Alzheimer’s Disease Pathology as a Clue to Pathogenesis DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Kristen E. Funk Graduate Program in Molecular, Cellular and Developmental Biology The Ohio State University 2012 Dissertation Committee: Jeffrey A. Kuret, PhD, Advisor Christopher J. Phiel, PhD David E. Somers, PhD Mariano S. Viapiano, PhD Copyright by Kristen E. Funk 2012 Abstract Alzheimer’s disease is characterized pathologically by two intracellular lesions, granulovacuolar degeneration and neurofibrillary tangles. Because Alzheimer’s disease is primarily sporadic, the traditional starting point for studying disease is pathology. It is still debated whether these hallmark lesions are markers or mediators of disease progression; however, the correlation between these lesions and disease progression warrants their use as clues to underlying disease processes. The molecular mechanisms of their development, their role in the disease process, and their connection to one another are not fully understood. Granulovacuolar degeneration involves the accumulation of large, double membrane-bound bodies within certain neurons during the course of disease. Because of their ultrastructure, it is hypothesized that the bodies are autophagic. To test this, colocalization of autophagic and endocytic markers with a marker for granulovacuolar degeneration was investigated in hippocampal sections prepared from post mortem late stage Alzheimer’s disease cases using double-label confocal fluorescence microscopy. The resultant immunohistochemical signature suggests that granulovacuolar degeneration bodies accumulate at the nexus of autophagic and endocytic pathways and that failure to complete autolysosome formation may correlate with their formation. Due to its far- ii reaching roles in cells, disruption of the endocytic pathways has the potential to act as a nidus central to disease onset and the development of granulovacuolar degeneration as well as neurofibrillary tangles and amyloid plaques. In sporadic Alzheimer’s disease, neurofibrillary tangle formation is preceded by extensive post-translational modification of tau. To identify the modification signature associated with tau lesion formation at single amino acid resolution, paired helical filaments immunopurified from Alzheimer’s disease brain were subjected to liquid chromatography, tandem mass spectrometry analysis. The resulting spectra identified Lys monomethylation as a new tau modification distributed among seven residues located in the projection and microtubule biding domains of tau protein. One site, K254, was found to be a substrate for a competing Lys modification, ubiquitylation. Double label confocal fluorescence microscopy demonstrated that methylation is wide-spread among neurofibrillary tangles in hippocampal sections prepared from post mortem late- stage Alzheimer’s disease cases. Together these data provide the first evidence that tau in neurofibrillary lesions is modified by Lys methylation. The tau methylation signature involves sites known to mediate disease-related modifications including ubiquitylation and phosphorylation, suggesting that methylation is a candidate modification for influencing tau aggregation, toxicity, and protein turnover. To extend the correlation between methylation occupancy and disease, the modification state of soluble tau protein isolated from cognitively normal human brain was investigated using proteomic methods. Results showed that normal soluble tau is hypermethylated relative to disease-derived tau in its microtubule binding domain. iii Furthermore, recombinant human tau subjected to reductive methylation in vitro retains the normal function of tau as a microtubule-binding and stabilizing protein but its aggregation propensity is greatly attenuated. These data establish Lys methylation as a normal tau post-translational modification in human brain that may protect against pathological tau aggregation during aging. Furthermore, data suggests that enzymes responsible for tau methylation, including methyltransferases and demethylases, may be tractable targets for disease-modifying therapies focused on halting neurofibrillary lesion formation in Alzheimer’s disease. iv Acknowledgements I would first like to thank my advisor, Dr. Jeff Kuret, for his intellectual support and guidance over the time I have been in the lab. He has been a great teacher and mentor always providing an excellent working environment. I would also like to thank my former and current labmates. Kelsey Schafer has been a great lab mate and contributed to the work presented in Chapter 4. Thanks to former lab members Drs. Bhaswati Bandypadhyay and Swati Naphade for teaching me cell culture and immunochemistry techniques. I am grateful for the positive experience and helpful discussions provided by other current and former lab members, Drs. Edward Chang, Katryna Cisek, Nicolette Honson, Jordan Jensen, and Sohee Kim as well as Grace Cooper. I am grateful to Dr. Austin Yang at the University of Maryland, Baltimore and Dr. Stefani Thomas at Johns Hopkins University for their mass spectrometry expertise that launched the studies presented in chapters 3 and 4. Many thanks are due to my graduate committee members, Drs. Christopher Phiel, David Somers, and Mariano Viapiano, for their guidance, suggestions, and time. Thank you to Paula Monsma, manager of the Molecular Neurobiology Imaging Core Facility, for training me on the use of the confocal microscope and providing v valuable feedback on troubleshooting. My gratitude is due to Dr. Robert Mrak at the University of Toledo, the late Dr. Mark Smith and Sandra Siedlak at Case Western Reserve University, and Drs. Paul Coleman and Linda Callahan at the University of Rochester as well as to the Buckeye Brain Bank and the NICHD Brain and Tissue Bank for Developmental Disorders at the University of Maryland, Baltimore for generous access to tissue resources. My sincere appreciation also goes to the individuals and the families of those who have donated the post mortem tissue made available to me, without whom the work herein could not have been done. Finally I would like to thank my parents, Nancy and Rustin Funk, my siblings, Jennifer Baker, Eric Funk and Jason Funk, and all of my family and friends for their love and support over the years. vi Vita 2004…………………………………………….……...Post Secondary Enrollment Option Marietta College 2007…………………………………………………………..Bachelor of Arts in Zoology Miami University 2007-Present………………………………………………...Graduate Research Associate, MCDB Graduate Program The Ohio State University Publications Chang E, Honson NS, Bandyopadhyay B, Funk KE, Jensen JR, Kim S, Naphade S, and Kuret J. Modulation and detection of tau aggregation with small-molecule ligands. Curr Alzheimer Res. 2009; 6: 409-414 Kim S, Jensen JR, Cisek K, Funk KE, Naphade S, Schafer K, and Kuret J. Imaging as a strategy for premortem diagnosis and staging of tauopathies. Curr Alzheimer Res 2010; 7: 230-234 Funk KE, Mrak RE, and Kuret J. Granulovacuolar degeneration (GVD) bodies of Alzheimer's disease (AD) resemble late-stage autophagic organelles. Neuropathol Appl Neurobiol 2011; 37: 295-306 Jensen JR, Cisek K, Funk KE, Naphade S, Schafer KN, and Kuret J. Research towards tau imaging. J Alzheimers Dis. 2011; 26 Suppl 3:147-57 Thomas SN*, Funk KE*, Wan Y, Liao Z, Davies P, Kuret J, and Yang AJ. Dual modification of Alzheimer's disease PHF-tau protein by lysine methylation and ubiquitylation: a mass spectrometry approach. Acta Neuropathol 2012; 123(1):105-117 vii Funk KE and Kuret J. Lysosomal dysfunction as a unifying hypothesis for Alzheimer’s disease pathology. 2012. [In Preparation] Funk KE, Thomas SN, Schafer KN, Yang AJ, and Kuret J. Idenification of lysine methylation of tau as a normal post-translational modification and its effect on normal and pathological function. 2012. [In Preparation] Cisek K, Jensen, J, Funk KE, Darby M, and Kuret J. Oxindole compounds as potential tau-selective imaging agents. 2012. [In Preparation] Field of Study Major Field: Molecular, Cellular and Developmental Biology viii Table of Contents Abstract ............................................................................................................................... ii Acknowledgements ............................................................................................................. v Vita .................................................................................................................................... vii Publications ....................................................................................................................... vii Table of Contents ............................................................................................................... ix List of Tables ................................................................................................................... xiv List of Figures ................................................................................................................... xv List of Abbreviations ....................................................................................................... xvi Chapters 1. Introduction ..................................................................................................................... 1 1.1. Alzheimer’s disease pathology................................................................................