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Downloaded Expression Data and Experimental Design Meta Data from GEO META-ANALYSIS OF GENE EXPRESSION IN MOUSE MODELS OF NEURODEGENERATIVE DISORDERS by Cuili Zhuang B.Sc. Biology, The University of British Columbia, 2009 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Bioinformatics) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) April 2017 © Cuili Zhuang, 2017 Abstract There is intense interest in understanding the molecular mechanisms that contribute to neurodegenerative disorders (NDs), which involve complex interplays of genetic and environmental factors. To catch early events involved in disease initiation requires investigation on pre-symptomatic brain samples. It is difficult to capture early molecular events using post- mortem human brain samples since these samples represent the late phase of the disorder with progressive brain damage and neurodegeneration. Disease mouse models are developed to study disease progression and pathophysiology. Here, I focus on two of the most studied NDs: Alzheimer’s disease (AD) and Huntington’s disease (HD). Mouse models developed for the disease (AD or HD) often share similar phenotypes mimicking human disease symptoms, which suggest potential common underlying mechanisms of disease initiation and progression across mouse models of the same disease. Investigation of gene expression profiles of pre-symptomatic animals from different mouse models may shed light on the mechanisms occurred in the early disease phase. Gene expression profiling analyses have been performed on mouse models and some of the studies investigate the molecular changes in pre-symptomatic phase of AD and HD respectively. However, their findings have not reached a clear consensus. To identify shared molecular changes across mouse models, I conducted a systematic meta-analysis of gene expression in mouse models of AD and HD, consisted of 369 gene expression profiles from 23 independent studies. The goal of this project is to identify transcriptional alterations shared among different mouse models of each disease respectively, especially changes during early disease phase that may link to disease-causing mechanisms, and potential common cross-disease changes. For both of the disorders, the results showed subtle but biologically interpretable changes shared across mouse models in the early disease phase that may contribute to the early disease progression: dysregulation of genes involved in cholesterol biosynthesis and complement system in AD mouse models and genes encoding mitochondrial respiratory chain complexes in HD mouse models. Cross-disease similarities in the late phase suggested that different brain regions may share mechanisms in response to neuronal loss and toxic protein aggregates. ii Preface The idea to perform a meta-analysis of gene expression of neurodegenerative disorders was initiated by my supervisor Dr. Paul Pavlidis. With his guidance, I was responsible for the design and analysis of the research presented. The motivation for investigating cross-disease similarities was from the NeuroGEM project, our collaboration with Dr. Jörg Gsponer and his group. I was responsible for the writing of this thesis, with useful suggestions and editing from Dr. Paul Pavlidis and Dr. Lilah Toker. None of the chapters or combination of this research has been published yet. However, manuscripts are planned. iii Table of Contents Abstract .......................................................................................................................................... ii Preface ........................................................................................................................................... iii Table of Contents ......................................................................................................................... iv List of Tables ................................................................................................................................ vi List of Figures .............................................................................................................................. vii Glossary ...................................................................................................................................... viii Acknowledgements ...................................................................................................................... ix Dedication .......................................................................................................................................x Chapter 1: Introduction ................................................................................................................1 1.1 Alzheimer’s disease ........................................................................................................ 1 1.1.1 AD pathological hallmarks: amyloid plaques and neurofibrillary tangles ................. 1 1.1.2 AD genetic risk factors ............................................................................................... 3 1.2 Huntington’s disease ....................................................................................................... 4 1.2.1 HD disease-causing gene: HTT ................................................................................... 4 1.2.2 HD genetic modifiers .................................................................................................. 5 1.3 Common mechanisms in AD and HD. ........................................................................... 6 1.4 Investigate early events involved in AD and HD initiation with disease mouse models in pre-symptomatic phase. .......................................................................................................... 6 1.5 Mouse models of AD and HD ........................................................................................ 7 1.5.1 AD mouse models ....................................................................................................... 7 1.5.2 HD mouse models ....................................................................................................... 8 1.6 Cell-type proportion changes in the brains of AD and HD. ......................................... 12 1.7 Transcriptomic analyses in AD and HD mouse models. .............................................. 12 1.7.1 Transcriptomic analyses in AD mouse models ......................................................... 13 1.7.2 Transcriptomic analyses in HD mouse models ......................................................... 13 1.8 Meta-analysis of gene expression ................................................................................. 13 1.8.1 Methods of meta-analysis ......................................................................................... 14 1.8.2 Meta-analysis on gene expression in AD.................................................................. 14 1.8.3 Meta-analysis on gene expression in HD.................................................................. 15 iv 1.9 Motivations ................................................................................................................... 15 Chapter 2: Materials and Methods ............................................................................................17 2.1 Data retrieval from GEO ............................................................................................... 17 2.2 Data pre-processing and quality control ....................................................................... 19 2.3 Dividing samples into early and late disease phases and combining data sets. ............ 19 2.4 Estimate cell-type proportion changes .......................................................................... 20 2.5 Fitting linear mixed-effects models and applying jackknife procedure to rank genes . 21 2.5.1 Linear mixed-effects model to correct for between-study variations. ...................... 22 2.5.2 Linear mixed-effects model to correct for between-study variations and cell-type proportion changes ................................................................................................................ 23 2.5.3 Jackknife procedure for gene ranking ....................................................................... 24 2.6 Functional enrichment analysis..................................................................................... 25 Chapter 3: Results........................................................................................................................29 3.1 Estimation of cell-type proportion changes .................................................................. 30 3.1.1 Estimation of cell-type proportion changes in AD mouse models ........................... 30 3.1.2 Estimation of cell-type proportion changes in HD mouse models ........................... 31 3.2 Meta-analysis of gene expression in Alzheimer’s disease mouse models .................... 36 3.3 Meta-analysis of gene expression in Huntington’s disease mouse models .................. 40 3.4 Cross-disease comparison revealed similarities in the late phase of AD and HD. ....... 67 Chapter 4: Discussion and Conclusion ......................................................................................68 4.1 Consistent transcriptomic alterations were identified across different mouse models for each disorder. ............................................................................................................................ 68 4.2 Applying
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