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Evaluating the Therapeutic Potential of the Pak1 and Tbk1 Kinases in Pancreatic Ductal Adenocarcinoma

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Evaluating the Therapeutic Potential of the Pak1 and Tbk1 Kinases in Pancreatic Ductal Adenocarcinoma EVALUATING THE THERAPEUTIC POTENTIAL OF THE PAK1 AND TBK1 KINASES IN PANCREATIC DUCTAL ADENOCARCINOMA Nicole Marie Baker A dissertation submitted to the faculty of the University of North Carolina at Chapel Hill in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Pharmacology Chapel Hill 2016 Approved by: Channing J. Der Adrienne D. Cox Lee M. Graves Gary L. Johnson M. Ben Major © 2016 Nicole Marie Baker ALL RIGHTS RESERVED ii ABSTRACT Nicole Marie Baker: Evaluating the therapeutic potential of the PAK1 and TBK1 kinases in pancreatic ductal adenocarcinoma (Under the direction of Channing J. Der) Pancreatic ductal adenocarcinoma (PDAC) is an extremely lethal cancer characterized by a high frequency (>95%) of activating mutations in the KRAS oncogene, which is a well-validated driver of PDAC growth. However, to date, no successful anti-KRAS therapies have been developed. Inhibitors targeting components of KRAS downstream signaling pathways, when used as monotherapy or in combination, have been ineffective for long-term treatment of KRAS -mutant cancers. Decidedly, the most studied and most targeted KRAS effector pathways have been the RAF-MEK-ERK mitogen-activated protein kinase (MAPK) cascade and the PI3K-AKT-mTOR lipid kinase pathway. The apparent lack of success exhibited by inhibitors of these pathways is due, in part, to an underestimation of the importance of other effectors in KRAS-dependent cancer growth. Additionally, compensatory mechanisms reprogram these signaling networks to overcome the action of inhibitors of the ERK MAPK and PI3K pathways. Consequently, the central hypothesis of my dissertation research is that a better understanding of the role of less studied KRAS effector signaling pathways may lead to more effective therapeutic strategies to block KRAS effector signaling and PDAC growth. Although the TIAM1-RAC1 small GTPase effector pathway has been validated as a driver of KRAS-mutant cancer growth, how RAC1 mediates this role has not been established. My studies aimed to address a possible critical role for the p21-activated kinase iii 1 (PAK1) in this effector pathway. In support of this, I found that PAK1 protein levels are overexpressed both in a subset of pancreatic cancer cell lines and in primary patient tumor samples. Moreover, I determined that stable shRNA-mediated suppression of PAK1 protein expression inhibited the anchorage-dependent and -independent growth of PDAC cell lines in vitro . I also observed that a pharmacologic inhibitor of PAK1 recapitulated the reduced growth phenotypes observed upon genetic ablation of PAK1. As KRAS -mutant tumors are known to upregulate certain cellular processes in order to support the increased metabolic demands of uncontrolled cellular proliferation, I sought to determine whether PAK1 signaling was partially accountable for ensuring that these metabolic needs were met. My studies confirmed a role for PAK1 in regulating macropinocytosis, a mechanism by which PDAC cells acquire macromolecules (e.g., proteins, polysaccharides, and lipids) from the extracellular environment as a source of nutrients. I found that both pharmacologic inhibition and genetic ablation of PAK1 resulted in markedly decreased macropinocytosis in PDAC cells. These data suggest inhibition of PAK1 in KRAS-mutant PDAC could interfere with PDAC metabolism and reduce tumor cell growth. I observed a further reduction in macropinocytosis upon inhibition of PAK1 together with concurrent ERK1/2 or PI3K inhibition. In summary, my results support PAK1 as a promising therapeutic target for pancreatic cancer. My lab and others have provided strong evidence for the key role of a second, less studied KRAS effector pathway, the RalGEF-RAL small GTPase effector pathway, in the growth of pancreatic and other cancers. One critical effector of RAL is the Sec5 component of the exocyst complex. How Sec5 contributes to the role of RAL in cancer remains unresolved. White and colleagues initially identified a Sec5 function independent of exocyst regulation that involved the TANK-binding kinase 1 (TBK1). When a study that searched for synthetic lethal partners of mutant KRAS identified TBK1, these findings suggested that iv TBK1 may be a critical mediator of RalGEF-RAL effector-driven cancer growth. However, a subsequent study questioned the role of TBK1 in the growth of KRAS-mutant cancers. When my lab obtained a novel pharmacologic inhibitor of TBK1, I embarked on studies to determine whether inhibition of TBK1 kinase activity could be an efficacious treatment strategy for PDAC. My studies revealed that inhibition of TBK1 alone led to limited growth inhibition in PDAC cell lines. Furthermore, I found that concurrent inhibition of TBK1 did not enhance the growth inhibitory activity of an ERK inhibitor. However, loss of TBK1 protein via shRNA or pharmacologic inhibition prompted the development of large, intracellular vesicles that appeared to be swollen autolysosomes and the product of non- productive autophagy. This work suggests that TBK1 may play a role in PDAC autophagic flux and provides a rationale for pairing a TBK1 inhibitor with other targeted therapies or chemotherapies to drive these tumor cells towards death. In summary, my studies support my hypothesis that concurrent inhibition of multiple KRAS effector pathways may provide more effective therapeutic strategies for PDAC. They emphasize that single agent therapies targeting KRAS effector signaling will not be effective, a reality that is emerging from ongoing clinical trials. While my studies took a rational approach to identifying these combinations, unbiased chemical library screens with PAK1 and TBK1 inhibitors will likely identify additional combinations of inhibitors for PDAC. v ACKNOWLEDGEMENTS This all started with my parents, aunt, and maternal grandmother. Instead of giving me dolls, Easy Bake Ovens, and other nonsense, they bought me Legos and books about dinosaurs. Instead of watching TRL on MTV, I was watching documentaries on outer space and blue whales. Somewhere in my genetics, I was also given the attitude that I wanted to be as intelligent as possible to better understand the world around me. I learned to eschew religion as a means of explanation, and sought my own answers through a deeper understanding of the natural world. So this really all starts with my parents, Bill and Joanne Baker, my aunt, Jean Dryden, and my grandmother, Grace St. Dennis, who gave me more than they ever had for themselves, and for whose influences I will be forever grateful. I urgently need to acknowledge and thank my elementary, junior high, and high school teachers, who saw enough of something in me to encourage me to reach a potential beyond that of most other children from my slice of the world. Specifically, I’d like to thank Mrs. Denise Cozzolino, Mr. Ken Bell, Ms. Barbara Samara, Mr. Dan Skidmore, Ms. Kathy Roumell, Mr. Gary Scheff, Mrs. Michelle Rollinger-Kaulfield, and Mr. Dan Chesher. Thank you for being excellent teachers and mentors, and for being a positive force of knowledge in my life. I’d be heavily amiss if I did not acknowledge my undergraduate research mentor at Michigan State University. To Dr. Jennifer Ekstrom, wherever you are now, I’m full of gratitude for you taking me into your lab and teaching me the first things I ever learned about research. vi At Pfizer, I’d like to thank John Ceglarek for granting me the opportunity to work in industry and helping me early on to realize my dream of being employed by the best pharmaceutical company in the world… and then promptly convincing me that, yes, I needed to go to graduate school. I have no proper words at my disposal to thoroughly express my gratitude to my mentor, Dr. Channing J. Der. Graduate school is a time of struggle for everyone, and I think especially so for me. I appreciate your understanding and guidance through this process and I’m immeasurably proud to be a part of your research lab and the truly wonderful group of people in it. Thank you for taking a gamble on me and helping me find the wherewithal to be successful, especially when times were tough for me mentally, which was nearly the entirety of graduate school. Also, please keep sending challenging recipes my way and exotic, spherical plants. I am eternally beholden to Dr. Adrienne D. Cox. From scientific suggestions to insight about life and the encouragement to just get out and find the career I really want, not the one that I think I’m supposed to have, I’m forever grateful. Thank you for being my free-of- charge psychoanalyst and therapist, a great theater date, and a cherished role model of incalculable value to my life. The Der Lab atmosphere may have been tempestuous over the course of my tenure as graduate student, but it’s never once been boring. Dr. Tim Martin and Dr. Jeran Stratford, thank you for excellent training and for your cynical attitudes that actually made everything more palatable for a person like me. Dr. Tikvah Hayes, thank you for enduring these years with me and for always being someone with whom I could share a knowing glance across the table… or the auditorium. Dr. Kirsten Bryant, you’re an inspiring role model, an exemplary scientist, a wonderful mother, and an absolute pleasure to work with in the lab. Thank you for your advice, your friendship, and your example. I cannot wait to watch your future lab erupt with methodologies to conquer cancer cell metabolism and defeat vii pancreatic cancer. Samuel George: Jimminy Christmas, I appreciate you for being just so much gosh-dang fun, and I thank you in advance for your cessation of daily “Dad Jokes.” To everyone else currently in the Der Lab, thank you for not being a bag of you-know-what. I truly adore each and every one of you. As for my friends, I quite literally would not be here without Kyle Bradford and Audrey Clemens.
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