Regulation of Bladder Cancer Invasion by Amy Lee Han A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Molecular and Cellular Pathology) in the University of Michigan 2016 Doctoral Committee: Professor Evan T. Keller, Chair Professor Mark L. Day Professor Celina G. Kleer Assistant Professor Scott A. Tomlins © Amy L. Han 2016 DEDICATION To my grandmother who passed away from liver cancer (Aug. 13, 2001). ii ACKNOWLEDGEMENTS I would like to first thank my advisor and mentor, Dr. Evan Keller, who took me into his lab and guided me throughout this whole graduate school process. His constant encouragement and support helped me continue to press on, especially when experiments did not seem to be working. He pushed me to think critically with the questions he asked and offered insight on potential directions to look into. I’m truly thankful for the vast amount of knowledge he has shared with me these past several years, always making time for me despite his busy schedule, and helping me develop skills necessary to be a good researcher in the scientific community. I would also like to acknowledge all my committee members: Dr. Mark Day, Dr. Celina Kleer, and Dr. Scott Tomlins, whose expertise, guidance, and support made it possible for me to develop and move my project forward. I appreciate all the time and effort they spend on providing me input and suggestions. Dr. Day’s lab, especially Layla El-Sawy and Kathie Day were also of tremendous help. Not only did they share their bladder cancer expertise and reagents with me, but they also passed on their established orthotopic mice bladder injection protocol. I would like to express gratitude to Brendan Veeneman and Dr. Tomlins who had analyzed the RNA-Seq results and helped identify the genes of which my research project was based on. Dr. Tomlins has continually been involved since the beginning of this bladder cancer project. I am truly thankful for all the patient tissues he had shared with us and all the counsel and pathology expertise he offered, especially in interpreting the numerous slides. iii I thank all the former and current Keller lab members. I am grateful for all the people I had met while being part of the Keller lab. As people who I saw and interacted with the most, they made coming to lab pleasant and enjoyable. I appreciate all the conversations we had (whether scientific or not), being able to share ideas/advice, and how we helped each other out with experiments and reagents. I would especially like to thank June Escara-Wilke who assisted me with the in vivo experiments and has continually been cheering me on. In addition, I would like to thank my family and friends for all their love, prayers, and support. I truly would not have been able to get to this point without their assistance. They would constantly check up on me making sure I was okay, listen to my struggles while encouraging me, and bless me with their thoughtfulness and gifts/care packages. I sincerely thank my parents who made it possible for me to be here continuing my studies. Their continual love and encouragement allowed me to persevere and push myself to work harder. I want to especially recognize my sister who is always there for me and would come visit me from time to time. Her positivity and joyfulness helped me to see the brighter side of things and to keep going. Finally, I would like to thank God for giving me the opportunity to come to the University of Michigan to study cancer in pursuit of my Ph.D. degree, allowing me to meet wonderful people in Ann Arbor, and providing me with all that I need. He has been my rock, refuge, strength, and source of hope during this whole process. iv TABLE OF CONTENTS DEDICATION…………………………………………………………….............................ii ACKNOWLEDGEMENTS……………………………………………….............................iii LIST OF FIGURES……………………………………………………….............................vii LIST OF TABLES…………………………………………………………………………...viii ABSTRACT……………………………………………………………….............................ix CHAPTERS I. Introduction to Bladder Cancer………………………………………………………1 a. Epidemiology…………………………………………………………………….1 b. Risk Factors……………………………………………………............................1 c. Clinical Presentation/Pathology………………………………………………….4 d. Molecular Pathology…………………………………………..............................5 e. Diagnosis/Treatment…………………………………………..............................10 f. Summary………………………………………………………............................14 g. References……………………………………………………..............................15 II. Identifying genes that regulate bladder cancer invasion……………………………..21 a. Abstract…………………………………………………………………………..21 b. Introduction……………………………………………………............................22 c. Materials and Methods………………………………………...............................23 d. Results……………………………………………………….…………………...26 e. Discussion………………………………………………….….............................32 f. References………………………………………………….….............................34 v III. Introduction to Fibulin-3……………………………………………………………..35 a. Fibulins………………………………………………...........................................36 b. Fibulin-3: Structure and Expression…………………………………..……….....37 c. Fibulin-3: Function………………………………….…………………..……..…37 d. Fibulin-3 and Cancer……………………………….…........... .............................39 e. Summary………………………………………….……………………...…....…42 f. References……………………………………….…….........................................43 IV. Role of fibulin-3 in regulating bladder cancer invasion……………………………..46 a. Abstract……………………………………………….……….............................46 b. Introduction…………………………………………..………..............................46 c. Materials and Methods…………………………….….……….............................47 d. Results………………………………………………..………..............................52 e. Discussion…………………………………………..………..…………..……....61 f. References………………………………………..…….……………..………….66 V. Discussion and Future Directions……………………………………….…...………69 vi LIST OF FIGURES Chapter I Figure 1-Bladder cancer stage classification based on depth of tumor invasion in the urothelium and presence of metastasis.……………………………….4 Chapter II Figure 2.1-Identification of candidate genes…………………………………………………26 Figure 2.2.-Validation of the candidate genes with bladder cancer cell lines…......................29 Figure 2.3-Fibulin-3 expression correlates with invasion……….…………………………...31 Figure 2.4-Fibulin-3 is overexpressed in MIBC vs. NMIBC..………………….……………32 Chapter III Figure 3-Family of fibulins characterized by their tandem arrays of epidermal growth-factor-like domains (cbEGF) and a distinct C-terminal fibulin-like domain.……………………………………………………………….35 Chapter IV Figure 4.1-Decreased fibulin-3 expression attenuates bladder cancer invasion and migration……………………………………………………………..................53 Figure 4.2-Fibulin-3 overexpression promotes bladder cancer cell invasion and migration………………………………………………………...................54 Figure 4.3-Fibulin-3 knockdown decreases muscle invasive bladder cancer in vivo…………………………………………………………………………56 Figure 4.4-IGFBP5 expression is downregulated with fibulin-3 knockdown………………...58 Figure 4.5-IGFBP5 rescues the invasive and migratory potential that is decreased through loss of fibulin-3 expression……………………………...................60 vii LIST OF TABLES Table 2.1-List of primers used in qRT-PCR experiments…………………………………….25 Table 2.2-Genes differentially expressed between T1 vs. T2……………………...................27 Table 4.1-List of primers used in qRT-PCR experiments…………………………………….51 viii ABSTRACT The most common type of bladder cancer is urothelial carcinoma (UC). Bladder cancers are categorized as either non-muscle invasive (stages Ta-T1) or muscle invasive (stages ≥T2). The majority of bladder cancers are non-muscle invasive at initial diagnosis; however, the recurrence rate for these tumors is high and a subset of them progress into T2. In this study, we aimed to determine if there is differential gene expression between T1 versus T2 bladder cancers that can help identify key regulators in bladder cancer progression and invasion. T1 and T2 bladder cancer tissues were subjected to RNA-Seq to evaluate differential mRNA expression amongst these stages. The Oncomine database was then examined to further limit potential candidates that differentiate T1 from T2. These efforts led to the identification of an extracellular matrix glycoprotein, fibulin-3 (also known as EFEMP1), as being highly expressed in T2s compared to T1s. Consistent with these findings, fibulin-3 expression level correlated with the invasive ability of several bladder cancer cell lines. Specifically, fibulin-3 expression was determined using both qRT-PCR and western blotting amongst the T24, UMUC-13, UMUC-3, RT4, and 5637 bladder cancer cell lines. The most invasive cell lines, T24 and UMUC-13, demonstrated the highest fibulin-3 expression. In contrast, the least invasive cells, RT4 and 5637, demonstrated the lowest fibulin-3 expression. Genetically-engineered modulation of fibulin-3 expression in bladder cancer cell lines was directly associated with their invasive ability. Knockdown of fibulin-3 in bladder cancer cell lines decreased the incidence of muscle invasive ix