Sequential Proteolysis by γ-Secretase and Its Implications for Alzheimer’s Disease The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Fernandez, Marty. 2015. Sequential Proteolysis by γ-Secretase and Its Implications for Alzheimer’s Disease. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:17467510 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Sequential proteolysis by !-secretase and its implications for Alzheimer’s disease A dissertation presented by Marty Alyse Fernandez to The Division of Medical Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Biological Chemistry and Molecular Pharmacology Harvard University Cambridge, Massachusetts May 2015 2015 - Marty Alyse Fernandez All rights reserved. Dissertation Advisor: Dr. Michael S. Wolfe Marty Alyse Fernandez Sequential proteolysis by !-secretase and its implications for Alzheimer’s disease Abstract The production and aggregation of the amyloid !-peptide (A!) is thought to play a central role in Alzheimer’s disease (AD) pathogenesis. The presenilin (PS)-containing "-secretase complex cleaves the amyloid !-protein precursor C-terminal fragment (APP CTF!) to generate A!s of 38-49 residues. Evidence suggests that these A!s are the result of successive "-secretase cleavages, which are thought to start at the # sites to generate A!48 or A!49, followed by C- terminal trimming mostly every three residues to produce secreted A!s. Specifically, two product lines have been proposed: the A!49-46-43-40 line and the A!48-45-42-38 line. An increased proportion of aggregation-prone A!42 compared to A!40 is believed to be important in AD pathogenesis. Despite the apparent relevance of the production of the A! C-terminus in AD, questions surround the mechanisms by which "-secretase generates the A! spectrum and how familial AD-causing (FAD) mutations alter A! production. This dissertation first examined the C-terminal trimming function of "-secretase and how PS FAD mutations alter this activity. We found that synthetic A!49, A!48, A!46, and A!45 are trimmed to A!40 and A!42 by "-secretase in vitro. Moreover, our results were consistent with the two-pathway model in which A!49 is primarily converted to A!40 and A!48 to A!42, but also demonstrated a small degree of crossover between the pathways. Most importantly, we iii found that PS1 FAD mutations dramatically reduce the efficiency of trimming of #-cleaved A!s, particularly the trimming of A!49 to A!40. We also investigated substrate determinants for # site endoproteolysis and C-terminal trimming of APP CTF! by "-secretase. The deletion of residues around the # sites indicated that upstream sequences, and not depth within the transmembrane domain, are the determinants of # site specificity. We also show that instability of the APP CTF! transmembrane helix near the # site increases endoproteolysis, and that instability near the carboxypeptidase cleavage sites facilitates C-terminal trimming by "-secretase. Last, the potential role of A!45-49 in AD pathogenesis was considered. We did not detect these A! species in AD brains by immunoprecipitation and western blot. However, we developed cellular systems to investigate their toxicity and obtained preliminary data suggesting that these A!s may be neurotoxic. iv TABLE OF CONTENTS Title Page Prefix: Table of figures and tables vi Acknowledgements and dedication viii Chapter 1: Introduction 1 Chapter 2: Alzheimer presenilin-1 mutations dramatically reduce trimming of 39 long amyloid !-peptides (A!) by "-secretase to increase 42-to-40-residue A! Chapter 3: Transmembrane substrate determinants for "-secretase processing 76 of APP CTF! Chapter 4: Investigation of the pathogenicity of #- and $-cleaved A! peptides 119 Chapter 5: Conclusions and future directions 149 Appendix: Supplementary figures 163 v TABLE OF FIGURES AND TABLES Figure Title Page Figure 1.1 Proteolytic processing of APP by %-, !-, and "-secretases 4 Figure 1.2 The components of the "-secretase complex 13 Figure 1.3 Dual "-secretase cleavage sites within APP CTF! 18 Figure 1.4 "-secretase processing of the APP CTF! transmembrane domain 20 Figure 2.1 "-secretase trims synthetic A!49 and A!48 to A!40 and A!42 in vitro 47 Figure 2.2 "-secretase modulators lower A!42 produced from A!49 and A!48 50 Table 2.1 A!42/A!40 ratios from trimming of #- and $-cleaved A!s 52 Figure 2.3 "-secretase trims p3/A!49 and p3/A!48 to p3/A!40 and p3/A!42 54 in cells Figure 2.4 "-secretase trims synthetic A!45, A!46, and A!47 to A!40 and A!42 56 in vitro Figure 2.5 A!49 and A!48 conversions to A!40 and A!42 by "-secretase are 59 dramatically reduced by PS1 FAD mutations Table 2.2 Vmax and Km of A! trimming events from WT and PS1 FAD-mutant 61 "-secretase Table 2.3 Catalytic efficiencies of trimming of A!49 and A!48 to A!40 and A!42 63 as a percent of WT PS1 Table 2.4 Rate of trimming A!46 and A!49 to A!40 as a percent of WT PS1 65 Figure 2.6 FAD-mutant PS1-"-secretase complexes increase A!42/40 independent 67 of effects on #-site endoproteolysis Figure 3.1 "-secretase trims A!49 and A!49 with a C-terminal amide to generate 85 primarily A!40 Figure 3.2. "-secretase has S1’, S2’, and S3’ pockets 88 vi Figure 3.3. Deletion of residues around the # sites does not alter the primary A! 90 cleavage products Figure 3.4. Depth within the transmembrane domain is not a determinant of 93 #-site specificity Figure 3.5. Helical instability between the # and $ sites is important for 97 endoproteolysis at the # site Figure 3.6. Helical instability between the # and $ sites and trimming 99 Figure 3.7. Helical instability between $ and " sites and " and "’ site does not 101 affect endoproteolysis at the # site Figure 3.8. Helical propensity between $ and " sites and " and "’ sites and 103 trimming Figure 4.1 A!45-49 are primarily in the cell membrane 129 Figure 4.2 Analysis of A!45-49 in AD brain samples 131 Figure 4.3 Development of inducible APP$- and APP#-expressing N2a cell lines 135 Figure 4.4 Analysis of long A! toxicity in differentiated SH-SY5Y cells 137 Figure S1 Mass spectrometric analysis of the A!s generated from CTF! 164 deletion mutants Figure S2 Mass spectrometric analysis of the A!s generated from # to $ site 166 helical stability mutant CTF!s Figure S3 Mass spectrometric analysis of the A!s generated from $ to " site 167 and " to " ‘ site helical stability mutant CTF!s vii Acknowledgements I would first like to thank Dr. Wolfe for allowing me to work on these projects and for being a patient, enthusiastic, and generous mentor and teacher. I am very lucky to have found a lab to join with a PI who is motivated not only by an endless interest in science, but also by a genuine desire to help people. Dr. Wolfe was always available for advice on problems large and small, and if I ever went into a meeting feeling anxious or discouraged by experimental troubles or negative results, I would always leave more excited than before to pursue a solution or new idea that had come up. In my mind, this is a sign of a great mentor. I also thank my labmates, who have been both friends and teachers to me. It has been a wonderful experience working with people who are always willing to help and who are happy to share their extensive knowledge and expertise. I could not have asked for a better group of people to have worked with and to have celebrated publications, new jobs, weddings, and birthdays with throughout the years. I also thank my colleagues in the CND for being an extension of my lab, always willing to help and great friends. They were also kind (or, should I say unkind?!) enough to select me as the involuntary president of the CND “Beer Camp,” during which we shared many a fun evening. I thank all of the students I had the opportunity to mentor for all of their hard work in the lab, their refreshing enthusiasm that was heart-warming to see on days that I was discouraged by failed experiments, and for allowing me to learn about teaching and managing students. I also thank my advisory committee. As a nervous student embarking on my PhD, I never thought I would say that committee meetings were fun, but my advisors were able to accomplish just that with their sage advice and thought-provoking conversations. I also thank my classmates in the viii BBS program for often teaching me as much as the class lecturers and for always being willing to lend a hand. Most importantly, I thank my family. I am indebted to my parents for their endless love, support, and encouragement. They instilled in me the importance of learning and doing well in school, and taught by example the value of working hard. I thank my brother for being my first and most loyal friend, my friends and extended family for making my life rich and fun, and my friends in Boston for making this city a home.