UC Berkeley UC Berkeley Electronic Theses and Dissertations Title Investigating Dysregulated Metabolic Pathways that Drive Cancer Pathogenicity Permalink https://escholarship.org/uc/item/9cw6c7sr Author Roberts, Lindsay Shayna Publication Date 2017 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California Investigating Dysregulated Metabolic Pathways that Drive Cancer Pathogenicity By Lindsay Shayna Roberts A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Metabolic Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Daniel K. Nomura, Chair Professor James Olzmann Professor Sarah Stanley Spring 2017 ABSTRACT Investigating Dysregulated Metabolic Pathways that Drive Cancer Pathogenicity by Lindsay Shayna Roberts Doctor of Philosophy in Metabolic Biology University of California, Berkeley Professor Daniel K. Nomura, Chair In the United States, it is estimated that over 200,000 women will be diagnosed with breast cancer and nearly 40,000 women will die of breast cancer in 20161. Mortality from breast cancer is almost always attributed to metastatic spread of the disease to other organs, thus precluding resection as a treatment method.2 Unfortunately, conventional chemotherapy fails to eradicate many aggressive breast cancers. Studies over the past decade have uncovered certain breast cancer cell-types, such as estrogen/progesterone/human epidermal growth factor receptor 2 (ER/PR/ HER2)- negative (triple-negative) breast cancers (TNBCs) that show poor prognosis and chemotherapy resistance within breast tumors.3–5 Eliminating these breast cancer types is critical in reducing the mortality associated with breast cancer. Current therapeutic strategies for breast cancer include resection, nonspecific therapies such as radiation or chemotherapy, and targeted strategies for combating certain types of breast cancers. However, there are no targeted strategies for combating the most aggressive types of breast cancers, including TNBCs. Cancer cells are known to possess altered metabolism that fuels their malignancy and pathogenicity. Most of what has been known about cancer cell metabolism focuses on the well-characterized central carbon pathways, however, the mapping of the human genome revealed that cellular metabolic networks extend far beyond that. In this dissertation I present some extensions of our understanding of dysregulated cancer cell metabolism in areas of lipid metabolism and membrane glycosylation. Furthermore, using drugs and drug candidates already in clinical trials or the clinic, I identify new metabolic targets that, when inhibited, contribute to or are responsible for killing TNBC cells. Increasing our understanding of cancer cell metabolism, especially in the context of small molecule inhibitors, will hopefully enable or promote the development of targeted therapeutics for these highly lethal and poorly treated cancers. 1 DEDICATION Achieving this goal of earning my Ph.D. was made possible by the help and support of many important people in my life to whom I would like to dedicate this dissertation: To all of my mentors – in science and in life. In science To Dr. Sharon Fleming and Mark Fitch, my first two mentors in research, for taking a chance on an excited, naïve, new freshman undergrad. Without that opportunity I would not have discovered and developed my love for research. To Dr. Marc Hellerstein, Dr. Matthew Bruss, Dr. Cyrus Khambatta, and Dr. Airlia Thompson for encouraging me, giving advice, and providing new opportunities for me to cultivate my scientific passions. To my Ph.D. advisor, Dr. Daniel Nomura, for pushing me to work harder and more thoughtfully that I knew possible. I’ve learned so much about research, science, and myself throughout this experience, and I thank you for giving me this opportunity. To Dr. Mela Mulvihill for being the first to welcome me into the lab and quickly becoming my go-to person for any help I needed scientifically or personally. To Dr. Rebecca Kohnz for being my science Google and “sialyl-mate”, I attribute so much of my scientific knowledge to you and your mentorship. To Dr. Leslie Bateman, thank you for being honest, direct, brilliant, and caring – your friendship and colleagueship is one of the best things to have come out of my graduate experience. To Peter Yan, my undergrad, for teaching me about mentoring and helping me learn things more thoroughly than ever before. To all the past and present members of the Nomura Research Group, I could not have done this without each of you -- you shared in my accomplishments and my struggles, you kept me going when I wanted to quit, you are why I wanted to come to work every day, and you are why I am so sad that this journey is over. Finally, to now Dr. Sharon Louie, my counterpart throughout these past five years. I am so honored to have shared this experience with you. I feel so lucky to have had an amazing friend and colleague next to me every step of the way and I know that was a major part of my success (and sanity!). I will truly miss working with you and will always be just a text or call away for any help or advice you need – science, personal, general, fitness, food, anything. #LindsayandSharonisPhinisheD! In life To my parents, Joan and Peter Roberts, for investing in my education, for encouraging me and enabling me to explore my passions, for supporting me and always being proud. To my brother, Kevin Roberts, for thinking everything I do is way cooler than it actually is and for always acting interested and trying to understand what I’m talking about. To my grandfather, “PopPop”, for your continued interest and excitement in my work – anytime I became jaded or bored, you kept me going. To my future in-laws, i Sharon Casey and George Littleton, thank you for your constant interest in my work, thank you for bragging for me and celebrating with me, and thank you for reminding me about how special and monumental this all is. To my best friends Marcy and Mac Matthews, thank you for always being available to distract me from science when I needed a break or to listen to me talk about my work when I was excited. Thank you for cooking for me when I was too stressed, and toasting with me when I had accomplishments to commemorate. Thank you for bringing Owen Matthews into my life. Or maybe, more accurately, thank you for letting me help bring Owen into my life. To little Owen, this dissertation is also dedicated to you and your future. I can’t wait to see your amazing accomplishments and contributions to this world, but just remember I put you in my dedication and, fair is fair, I better be in yours! To my amazing fiancé, Dr. Casey Stark, thank you for always knowing how to help me. Thank you for pushing me when I needed a kick, thank you for catching me when I collapsed, thank you for forgiving me when I was stressed and lashed out, thank you for supporting me in every meaning of the word. And to our fur-baby, Kaia Starberts, thank you for reminding me how much more there is to life than science. Thank you for getting us outside to enjoy family time together, breathe in fresh air, and see the natural beauty of the bay area. To my “health team” at the Recreational Sports Facility, Geoffrey Suguitan and Devin Wicks, thank you for providing classes so physically challenging that I forgot about everything else – no matter what was going on at work, I could always handle it after getting some clarity and perspective in one of your classes. Also, thank you for being my friends and allies; I will miss my exercise routine and gossiping with you guys every week. Again, thank you to everyone in this dedication and everyone else with whom I crossed paths these past five years, you all made this work possible. With gratitude (and relief), Lindsay S. Roberts Dr. Lindsay S. Roberts ii TABLE OF CONTENTS CHAPTER ONE: Understanding and Identifying Metabolic Nodes Driving Cancer Cell Pathogenicity Towards Improvements in Future Therapeutic Options.............................1 Introduction ...................................................................................................................2 Metabolomics profiling to reveal new important pathways in cancer............................3 Untargeted, discovery-metabolite profiling as an unbiased metabolomics screening approach.......................................................................................................................6 Activity-based protein profiling to assess enzyme functionality ....................................7 isoTOP-ABPP to map proteome-wide ligandable hotspots ..........................................9 Conclusions ................................................................................................................10 Figures........................................................................................................................11 CHAPTER TWO: Mechanisms Linking Obesity and Cancer .........................................16 Introduction .................................................................................................................17 Inflammation ...............................................................................................................17 Insulin signaling ..........................................................................................................19 Adipokines ..................................................................................................................21