The Prion Protein Is Embedded in a Molecular Environment That Modulates Transforming Growth Factor Β and Integrin Signaling
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The Prion Protein is Embedded in a Molecular Environment that Modulates Transforming Growth Factor β and Integrin Signaling by Farinaz Ghodrati A thesis submitted in conformity with the requirements for the degree of Master of Science Department of Laboratory Medicine and Pathobiology University of Toronto © Copyright by Farinaz Ghodrati 2018 The Prion Protein is Embedded in a Molecular Environment that Modulates Transforming Growth Factor β and Integrin Signaling Farinaz Ghodrati Master of Science Department of Laboratory Medicine and Pathobiology University of Toronto 2018 Abstract The prion protein (PrP) is known for its fundamental role in a group of neurodegenerative disorders, aptly called prion diseases. The function of the normal cellular prion protein (PrPC) as well as the underlying molecular mechanisms that lead to neurotoxicity in disease are still unresolved. The previously discovered evolutionary relationship between PrP and ZIP zinc transporters implicated PrPC in morphogenetic reprogramming events but also uncovered surprising differences when comparing signaling pathways downstream of PrPC in separate cellular paradigms. To extend this line of research, we combined CRISPR-Cas9-based genetic engineering to generate four relevant murine PrP-deficient cell models, with quantitative mass spectrometry-based analyses to compare the molecular environment of PrP in these models. Interestingly, a unified theme emerged from these studies that placed PrPC in a specialized membrane domain that modulates TGF beta and integrin signaling. ii Acknowledgments First and foremost, I would like to wholeheartedly thank my supervisor, Dr. Gerold Schmitt-Ulms for his exceptional mentorship and unwavering support throughout my studies. I credit his genuine passion and dedication to research and his keen scientific mind with helping me grow both personally and professionally over these last two years. Though my time under his mentorship has now ended, I will take the lessons I’ve learned here with me onwards through my career. I would also like to extend my thanks to the members of my advisory committee – Dr. Joel Watts and Dr. Sunit Das. Their advice and guidance have helped me immensely in my research. Additionally, many thanks to the tireless efforts of the Department of Laboratory Medicine and Pathobiology’s Graduate Coordinator, Dr. Harry P. Elsholtz, and the Graduate Administrator, Rama Ponda. I am also tremendously grateful for the pleasure and privilege of collaborating with past and present members of the Schmitt-Ulms lab – Dr. Hansen Wang, Louisa Wang, and Michael Solarski. My time here would not have been as productive or enjoyable without them. Special thanks to Dr. Declan Williams, who helped move this project leaps and bounds with his invaluable guidance and expertise in the field of mass spectrometry. And finally, this entire project would not have been possible without the accomplishments of Dr. Mohadeseh Mehrabian. To her, I express my immense gratitude for her untiring mentorship, guidance and, above all, friendship. Lastly, I would like to thank my friends and family for their love, patience, and support over the years, specifically, AS, NS, NR, NM and ABZ, for your unique sense of humour. I would also want to express my thanks to the colleagues at the Tanz CRND who provided me with tremendous scientific and personal support during my degree. And above all, my utmost appreciation to my parents for being such amazing sources of strength and support. iii Table of Contents Acknowledgments .................................................................................................................. iii Table of Contents ................................................................................................................... iv List of Tables ......................................................................................................................... vii List of Figures ....................................................................................................................... viii List of Appendices .................................................................................................................. ix Abbreviations .......................................................................................................................... x Chapter 1 ............................................................................................................................... 1 The Prion Protein: What We Do and Don’t Know ............................................................ 1 1.1 Introduction ......................................................................................................................... 1 1.2 Prion diseases ...................................................................................................................... 1 1.2.1 Overview of prion diseases ..................................................................................................... 1 1.2.2 Inherited human prion diseases ............................................................................................. 2 1.2.3 Acquired human prion diseases ............................................................................................. 3 1.2.4 Sporadic human prion diseases .............................................................................................. 5 1.3 Prion propagation ................................................................................................................ 7 1.3.1 How the prion concept came to be ........................................................................................ 7 1.3.2 PrPC expression is essential for prion infection ....................................................................... 8 1.3.3 Prion toxicity ........................................................................................................................... 9 1.4 Structure of the prion protein ............................................................................................ 10 1.4.1 Overview of the structural features of PrP ........................................................................... 10 1.4.2 Proteolytic processing of PrP ................................................................................................ 11 1.5 Evolutionary origin of the prion protein ............................................................................. 12 1.5.1 Discovery of the PrP-ZIP connection .................................................................................... 12 1.5.2 How PrP evolved from ZIP ancestors .................................................................................... 13 1.5.3 Further proof on the family reunion of PrP and ZIPs ............................................................ 14 1.6 Proposed functions of the prion protein ............................................................................. 15 1.6.1 Overview of the roles ascribed to PrPC ................................................................................. 15 1.6.2 Epithelial-to-mesenchymal transition .................................................................................. 16 1.6.3 Additional PrP-related phenotypes ...................................................................................... 17 iv 1.7 Methodology background .................................................................................................. 18 1.7.1 Overview of the experimental workflow .............................................................................. 18 1.7.2 Cell models ........................................................................................................................... 19 1.7.3 CRISPR-Cas9 knockout technology ....................................................................................... 20 1.7.4 Affinity capture matrix .......................................................................................................... 22 1.7.5 Mass spectrometry ............................................................................................................... 22 Chapter 2 .............................................................................................................................. 25 Rationale, Hypothesis and Objectives ............................................................................ 25 2.1 Rationale for the ZIP study ................................................................................................. 25 2.2 Rationale for the PrP interactome study ............................................................................ 26 Chapter 3 .............................................................................................................................. 28 ZIP6-mediated NCAM1 Phosphorylation ........................................................................ 28 3.1 Introduction ....................................................................................................................... 29 3.2 Results ............................................................................................................................... 30 3.2.1 In vitro phosphorylation of the longest NCAM1 isoform by GSK3B ..................................... 30 3.3 Discussion .......................................................................................................................... 32 3.4 Methods ...........................................................................................................................