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UC San Diego Electronic Theses and Dissertations UC San Diego UC San Diego Electronic Theses and Dissertations Title Systems analysis of model organisms in the study of human disease phenotypes Permalink https://escholarship.org/uc/item/665114b4 Author Gersten, Merril Joy Publication Date 2011 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Systems Analysis of Model Organisms in the Study of Human Disease Phenotypes A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics and Systems Biology by Merril Joy Gersten Committee in charge: Professor Shankar Subramaniam, Chair Professor Gabriel G. Haddad, Co-Chair Professor Christopher K. Glass Professor Trey Ideker Professor Wei Wang 2011 Copyright (or ©) Merril Joy Gersten, 2011 All rights reserved. The Dissertation of Merril Joy Gersten is approved, and it is acceptable in quality and form for publication on microfilm and electronically: _____________________________________________________________________ _____________________________________________________________________ _____________________________________________________________________ _____________________________________________________________________ Co-Chair _____________________________________________________________________ Chair University of California, San Diego 2011 iii DEDICATION To my parents Who inspired me To my children Whom I try to inspire And to my husband Who makes all things possible iv TABLE OF CONTENTS Signature Page ............................................................................................................. iii Dedication ..................................................................................................................... iv Table of Contents .......................................................................................................... v List of Figures ............................................................................................................ viii List of Tables ................................................................................................................ ix List of Supplemental Figures ....................................................................................... x List of Supplemental Tables ....................................................................................... xi Acknowledgements ..................................................................................................... xii Vita ............................................................................................................................... xv Abstract of the Dissertation ...................................................................................... xvi 1. INTRODUCTION ................................................................................................... 1 2. AN INTEGRATED SYSTEMS ANALYSIS IMPLICATES EGR1 DOWNREGULATION IN SIVE- INDUCED NEURAL DYSFUNCTION .................................................................................................... 10 Abstract .................................................................................................................... 10 Introduction .............................................................................................................. 11 Results ...................................................................................................................... 13 Expression analysis of SIV-infected macaques ................................................... 13 Identification of transcriptionally active network modules ................................. 13 Functional enrichment of active network modules .............................................. 17 Network module analysis implicates EGR1 in SIVE-induced dementia ............. 18 EGR1 expression in neurons ............................................................................... 21 CCL8 downregulates EGR-1 in differentiated SK-N-MC cells ........................... 22 Discussion ................................................................................................................ 25 Materials and Methods ............................................................................................. 31 Ethics Statement .................................................................................................. 31 Human Protein Interaction Network ................................................................... 31 Rhesus Macaques ................................................................................................ 32 Microarray .......................................................................................................... 33 Immunohistochemistry ......................................................................................... 34 v Data Integration .................................................................................................. 35 Cell Culture ......................................................................................................... 36 Flow Cytometry ................................................................................................... 37 Macrophage Supernatant .................................................................................... 38 Western Blot ........................................................................................................ 38 RT-PCR ............................................................................................................... 39 Supplemental Figures ............................................................................................... 41 Supplemental Tables ................................................................................................ 43 Acknowledgements .................................................................................................. 67 3. GENOMIC SEQUENCING OF HYPOXIA-ADAPTED FLIES ...................... 68 Introduction .............................................................................................................. 68 Methods and Results ................................................................................................ 72 Notch Signaling Pathway .................................................................................... 72 Wnt Signaling Pathway ....................................................................................... 80 Discussion ................................................................................................................ 87 Supplemental Figures ............................................................................................... 92 Supplemental Tables ................................................................................................ 94 Acknowledgements ................................................................................................ 111 4. TRANSCRIPTIONAL ANALYSIS OF HYPOXIA-ADAPTED FLIES........ 112 Introduction ............................................................................................................ 112 Methods .................................................................................................................. 114 Results .................................................................................................................... 118 Discussion .............................................................................................................. 134 Supplemental Tables .............................................................................................. 140 Acknowledgements ................................................................................................ 145 5. EXPERIMENTAL VALIDATION OF WNT PATHWAY ACTIVATION IN TOLERANCE TO HYPOXIA IN FLIES .................................................... 146 Introduction ............................................................................................................ 146 Methods .................................................................................................................. 149 Results .................................................................................................................... 151 Neurons ............................................................................................................. 151 Hemocytes ......................................................................................................... 155 Discussion .............................................................................................................. 159 Supplemental Tables .............................................................................................. 162 Acknowledgements ................................................................................................ 166 6. CONCLUSIONS .................................................................................................. 167 vi REFERENCES ......................................................................................................... 170 vii LIST OF FIGURES Figure 2.1 Overview of analysis process .................................................................. 14 Figure 2.2 Highest scoring significant modules ....................................................... 16 Figure 2.3 Significant modules containing selected downregulated genes and RT-PCR confirmation ............................................................................
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