Comparative genome analysis in rodent models of Parkinson’s disease and spinocerebellar ataxia type 3 by Nivretta Thatra B.S. Neurobiology, The University of Washington, 2014 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) May 2019 © Nivretta Thatra, 2019 The following individuals certify that they have read, and recommend to the Faculty of Graduate and Postdoctoral Studies for acceptance, a thesis/dissertation entitled: Comparative genome analysis in rodent models of Parkinson’s disease and spinocerebellar ataxia type 3 submitted by Nivretta Thatra in partial fulfillment of the requirements for the degree of Master of Science in Bioinformatics Examining Committee: Dr. Jörg Gsponer Co-supervisor Dr. Paul Pavlidis Co-supervisor Dr. Sara Mostafavi Supervisory Committee Member Dr. Weihong Song Additional Examiner Additional Supervisory Committee Members: Dr. Martin Hirst Supervisory Committee Member Supervisory Committee Member ii Abstract The shared hallmarks of neurodegenerative diseases (NDs) – notably, the existence of protein deposits,1 selective vulnerability of cell types,2 chronic neuroimmune response,3 and early dysfunction in brain vasculature4 – support the idea of studying different transgenic models relevant to NDs in concert rather than separately. Indeed, transgenic models of different NDs, namely Parkinson’s disease (PD) and spinocerebellar ataxia type 3 (SCA3), show comparable behavioral abnormalities and some similarities in cell loss. In this project, we hypothesized the reflection of these previously characterized similarities at the transcriptomic level in transgenic models of PD and SCA3, and that prioritizing overlaps in gene expression across transgenic models might allow the identification of genes that are involved in pathological pathways relevant to more than one ND. I show in an unpublished dataset of rodent transcriptomes from two time points and up to three brain regions that most overlaps in gene expression patterns are specific both to the brain region and time point from which samples are obtained. Overlaps in gene expression are found between transgenic models that study the effects of the same gene, synuclein alpha (Snca). In examining the overlaps of the interpretations of gene expression via cell type proportional estimations and functional analysis, I find commonalities across models suggesting changes in endothelial cells at the earlier time point and oligodendrocytes at the later time point. iii Lay Summary Many neurodegenerative diseases (NDs) share common features, like the death of specific brain cells and protein deposits in brain cells. With therapeutic aims, researchers hope to find genes associated with these protein deposits or dying brain cells that can be targeted by drugs to help those with NDs. Since brain tissue from humans is difficult to obtain, many investigations are conducted with animal models that are relevant to human disease. In this project, I looked for gene overlaps in rodent models that are relevant to two human NDs (Parkinson’s disease and spinocerebellar ataxia type 3). I show that most overlaps in gene expression occur when the rodent models are related to each other. Otherwise, overlaps in gene expression seem to be associated with changes in brain cell type proportion estimations, perhaps due to cell death. iv Preface The research initiative presented in this paper – to compare different transgenic models of neurodegenerative diseases – was originally proposed in the NeuroGEM project, which both my supervisors Dr. Jörg Gsponer and Dr. Pavlidis are a part of. Our collaborator and NeuroGEM member Dr. Olaf Riess of The University of Tübingen was responsible for overseeing collection of the data by members of his group before it was sent our way. Following data transfer, I was responsible for the analysis of the data presented here. I wrote this thesis with suggestions from Drs. Gsponer and Pavlidis. All chapters and results are as yet unpublished, though manuscripts are planned. v Table of Contents Abstract ......................................................................................................................................... iii Lay Summary ............................................................................................................................... iv Preface .............................................................................................................................................v Table of Contents ......................................................................................................................... vi List of Tables ............................................................................................................................... xii List of Figures ............................................................................................................................. xiii List of Abbreviations ................................................................................................................. xiv Acknowledgements ......................................................................................................................xv Dedication ................................................................................................................................... xvi Chapter 1: Introduction ................................................................................................................1 1.1 Parkinson’s disease ......................................................................................................... 2 1.1.1 SNCA ........................................................................................................................... 3 1.1.2 Aggregation and toxicity of α-synuclein .................................................................... 4 1.2 Spinocerebellar ataxia type 3 .......................................................................................... 5 1.2.1 ATXN3 ......................................................................................................................... 5 1.2.2 Aggregation and toxicity of ataxin-3 .......................................................................... 5 1.3 Overlapping pathways in neurodegenerative diseases .................................................... 6 1.3.1 Aggregation................................................................................................................. 7 1.3.2 Specific cell types ....................................................................................................... 8 1.3.2.1 Cell types in PD .................................................................................................. 9 1.3.2.2 Cell types in SCA3............................................................................................ 10 vi 1.3.2.3 Cell type proportion estimation ........................................................................ 10 1.3.3 Microglia and inflammation ..................................................................................... 11 1.3.4 Parkinsonism and levodopa-responsive PD in SCA3 ............................................... 12 1.4 Current state of rodent models of NDs ......................................................................... 13 1.4.1 Current state of rodent models of PD ....................................................................... 14 1.4.2 SNCA overexpression rat model relevant to PD ....................................................... 15 1.4.3 Snca KO mouse model relevant to PD ..................................................................... 16 1.4.4 Snca KO and SNCA overexpression mouse model relevant to PD ........................... 16 1.4.5 Current state of rodent models of SCA3 ................................................................... 17 1.4.6 Mutant ATXN3 model of SCA3 ................................................................................ 18 1.5 Transcriptional analyses................................................................................................ 18 1.5.1 Transcriptional analyses in rodent models of PD ..................................................... 19 1.5.2 Transcriptional analyses in rodent models of SCA3................................................. 19 1.6 Methods of assessing overlaps of gene lists ................................................................. 20 1.7 Aims .............................................................................................................................. 20 Chapter 2: Materials and methods .............................................................................................22 2.1 Data ............................................................................................................................... 22 2.2 Data quality control and pre-processing ....................................................................... 24 2.3 Fitting linear models ..................................................................................................... 27 2.3.1 Sub-setting the data by age ....................................................................................... 27 2.3.2 Sub-setting the data by age and tissue ...................................................................... 28 2.4 Functional enrichment .................................................................................................