective screening system by exploiting lentiviral shRNA libraries and tetracycline inducible-hTERT cell lines that is hTR deficient but expressing mutant hTR. Thus, the overall strategy of the screening system may be considered a “synthetic rescue screen”. In brief this screen was set up to rescue cells from apoptotic death due to mutant sequence incorporation at telomeres by reducing the gene expressions with lentiviral shRNA libraries. This allows us to look a set of genes involved in pathways involved in functional aspects of telomerase actions, not based on structural association with telomerase. During the work, I have established multiple lines of inducible-hTERT cells to use in selective screening systems. I have also developed a method for rapid construction of high-complexity custom shRNA libraries for targeted screening and re-evaluate hundreds of primary candidate genes to identify smaller numbers of secondary candidate genes by removing false positives. In order to analyze the pooled shRNA screening result, I have developed a method for quantitative identification of half-hairpins from a pooled shRNA library based on the pGIPZ vector. Introducing multiplexing codes and refining sample preparation schemes resulted in the predicted ability to detect two-fold enrichments followed by massive parallel sequencing. Development of those methods allowed me to identify several candidate proteins, which may be involved in telomerase actions. vii TABLE OF CONTENTS TITLE ... ............................................................................................................................ i DEDICATION .................................................................................................................. ii TITLE PAGE ................................................................................................................... iii COPYRIGHT ................................................................................................................... iv ACKNOWLEDGEMENTS .............................................................................................. v ABSTRACT ..................................................................................................................... vi TABLE OF CONTENTS ............................................................................................... viii PRIOR PUBLICATIONS ................................................................................................. xi LIST OF FIGURES ........................................................................................................ xii LIST OF TABLES .......................................................................................................... xv LIST OF DEFINITIONS ............................................................................................... xvi CHAPTER ONE: INTRODUCTION AND LITERATURE REVIEW ........................... 1 THE HISTORY OF TELOMERES AND TELOMERASE ...................................... 1 TELOMERASE AND CANCER ............................................................................... 8 TELOMERE ARCHTECHTURE ............................................................................ 10 THE PROTEIN COMPONENTS OF MAMMALIAN TELOMERES ................... 14 TELOMERASE AS RIBONUCLEOPROTEINS .................................................... 18 viii CHAPTER TWO: ESTABLISHMENT OF INDUCIBLE TELOMERASE CELLS .... 22 ABSTRACT ............................................................................................................. 22 INTRODUCTION .................................................................................................... 24 RESULTS ................................................................................................................. 27 CONCLUSIONS ...................................................................................................... 43 DISCUSSION .......................................................................................................... 45 MATERIALS AND METHODS ............................................................................. 55 CHAPTER THREE: WHOLE-GENOME SHRNA LIBRARY SCREENING FOR FACTORS INVOLVED IN TELOMERASE ACTIONS .............................................. 59 INTRODUCTION .................................................................................................... 59 RESULTS ................................................................................................................. 62 CONCLUSIONS ...................................................................................................... 75 DISCUSSION ......................................................................................................... 76 MATERIALS AND METHODS ............................................................................. 81 CHAPTER FOUR: DEVELOPMENT OF METHODS FOR QUANTITATIVE IDENTIFICATION OF POOLED SHRNAS BY MASS SEQUENCING .................... 93 INTRODUCTION ...................................................................................................
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