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CARBOPLATIN and PACLITAXEL a Dissertation SUBMITTED PHARMACOGENOMICS OF CHEMOTHERAPEUTIC AGENTS: CARBOPLATIN AND PACLITAXEL A Dissertation SUBMITTED TO THE FACULTY OF UNIVERSITY OF MINNESOTA BY Taraswi Mitra Ghosh IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Dr. Jatinder K. Lamba May 2017 © Taraswi Mitra Ghosh, 2017 ACKNOWLEDGEMENTS At this special moment when I have reached the concluding stages of my Doctoral research and am ready to embark upon another voyage in my scientific career, I would like to take the opportunity to acknowledge the contributions of the people who have shaped up my life and career. First and foremost, I would like to thank Almighty God for giving me the strength to overcome all the challenges, for giving me the motivation to learn and to acquire knowledge. I would like to thank Dr. Jatinder Lamba, my adviser. I have learned a lot from her and am extremely thankful to her. She has helped me develop my scientific temper and inquisitive thinking. I would like to express my sincere gratitude towards my committee members. Dr. Mark Kirstein, my committee chair, has been a constant support. He has helped me develop my concepts in Pharmacokinetics. His insightful questions during our discussions have encouraged me to think deep and broaden my knowledge base. Dr. Angela Birnbaum, my committee member and DGS, has always been a strong support. Working with her was a very nice and cherishable experience for me. She has provided me the confidence to undertake independent projects- an experience which I am sure will be helpful in my future as a Scientist. I would like to thank Dr. Natalia Tretyakova for her invaluable suggestions and helpful guidance in Drug metabolism. I am grateful to my collaborators at the University of Kansas (Dr. Brooke Fridley and Dr. Rama Raghavan), Minneapolis VA Healthcare (Dr. Pankaj Gupta) and the Mayo Clinic (Dr. Ellen Goode) for their support during my research. My heartiest thanks to Prof. Esam El-Fakahany, Prof. Brian Van Ness and Dr. Robert Straka for standing by me when things were not on brighter side. It was an honor for me to be associated with them throughout my scientific quest. I I am extremely grateful to all my professors and teachers who have enriched my knowledge and understanding of various fields. Especially, I would like to mention Dr. Demerath, Dr. Foster, Dr. Zimmerman and Dr. Susan Telke in University of Minnesota and Prof. Ashish Kumar DuttaGupta, Prof. Trilochan Midya, Prof. Arun Chatterjee, Dr. Nihar Ranjana Chatterjee, Dr. Srikanta Kumar Rath, Atanu Banerjee, Nandita Chatterjee, and Cindy Brown for their contributions. I would like to acknowledge the help of all the members of ECP administrative staff Carol Ann, Dede, Karla, Mary, Erin for their help whenever I needed. I am very grateful to Jan Morse for providing the support and confidence I needed during difficult times in my PhD career. My special thanks to Tanya Feldberg for being such a wonderful person through her continued support and encouragement. I would like to thank Dr. Neha Bhise for being an excellent lab member and above all a great friend and confidante. I am also thankful to Dr. Lata Chauhan for her help and for being a cordial host in Florida. I would like to thank my friends at University of Minnesota Manoj, Kinjal, Sam, Youssef, Mariam, Chay, Ritu, Shuang, Ashwin, Vaishnavi and University of Florida Miyoung and Bradley who have shared my journey through my graduate student life. I am extremely thankful to all my friends Arpita, Shahida di, Nlanjana di, Bubai da, Subhrajit, Ujjal da, Sohan, Debarchana, Smita, Moumita, Joyeeta, Sraboni di, Rita di and Kathak dance buddies. Without their support my journey would have been impossible to complete. I consider myself lucky to have very supportive parents. My parents have taught me that education is the door to freedom. I will always be grateful to them for instilling in me the urge to acquire knowledge. I realized during my PhD that they are willing to sacrifice anything for my education when they decided to leave their country and live with me during my final graduation year. II I have heartfelt love for my loving sister, Tanushri, who has always unconditionally believed in me. I always remember and admire all her support right from our childhood. I would also like to thank Abhijit, my brother-in-law, who takes care of my parents in my absence. I am extremely grateful to my in-laws and my extended family. As I am writing these acknowledgements I feel sad that my father-in-law, who passed away last month, will not be here to share the joy of my PhD degree completion with me. I would like to thank my friend and fortunately my husband, Amit, who has been the pillar of my strength through all the trials and tribulations over the past 17 years. He is the biggest critique as well as the biggest admirer of all my work. He has forever handled my gloomy phases with immense patience. This journey was possible because of him. Last but not the least, I would like to express my deepest love for our son, Adhrit (Tintin), the emperor of our hearts. III DEDICATION To my beloved companion, Amit IV TABLE OF CONTENTS LIST OF TABLES ………………………………………………………………………………………………………………………IX LIST OF FIGURES ……………………………………………………………………………………………………….……………XI CHAPTER 1 Literature review ...................................................................................................... 1 1.1 Ovarian cancer ................................................................................................................. 2 Introduction ............................................................................................................. 2 Risk factors ............................................................................................................... 4 Prognosis of Ovarian cancer .................................................................................... 6 Treatment of Ovarian epithelial cancer ................................................................... 6 Ovarian cancer clinical trials using Platinum/Paclitaxel chemotherapy .................. 8 1.2 Lung cancer: Non-small cell lung cancer (NSCLC) .......................................................... 11 Introduction ........................................................................................................... 11 Risk Factors ............................................................................................................ 14 Symptoms and Diagnosis ....................................................................................... 14 Prognostic factors .................................................................................................. 14 Treatment of Non-Small cell lung cancer (NSCLC) ................................................. 15 NSCLC clinical trials using Platinum/Paclitaxel combination therapy .................... 15 1.3 Platinum drugs ............................................................................................................... 19 Introduction ........................................................................................................... 19 Mechanism of action of Platinum drugs ................................................................ 20 Metabolic pathway of platinum drugs ................................................................... 22 Pharmacogenomics of platinum drug pathway genes .......................................... 35 1.4 Paclitaxel chemotherapy................................................................................................ 83 Introduction ........................................................................................................... 83 V Mechanism of action of paclitaxel ......................................................................... 84 Metabolic (PK/PD) pathway of paclitaxel .............................................................. 88 Pharmacogenomics of paclitaxel (PK/PD) pathway genes .................................... 93 1.5 Research Study Objectives ........................................................................................... 105 Gaps in literature ................................................................................................. 105 Objectives and Specific Aims ............................................................................... 106 CHAPTER 2 Pharmacogenomic markers influence the variation of in vitro chemosensitivity to carboplatin and paclitaxel as single agents and as combination: a pathway based approach ... 108 2.1 Introduction ................................................................................................................. 109 2.2 Materials and Methods ................................................................................................ 111 Creation of EBV-transformed Ovarian cancer LCLs.............................................. 111 Cell Culture ........................................................................................................... 111 Drugs .................................................................................................................... 111 In vitro cytotoxicity assays ................................................................................... 111 Caspase-Glo 3/7 activity Assay ............................................................................ 112 Cell cycle analysis ................................................................................................. 112 SNP Genotyping ..................................................................................................
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