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Canada Archives Canada Published Heritage Direction Du Branch Patrimoine De I'edition University of Alberta UNDERSTANDING THE MOLECULAR BASIS OF SPINAL MUSCULAR ATROPHY by Victoria Elizabeth Cook © A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Master of Science The Centre for Neuroscience Edmonton, Alberta Fall 2008 Library and Bibliotheque et 1*1 Archives Canada Archives Canada Published Heritage Direction du Branch Patrimoine de I'edition 395 Wellington Street 395, rue Wellington Ottawa ON K1A0N4 Ottawa ON K1A0N4 Canada Canada Your file Votre reference ISBN: 978-0-494-47196-8 Our file Notre reference ISBN: 978-0-494-47196-8 NOTICE: AVIS: The author has granted a non­ L'auteur a accorde une licence non exclusive exclusive license allowing Library permettant a la Bibliotheque et Archives and Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par telecommunication ou par Plntemet, prefer, telecommunication or on the Internet, distribuer et vendre des theses partout dans loan, distribute and sell theses le monde, a des fins commerciales ou autres, worldwide, for commercial or non­ sur support microforme, papier, electronique commercial purposes, in microform, et/ou autres formats. paper, electronic and/or any other formats. The author retains copyright L'auteur conserve la propriete du droit d'auteur ownership and moral rights in et des droits moraux qui protege cette these. this thesis. Neither the thesis Ni la these ni des extraits substantiels de nor substantial extracts from it celle-ci ne doivent etre imprimes ou autrement may be printed or otherwise reproduits sans son autorisation. reproduced without the author's permission. In compliance with the Canadian Conformement a la loi canadienne Privacy Act some supporting sur la protection de la vie privee, forms may have been removed quelques formulaires secondaires from this thesis. ont ete enleves de cette these. While these forms may be included Bien que ces formulaires in the document page count, aient inclus dans la pagination, their removal does not represent il n'y aura aucun contenu manquant. any loss of content from the thesis. Canada ABSTRACT Spinal Muscular Atrophy (SMA) is a neuromuscular disorder caused by mutations in the SMNJ gene. Analysis of ChAT, GAP-43 and MyHC proteins in a murine model of mild SMA indicated normal neuromuscular development and regeneration. However, we detected significant delays in denervation-induced muscle fiber atrophy in SMA muscles, which displayed a 29.4% reduction in average fiber CSA while that from WT animals was reduced by 52% 14d post-denervation. This finding may indicate alterations in PI3K/Akt signaling-mediated activation of the ubiquitin-proteasome system. Microarray analysis found substantial overlap of transcriptional changes between spinal cord and skeletal muscle of SMA animals, supporting a common molecular cause of disease in both tissues. We found significant overrepresentation of signaling-related genes, with KEGG pathway analysis specifically implicating MAPK and Wnt signaling. Collectively, findings implicate cell-signaling misregulation in development of SMA pathology. Further work will determine affectedness of PI3K/Akt, MAPK and Wnt signaling in SMA. ACKNOWLEDGEMENTS I would like to thank my supervisors, Drs. Tessa Gordon and Ted Putman, for their extensive help and guidance. I feel privileged to have learned from two individuals so enthusiastic about science. Dr. John Greer has also been very helpful through his role as committee member. I feel extremely grateful for the technical assistance of Ian MacLean and Neil Tyreman, who were not only helpful in the lab, but have also played an important role as friends. I had the pleasure of working with Max Levine as a summer student, and Jo-An Padberg as a practicum student. Both were successful in contributing work for the completion of my thesis. I would like to express my appreciation for the help of Yang Shu, Dr. Esther Udina and Dr. Luke Harris, whose technical assistance and creative guidance were instrumental to the completion of this work. Finally, Karen Martins and Dr. Maria Gallo made the laboratory a positive place to work, and were excellent resources for technical information. I am also grateful to NSERC for their support in the form of a Canada Graduate Scholarship. I am very lucky to have worked with such wonderful individuals, and would like to thank them for making my entire experience enjoyable. Finally, I would like to thank my amazing parents, Elizabeth and Alan, and my incredible friends, especially Dion and Troy. You have all been continually supportive of my work, and actually took the time to read my lengthy thesis drafts and provide constructive feedback. I hope to always make you proud! TABLE OF CONTENTS CHAPTER 1 11 INTRODUCTION 1 1.1.1 Clinical aspects of SMA I 1.1.2 Genetic cause of SMA and modifier genes 3 1.1.3 Effects of SMN deficiency outside of the neuromuscular system 4 1.1.4 Expression and localization ofSMN 5 7.7.5 SMN is essential for snRNP biogenesis 7 1.1.6 SMNfiinctions in neurite outgrowth and mRNA trafficking 9 1.1.7 SMN plays a role in cytoskeletal integrity and actin organization 10 1.1.8 SMN affects actin dynamics in MN 11 1.1.9 SMN affects actin dynamics at the NMJ 13 1.1.10 Animal models of SMA 14 1.1.11 Mouse models used in the present study 17 1.1.12 Proteins integral to neu romuscular growth and development evaluated in the present study 17 1.2 STUDY RATIONALE 19 7.27 Delayed development hypothesis 19 1.2.2 Whole genome expression analysis 19 1.3 REFERENCES 20 CHAPTER 2: EVALUATION OF A DELAYED DEVELOPMENT HYPOTHESIS IN SMA 2.1 INTRODUCTION 37 2.2 METHODS AND MATERIALS 39 2.2.1 Animals 39 2.2.2 Surgeries and tissue removal 39 2.2.3 Choline acetyltransferase activity assay 3 9 2.2.4 Western blot analysis 40 2.2.5 Antibodies for immunohistochemistry 41 2.2.6 Immunohistochemistry 41 2.2.7 Immunohistochemical analyses 42 2.3 RESULTS 43 2.3.1 Choline acetyltransferase activity 43 2. 3.2 Western blot analysis ofGAP-43 in axotomizedMN 45 2.3.3 Immunohistochemical analysis of muscle proteins 50 2.3.3.1. MyHC distribution 50 2.3.3.2. N-CAM expression 50 2.3.3.3. Cytoskeletal protein analysis 61 2.3.3.4. Analysis of muscle atrophy 68 2.4 DISCUSSION 73 2.4.1 Choline acetyltransferase expression 73 2.4.2 GAP-43 expression is not differentially expressed in SMAIII tissue and is upregulated similarly to WT after axotomy 73 2.4.3 Embryonic MyHC expression of does not persist, mature MyHC isoform distribution is unaffected in SMAIII skeletal muscle, and N-CAM staining provides no evidence for denervation in examined tissues 74 2.4.4 Staining for dystrophin, desmin and vimentin in skeletal muscle from Smn-'+-C57Bl'6 and smn-/-A2G-FVB is unremarkable 76 2.4.5 Denervation induced muscle atrophy as measured by fiber CSA is delayed in TAfrom 3 month smn-/-A2G-FVB mice 78 2.4.6 No evidence of developmental delays in nerve or skeletal muscle from SMAIII mice, but discovered delays in denervation-induced atrophy of skeletal muscle, and potential disorganization of the cytoskeletal protein dystrophin 81 2.4.7 Implication of present findings for delayed development hypothesis 82 2.5 REFERENCES 85 CHAPTER 3: GENE EXPRESSION ANALYSIS OF SMAIII MUSCLE AND NERVE 31 INTRODUCTION 96 3.2 METHODS 101 3.2.1 Animals 101 3.2.2 Tissue Removal and RNA extraction 101 3.2.3 cDNA labeling, array hybridization, and scanning 101 3.2.4 Data analysis 102 33 RESULTS 102 3.3.1 Microarray data quality assessment 102 3.3.2 Gene transcription in SMAIIISmn-/-A2G-FVB SpC and SkMrelative to WT-FVB control tissues 104 3.3.3 Incorrect splicing of extracellular matrix and transporter-related genes in SMAII does not lead to overrepresentation of these genes among those affected in SMAIII SpC and SkM 106 3.3.4 Genes showing > 4 fold changes in expression are involved in protein breakdown, energy production, and signaling 108 3.3.5 Significant overlap exists between differentially regulated genes from SpC and SkM from SMAIII Smn-/-A2G-FTrB mice 114 3.3.6 Functional grouping of differentially regulated genes in SpC and SkM from SMAIII Smn--A2G-FVB mice. 117 3.3.6.1. Representation of genes with protein products involved in Development 117 3.3.6.2. Representation of genes with protein products involvedin RNA transport and localization 118 3.3.6.3. Representation of genes with protein products involvedin RNA processing and protein production 119 3.3.6.4. Representation of genes involvedin cell cycle andapoptosis 120 3.3.6.5. Representation of genes with cytoskeleton-related protein Products 121 3.3.6.6. Representation of genes with signaling-related protein Products 122 3.3.7 KEGG pathway analysis of differentially regulated genes in SMAIII Smn--A2G-FVrB SpC and SkM 128 3.4 DISCUSSION 135 3.4.1 More genes were differentially regulated in SMAIII SpC than in SkM 135 3.4.1.1 No sigiiificant overlap between differentially regulated genes in SMAIII SpC and SkM and genes incorrectly spliced in SMAII SpC 136 3.4.1.2 Genes differentially regulated >4fold in SMAIII SpC and SkM have roles in cell signaling, fatty acid oxidation and the proteasome pathway 136 3.4.1.3 Many transcriptional changts are shared and consistent between SMAIII SpC and SkM supporting the idea of a primary lesion common to both tissues in SMA 137 3.4.2 Differentially regulated genes in SMAIII SpC and SkM are NOT overrepresented among RNA-transport.
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