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Limb Girdle Muscular Dystrophy in the Hutterite Population of North America

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Limb Girdle Muscular Dystrophy in the Hutterite Population of North America Limb Girdle Muscular Dystrophy in the Hutterite Population of North America by Patrick Frosk A Thesis Submitted to the Faculty of Graduate Studies in Fulfilment of the Requirements for the Degree of Doctor of Philosophy Department of Biochemistry and Medical Genetics University of Manitoba Winnipeg, Manitoba ©Patrick Frosk, April 2005 Table of Contents Table of Contents i Abstract iv Acknowledgements vi List of Figures viii List of Tables ix List of Abbreviations x List of Manufacturers xii Chapter 1: Introduction 1 Chapter 2: Review of Limb Girdle Muscular Dystrophies 3 2.1 General Features of LGMD 3 2.2 Dominant Forms 6 (A) LGMD1A 6 (B) LGMD1B 9 (C) LGMD1C 18 (D) LGMD1D 24 (E) LGMD1E 25 (F) LGMD1F 26 (G) LGMD1G 27 2.3 Recessive Forms 28 (A) LGMD2A 28 (B) LGMD2B 31 (C) LGMD2C – 2F, Sarcoglycanopathies 34 (D) LGMD2G 39 (E) LGMD2H 42 (F) LGMD2I 42 (G) LGMD2J 42 2.4 Pathogenic Themes 46 Chapter 3: Materials and Methods 52 3.1 Patient Resources 52 3.2 Genomic DNA Isolation 53 3.3 Polymerase Chain Reaction (PCR) 54 (A) Primer design 54 i (B) General method 54 (C) Fragment analysis 56 3.4 Genotyping and Analysis 57 (A) Short tandem repeats (microsatellites) 57 (B) Single nucleotide polymorphisms (SNP) 57 (C) Linkage analysis 58 (D) Haplotype analysis 58 3.5 Mutation Screening 58 (A) Single stranded conformational polymorphism analysis 58 (B) Sequencing, alignments, and analysis 59 3.6 Northern Blot 60 3.7 Plasmid Production 61 3.8 Protein Electrophoresis 63 (A) Sodium dodecyl sulfate - polyacylamide gel electrophoresis 63 (B) General protein stains 64 (C) Immunoblot 64 3.9 Cell Culture 65 3.10 Immunofluorescence 66 3.11 Bacterial Two Hybrid Screening 67 Chapter 4: Identification and characterization of the LGMD2H gene 70 4.1 Introduction 71 4.2 Results 72 (A) Subjects 72 (B) Haplotype analysis 74 (C) Physical mapping 74 (D) Mutation screening 78 (E) Tissue specific expression 83 (F) Subcellular localization 91 (G) Interaction screening 96 4.3 Discussion 101 Chapter 5: Identification of the LGMD2I gene 108 5.1 Introduction 109 5.2 Results 111 (A) Subjects 111 ii (B) Genome scan and haplotype analysis 113 (C) Mapping and mutation identification 114 (D) Genotype-phenotype correlations 120 (E) Natural history of the common LGMD2I mutation 127 5.3 Discussion 133 Chapter 6: Identification of the STM gene 137 6.1 Introduction 138 6.2 Results 139 (A) Subjects 139 (B) DNA analysis 140 (C) Muscle pathology 140 6.3 Discussion 144 Chapter 7: Conclusions and future directions 150 References 156 Appendices 183 1. Consent form for patients and family 2. Ethics approval 3. Primer sequences 4. Plasmid maps iii Abstract Limb girdle muscular dystrophies (LGMDs) are a clinically and genetically heterogeneous group of myopathies characterized by weakness and wasting of the proximal musculature. There are currently seventeen loci associated with different LGMDs, seven with an autosomal dominant mode of inheritance (LGMD1A–1G) and 10 with an autosomal recessive mode of inheritance (LGMD2A– 2J). The cumulative worldwide prevalence of LGMD is thought to be ~1/15,000.191 In the Hutterite population of North America there is an over-representation of autosomal recessive LGMD with a prevalence estimated to be >1/400. The objective of this work was to delineate the genetic basis of LGMD in this large genetically isolated population. A genome-wide scan was performed on Hutterite LGMD patients and their families in order to locate the mutant gene. This allowed us to identify a novel locus at chromosome region 9q31-33 that was named LGMD2H.279 Extensive haplotyping and mutation screening led to the discovery of c.1459G>A in TRIM32 as the causative mutation of LGMD2H.91 We then found that this same mutation was the cause of another previously described myopathy in the Hutterites, sarcotubular myopathy (STM). Analysis of the TRIM32 gene product revealed that it is a potential E3-ubiquitin ligase, is expressed in many human tissues including muscle and brain, and has a punctate cytoplasmic distribution. During the analysis of the LGMD2H region, it became apparent that there were Hutterite LGMD patients not linked to the LGMD2H locus. In order to identify the causative gene(s) in the remaining families, we performed a genome-wide scan. A locus at chromosome 19q13 was found to correspond to disease inheritance, the site of a previously iv described LGMD locus, LGMD2I.66 No causative gene had yet been identified at this locus so haplotyping and mutation screening was performed. We were able to identify c.826C>A in FKRP as the causative mutation in our remaining cohort of LGMD patients. The same mutation has since been found in many other populations, and is apparently a relatively common cause of LGMD. We obtained DNA from 19 non-Hutterite LGMD2I patients of diverse origins with c.826C>A and determined that it is an old founder mutation.90 There is no further evidence of any other loci causing autosomal recessive myopathy in the Hutterites. With the identification of c.1459G>A in TRIM32 and c.826C>A in FKRP we appear to have delineated the genetic cause of all myopathies of increased prevalence in the Hutterite population. To date, we have been able to provide accurate, non-invasive diagnosis to over 70 patients and have provided carrier testing to approximately 120 at-risk family members. This kind of DNA-based approach is not feasible in the general population due the enormous amount of locus, allelic, and clinical heterogeneity among myopathy patients. v Aknowledgements First and foremost I would like to thank the patients and their families for participating in our studies. The many Hutterite communities that we have visited have always been gracious and helpful. Without their constant support we would not have been able to do any of the work presented in this thesis. I am grateful to my co-supervisors Drs. Klaus Wrogemann and Cheryl Greenberg for providing me with this very fruitful opportunity, not just the project but the lab environment as well. I have been given an enormous amount of independence and responsibility and I hope that I have repaid that trust by providing our group with solid meaningful results. I don’t think that I could have found a laboratory better suited to my personality and interests. In addition, I am indebted to the many individuals that have been part of the lab at one time or another that have contributed to the work discussed in this thesis. Specific contributions will be mentioned prior to each chapter. I have had the pleasure of working with quite a few investigators in the course of my work and would specifically like to thank: Dr. Andrew Halayko & Gerald Stelmack (immunocytochemistry / microscopy), Drs. Andrew Engel & Marc Del Bigio (muscle pathology), Drs. Benedikt Schoser & Hanns Lochmuller (STM manuscript), Dr. Ken Morgan & Mary Fujiwara (linkage analysis and manuscript preparation), Drs. Mayana Zatz, Kate Bushby, & Volker Straub (non-Hutterite LGMD2I samples), Dr. Molly Kulesz-Martin (discussions involving the role of TRIM32 in skin cancer), Dr. Jody Berry (production of anti-TRIM32 antiserum), Dr. Richard Hammond (teaching me cell culture technique and immunoblotting), and Dr. Eric Shoubridge & Timothy Johns (production of human myoblast vi lines). In addition, the investigators in our department have always been available for questions and/or intriguing discussions, particularly Drs. Barb Triggs-Raine, Steven Pind, and Theresa Zelinski. I would also like to thank my examining committee (Drs. Peter Ray, Mary Lynn Duckworth, Barb Triggs-Raine, Cheryl Greenberg, and Klaus Wrogemann) for thoroughly reading this thesis and providing such useful comments. Special thanks to Dr. Peter Ray as the external examiner for making the effort to come to Winnipeg in order to attend my thesis defense. Finally I would like to thank my family for all their support and encouragement. The ten years (ouch!!) that I have spent in university would not have been bearable without them. Heartfelt thanks go to my partner Dan who has put up with a considerable amount of boring science talk and the occasional depression due to failed experiments for many years. Hopefully I will have a real job soon so I can support you for once! This work was supported by many funding agencies including Manitoba Health Research Council (MHRC), Manitoba Institute of Child Health (MICH), University of Manitoba Graduate Fellowship (UMGF), Muscular Dystrophy Association (MDA), and Canadian Institutes of Health Research (CIHR). vii List of Figures Figure 1: Muscular dystrophy proteins found in the sarcomere 8 Figure 2: Muscular dystrophy proteins found in the nucleus 10 Figure 3: Muscular dystrophy proteins found at the sarcolemmal membrane 19 Figure 4: Stratagene Bacteriomatchtm bacterial two hybrid system 68 Figure 5: LGMD2H pedigrees 73 Figure 6: Chromosome region 9q31-33 haplotypes 75,76 Figure 7: Physical map of the LGMD2H candidate region 77 Figure 8: Segregation of the four LGMD2H variants 81 Figure 9: Tissue distribution of the TRIM32 transcript 85 Figure 10: TRIM32 protein sequence 87 Figure 11: The TRIM family of proteins 88 Figure 12: Specificity of anti-TRIM32 antibody by immunoblotting 89 Figure 13: Multiple tissue immunoblot for TRIM32 90 Figure 14: Specificity of anti-TRIM32 antibody by immunofluorescence 92 Figure 15: TRIM32 in normal and patient cells 93 Figure 16: TRIM32 in fused myoblasts 94 Figure 17: TRIM32 in muscle sections 95 Figure 18: Schematic of the proposed pathogenic mechanism of LGMD2H 105 Figure 19: LGMD2I Pedigrees 112 Figure 20: Chromosome
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