Copyright is owned by the Author of the thesis. Permission is given for a copy to be downloaded by an individual for the purpose of research and private study only. The thesis may not be reproduced elsewhere without the permission of the Author. A GENETIC TEST FOR MALIGNANT HYPERTHERMIA A dissertation presented to Massey University in partial fulfilment of the requirements for the degree of Doctor of Philosophy in biochemistry. Rosemary L. Brown 2000 ACKNOWLEDGEMENTS I would like to extend my sincere gratitude to my principal supervisor, Dr. Kathryn Stowell for her enduring encouragement, dedication and reassurance, throughout the (prolonged) term of my PhD studies. Thanks also to Prof, John Tweedie for guidance, and enthusiastic assistance with computer-related tasks. This work would not have been possible without the dedication ofNeil Pollock, (specialist anaesthetist, Palmerston North hospital), who organised the collection ofblood and tissue samples and provided vital clinical expertise in the field ofMH. I would also like to thank other members of the Palmerston North hospital department of Anaesthesia and intensive care, for the provision of IVCT data and helpful discussion, particularly Ken Couchman and Mike Hodges. Many members of the former Department ofBiochernistry and the current IMBS have provided assistance, encouragement and enjoyable diversion along the way. In particular, I am indebted to Danielle James for her persistently cheerful dedication of to the task of endless DNA extractions, and for keeping tabs on the pedigree data. Much of this work also relied on the efficiency of Lorraine Berry, who was in charge the automatic sequencing. I would also like to thank friends and colleagues in the Twilight Zone, for friendship and technical advice, especially, Catherine, Robyn, Jakki, Bee and Carole. Special thanks to Stan Moore for his dedicated provision of comic relief, and likewise, the members of the IMBS touch team, numerous flatmates, and friends from the Massey alpine club. I am particularly indebted to Lee Davies for helping to salvage my data, and for reformatting and replacing my hard drive (sadly, on more than one occasion). I am sincerely grateful to my parents for their support and acceptance throughout the duration of my studies, and to Andrew, for his love and continued encouragement during my PhD and for abiding the protracted separation associated with the preparation of this thesis. TABLE OF CONTENTS ABSTRACT ......................................................................................................................................................................................................... i ABBREVIATIONS ............................................................................................................................................................................................. ii LIST OF FIGURES ............................................................................................................................................................................................ iii CHAP'fER ONE: INTRODUCTION ................................................................................................................ 1 1.1 OVERVIEW OF THE GENETICS AND BIOCHEMISTRY OF MALIGNANT HYPERTHERMIA ........................................................ I 1.2 CLINICAL FEATURES OF MALIGNANT HYPERTHERMIA ................................................................................................................... 2 1.3 THE PORCINE MODEL OF MALIGNANT HYPERTHERMIA .................................................................................................................. 3 1.4 DIAGNOSIS OF MALIGNANT HYPERTHERMIA ...................................................................................................................................... 4 1.5 MOLECULAR COMPONENTS OF SKELETAL MUSCLE CONTRACTION ........................................................................................... 6 1.6 THE PATHOPHYSIOLOGY OF MH ............................................................................................................................................................ 10 1.7 MUSCLE DISORDERS ASSOCIATED WITH MH ........................................ ............................................................................................. l2 1.8 THE GENETIC BASIS OF MALIGNANT HYPERTHERMIA ................................................................................................................... l3 1.9 THE RY ANODINE RECEPTOR: STRUCTURE AND FUNCTION .......................................................................................................... 16 1.10 EXCITATION-CONTRACTION COUPLING .............. ....................................... ............................................................................... ... 21 1.11 MOLECULAR PREDICTIONS FOR MHS MUTATIONS .................................................................................................................... 23 1.12 BIOCHEMICAL CHARACTERISATION OFMHS MUTATIONS ..................................................................................................... 24 1.13 RESEARCH GOALS ................................................................................................................................................................................. 26 CHAP'fER 1WO: MATERIALS AND METHODS ...................................................................................... 28 2.1 PURITICATION OF GENOMIC DNA. .......................................................................................................................................................... 28 2.2 PURITICATION OF HUMAN SKELETAL MUSCLE RNA ................................................................................... ..................................... 29 2.3 STANDARD PCR PROCEDURES ................................................................................................................................................................. 32 2.4 PROCEDURES FOR OPTIMISIMG PCR .................................................................................................................................................. , ... 34 2.5 METHODS OF MUTATION DETECTION .................................................................................................................................................. 35 2.6 ANALYSIS OF CHROMOSOME 19Q MARKERS ............................................................. ......................................................................... 40 2.7 GENETIC LINKAGE ANAL YSIS .................................................................................................................................................................. 44 2.8 SCREENING FOR NOVEL RYRI MUTATIONS BY RT-PCR .................................................................................................................. 46 2.9 REAGENTS AND CHEMICALS .................................................................................................................................................................... 49 CHAP'fER THREE: SCREENING FOR PUBLISHED RYRl MUTATIONS ............................................. 50 3.1 APPROACH TO THE SEARCH FOR REPORTED MH MUT ATIONS ..................................................................................................... 50 3.2 MUTATION SCREENING BY PCR-RFLP ANALYSIS .............................................................................................................................. 52 3.3 SCREENING FOR PUBLISHED RYRI MUTATIONS BY DIRECT SEQUENCE ANAL YSIS ............................................................. 69 CHAP'fER FOUR: GENETIC LINKAGE ANALYSIS OF A LARGE MHS PEDIGREE .......................... 72 4.1 CH PEDIGREE STRUCTURE ........................................................................................................................................................................ 72 4.2 PRINCIPLES OF GENETIC LINKAGE ANALYSIS ................................................................................................................................... 73 4.3 DATA COLLECTION ..................................................................................................................................................................................... 83 4.4 SEGREGATION OF MHS WITH CHROMOSOME 19Q MARKERS IN THE CH FAMILY ................................................................. 93 4.5 TWO-POINT LINKAGE ANALYSIS .......................................................................................................................................................... 105 4.6 MUL TIPOINT LINKAGE ANALYSIS ........................................................................................................................................................ 112 4.7 DISCUSSION OF RESULTS ........................................................................................................................................................................ 116 CHAPTER FIVE: IDENTIFICATION OF MUTATIONS BY SEQUENCE ANALYSIS OF RYRl cDNA .............................. 122 5.1 SEARCH FOR A NOVEL RYRI MUTATIONIN THE CH FAMILY ..................................................................................................... l22 5.2 RT?PCR STRATEGY ..................................................................................................................................................................................... l25 5.3 RT-PCR METHODOLOGY .......................................................................................................................................................................... 130 5.4 RESULTS: RT-PCR AND RYRI SEQUENCE ANALYSIS ...................................................................................................................... 132 5.5 IDENTFICATION OF RYRI MUTATIONS IN OTHER MHS PROBANDS .......................................................................................... !40 5.6 IDENTIFICATION OF NOVEL RYRI MUTATIONS IN MHS PROBANDS BY SSCP ANALYSIS ................................................. 148 5.7 OVERVIEW OF RYRI MUTATION ANALYSIS ...................................................................................................................................... l53 CHAPTER SIX: GENOTYPE I PHENOTYPE RELATIONSHIPS FOR RYRl MUTATIONS ............... 158 6.1 INVESTIGATING LINKAGE BETWEEN MHS AND T48261... .............................................................................................................. 158 6.2 THE RELATIONSHIP BETWEEN IVCT THRESHOLDS AND EVIDENCE FOR LINKAGE ............................................................ 160 6.3 STATISTICAL ANALYSIS OF THE IVCT DATA .................................................................................................................................... l63 6.4 IDENTIFICATION AND DISCUSSION OF DATA INCONSISTENCIES .............................................................................................. l69 6.5 FACTORS CONTRIBUTING TO GENOTYPE/PHENOTYPE DISCREPANCIES IN THE CH FAMILY .......................................... 172 6.6 COMPARISON OF PHENOTYPES ASSOCIATED WITH DIFFERENT RYRI MUTATIONS ........................................................... l76 6.7 MHS IN ASSOCIATION WITH SUDDEN INFANT DEATH IN THE LARGE MAORI FAMILY ...................................................... l80 6.8 SUMMARY AND IMPLICATIONS FOR DIAGNOSIS ............................................................................................................................. l82 6.9 IMPLICATIONS FOR THE STRUCTURE AND FUNCTION OF THE CALCIUM RELEASE CHANNEL ....................................... 189 6.10 FUilJRE MOLECULAR CHARACTERISATION OF THE NOVEL THR4826ILE MUTATION ................................................. 198 REFERENCES ................................................................................................................................................. 200 APPENDICES .................................................................................................................................................. 224 A I PRIMERS FOR PCR AND SEQUENCING ................................................................................................................................................... AI A2 RYRI CDNA SEQUENCE, PRIMERS AND POL YMORPHISMS ............................................................................................................ A5 A3 ONLINE RESOURCES: GENETIC MAPS AND MARKERS .................................................................................................................. Al4 A4 CHROMOSOME !9 Q MAP ......................................................................................................................................................................... Al5 A5 NZ MHS FAMILIES: SUMMARY OF IVCT AND GENETIC INVESTIGATION ................................................................................ Al7 ?6 CLINICAL CASE REPORTS FOR PATIENTS WITH RYR! MUTATIONS ......................................................................................... Al9 ?7 PATIENT CONSENT FORMS, GENETIC TESTING ............................................................................................................................. A23 AS STNnSTICAL METHODS AND FORMULAE ........................................................................................................................................ A29 -?? THE SEGREGATION OF THE T48261 WITH MHS IN THE COMBINED CH FAMILY PEDIGREE ...................................... INSERT , . ABSTRACT Malignant Hyperthermia (MH) is an inherited disorder of skeletal muscle in which an abnormality in the regulation of calcium release from internal stores can result in a fatal hypermetabolic reaction on exposure to general anesthetics. Mutations in the gene encoding the skeletal muscle ryanodine receptor/ calcium release channel (R YR 1) have been linked to MHS in 50% of overseas families examined, and at least five additional MH susceptibility loci have since been proposed. Current diagnosis of MH in New Zealand relies on the in vitro contracture testing ( IVCT) of excised muscle bundles with caffeine and halothane. The genetic basis ofMH in NZ families was investigated, with the goal of developing genetic tests to replace the muscle biopsy test. A search for previously published RYR1 mutations in susceptible members of 33 NZ MH families revealed three RYR1 mutations; Arg163Cys, Gly34 1Arg, and Gly2434Arg, which eo-segregated completely with susceptibility to MH (MHS). None of the 1 7 published RYRI mutations were detected in a local MHS Maori family in which several anaesthetic deaths have occurred. This is the largest characterised MH family in the world. An examination of the segregation of a panel of chromosome 1 9q markers with MHS in over 200 members of this family revealed that MHS was linked to the RYR1 -flanking markers. This implicated the involvement of a novel RYRI defect . The entire 1 5 . 3 kb R YR 1 coding region was combed for mutations by R T-PCR and automatic sequence analysis. A novel point mutation was detected that changed threonine 4826 to isoleucine in the C-terminal region of the RyR l protein. This mutation was not found in 220 chromosomes from the normal population, or in 94 members of the family who had been diagnosed MHN (normal) . A screen for the mutation in 2 1 0 key family members revealed a direct correlation between inheritance of the mutation and highly abnormal muscle contracture results in 36 individuals. 22 MHS individuals lacked the mutation; consequently the false positive rate of the IVCT and the possible segregation of at least one additional MHS gene complicated genetic linkage analysis. These problems were addressed by investigating increasingly stringent models for MH diagnosis . Four additional novel R YR 1 mutations were detected in other MHS families investigated by sequence analysis of cDNA and genomic DNA, Arg40 1 Cys, Arg2452Trp, Arg2454His and His4833Tyr. The detection of the Thr4826IIe and His 4833Tyr mutations established the channel domain of the ryanodine receptor as a new MHS domain. Genetic testing for MHS can now be applied with caution to predict MH susceptibility in approximately 40 % of at-risk individual in NZ, thus reducing the number of patients requiring an expensive and invasive surgical procedure. A ACRS ARMS ASO bp BRL cDNA Caf. CaM CFLP CHCT CK CS ddNTP dH20 DEPC DHPR DMD DMSO dNTP ds DNA DTT ECC EDTA EEO EMHG EtBr Ha I. HE PES IP3R IVCT kb KR MH MBE MHN MHS MPC m RNA MOPS NCE PAGE PCR PMCA PSS RE ABBREVIATIONS absorbance amplification-created restriction site amplification refractory mutation system allele-specific oligonucleotide base pair Bethseda research laboratories complementary DNA Caffeine calmodulin cleavase fragment length polymorphism caffeine/halothane contracture test (North American protocol) Creatine phosphokinase chromosome 2' ,3 '-dideoxyribonucleotide 5 '-triphosphate distilled water diethylpyrocarbonate dihydropyridine receptor Duchenne muscular dystrophy dimethyl sulphoxide deoxyribonucleoside 5 '-triphosphate double-stranded DNA dithiothreitol Excitation-contraction coupling ethylene diamine tetra-acetate electroendosmosis European Malignant Hyperthermia Group ethidium Bromide halothane N-[2-hydroxyethyl]piperazine-N'-[ 4-butanesulphonic acid] inositol 1 , 4 ,5-trisphosphate receptor in vitro contracture test (European protocol) kilo base Krebs-Ringer malignant hyperthermia malignant hyperthermia equivocal diagnosis malignant hyperthermia negative diagnosis malignant hyperthermia susceptible diagnosis magnetic particle concentrator Messenger RNA 3-[N-morpholino ]propanesulphonic acid Na+1Ca+2 exchanger polyacylamide gel electrophoresis polymerase chain reaction plasma membrane calcium ATPase porcine stress syndrome restriction endonuclease 11 RFLP RNase rRNA RT RT-PCR RYR RyR SDS SERCA ss DNA SSCP SR TAE Taq TBE TC TE TEMED Tm restriction fragment length polymorphism ribonuclease ribosomal RNA reverse transcriptase reverse transcription-polymerase chain reaction ryanodine receptor (gene) ryanodine receptor (protein) sodium dodecyl sulphate Sarco( en do )plasmic reticulum A TPase single-stranded DNA single-stranded conformation polymorphism sarcoplasmic reticulum Tris-acetate-EDTA buffer Thermus aquaticus Tris-borate-EDT A buffer Terminal cisternae Tris-EDTA buffer N,N,N' ,N' -tetramethylenediamine melting temperature lll LIST OF FIGURES FIGURE 1-1 ION CHANNELS INVOLVED IN SKELETAL MUSCLE ECC COUPLING ....................... ..................... 9 FIGURE 1-2 A PROPOSED :MECHANISM FOR THE INDUCTION OF HUMAN AND PORCINE MH .................... 11 FIGURE 1-3 TIIREE-DI:MENSIONAL STRUCTURAL RECONSTRUCTION OF RYR . ......... ................................ 18 FIGURE 1-4 PROPOSED INTERACTIONS BETWEEN TilE DHPR a1 SUBUNIT AND RYR1 ................................ 22 FIGURE 1-5 LOCATION OF RYR1 MHS AND CCDMUTATIONS ...................................... ................................... 24 FIGURE 3-1 EFFECTS OF [MG+2] ON PCR AMPLIFICATION YIELD AND SPECIFICITY .. ................. . . ... 53 FIGURE 3-2 SCREENING FOR PUBLISHED RYR1 MUTATIONS BY PCR-RFLP.................................. .. 54 FIGURE 3-3 DETECTION OF THE C487T (ARG163CYS) MUTATION BY PCR-RFLP ........... . ..... 55 FIGURE 3-4 MANUAL SEQUENCE ANALYSIS OF TilE C487T (ARG163CYS) MUTATION ............................... . 56 FIGURE 3-5 AUTOMATED SEQUENCE ANALYSIS OF THE C487T (ARGI63CYS) MUTATION ........ ................ 56 FIGURE 3-6 SEGREGATION TilE ARG163CYS (C487T) MUTATION IN FAMILY 35 ..................... ................... 58 FIGURE 3-7 PCR-RFLPDETECTION OF TilE GL Y2434ARG MUTATION IN FAMILY 5 ....................................... 59 FIGURE 3-8 CONFIRMATION OF TilE GLY2434ARG MUTATION BY AUTOMATIC DNA SEQUENCE ANALYSIS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 00 FIGURE 3-9 SEGREGATION OF THE ARG3434CYS MUTATION IN FAMILY 24 .................................................. 62 FIGURE 3-10 PCR-RFLP SCREEN FOR ARG2458IDS/CYS AND ARG2163CYS MUTATIONS ........... .................. . 64 FIGURE 3-11 CORRECTION OF SEQUENCE ERRORS IN INTRON 46 ................................................ ................ ... 65 FIGURE 3-12 AMPLIFICATION CREATED RESTRICTION SITES TO SCREEN FOR TYR522SER . ...................... 67 FIGURE 3-13 DEMONSTRATION OF ACRS SCREEN FOR TilE TYR522SER MUTATION.............. .. ................ 68 FIGURE 3-14 DIRECT MANUAL SEQUENCE ANALYSIS OF PUBLISHED RYRl MUTATION SITES ................... 70 FIGURE 4-1 TilE EFFECT OF THIRD GENERATION DATA ON PHASE DETERMINATION ............................... 71 FIGURE 4-2 SEGREGATION OF RYRl RFLP MARKERS IN NZ :MEMBERS OF FAMILY 94 .................. ... ..... 84 FIGURE 4-3A RFLP ANALYSIS OF TilE SER2862 POL YMORPIDSM WTIB CFO L . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . .. . . . . . . . 85 FIGURE 4-3B PCR-RFLP ANALYSIS OF RYRl POL YMORPIDSMS WTIB TAQ I AND FOK I . . . .. . . . . . . . .. . . .. .. . . . ... . . .. . . 86 FIGURE 4-4 LOCATION OF RYRl MARKERS ............................................................. .......................................... 87 FIGURE 4-5 ANALYSIS OF THE R YR-CA DINUCLEOTIDE REPEAT MARKER IN THE CHEA PEDIGREE .. .... 90 FIGURE 4-6 ANALYSIS OF TilE Dl9S220 DINUCLEOTIDE REPEAT MARKER IN THE CHES PEDIGREE .... ... 90 FIGURE 4-7 ANALYSIS OF TilE Dl9S47 DINUCLEOTIDE REPEAT MARKER IN THE CHEH PEDIGREE ..... .... 91 FIGURE 4-8 ANALYSIS OF TilE Dl9S47 DINUCLEOTIDE REPEAT MARKER IN THE CHES PEDIGREE ....... .. 91 FIGURE 4-9 ANALYSIS OF THE Dl9S 190 TRINUCLEOTIDE REPEAT MARKER IN THE CHEA PEDIGREE ...... 92 FIGURE 4-10 SEGREGATION OF CHROMOSOME 19Q MARKERS WTIB MHS IN THE CHEHPEDIGREE ........ .. 94 FIGURE 4-11 SEGREGATION OF CHROMOSOME 19Q MARKERS WTIB MHS IN THE CHEH PEDIGREE .......... 96 FIGURE 4-12 SEGREGATION OF CHROMOSOME 19Q MARKERS WTIB MHS IN THE CH2 PEDIGREE ............ 98 FIGURE 4-13 SEGREGATION OF CHROMOSOME 19Q MARKERS WTIB MHS IN THE CH3 PEDIGREE ........... 101 FIGURE 4-13 ANALYSIS OF THE TAQ I MARKER IN TilE FAMILY OF A SIDS CHILD ....... ........................... .. 103 FIGURE 4-14 ASSOCIATION OF THE MHS-LINKED HAPLOTYPE WTIB SUDDEN UNEXPLAINED DEATH . . . 104 FIGURE 4-15 INFLUENCE OF THE PHENOCOPY PARA:METER ON SUPPORT FOR LINKAGE TO RYR1 ......... 107 FIGURE 4-17 MULTIPOINT LINKAGE ANALYSIS OF TilE CHI PEDIGREE ......................................................... 114 FIGURE 4-18 MULTIPOINT LINKAGE ANALYSIS OF TilE CH2 PEDIGREE ......................................................... 115 IV FIGURE 4-19 MULTIPOINT LINKAGE ANALYSES OF DIE CH3 PEDIGREE ........................................................ 115 FIGURE 5-1 SUBJECTS CHOSEN FOR Ml.ITATION SCREEN ............................................................................... 124 FIGURE 5-2 RNA GEL ELECTROPHORESIS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125 FIGURE 5-3 STRATEGY FOR THE AMPLIFICATION OF RYR1 CDNA ............................................................... 127 FIGURE 5-4 DETECTION OF A PROBABLE UV-INDUCED MUTATION AMPLIFIED lN SECONDARY PCR .... 133 FIGURE 5-5 PCR-ASSOCIATED DELETIONS lN RYR1 5' UTR AMPLIFIED FROM CDNA ................................. 135 FIGURE 5-6 DETECTION OF NOVEL RYR1 POL YMORPHISMS BY SEQUENCE ANALYSIS OF CDNA .......... 136 FIGURE 5-7 SEQUENCE ANALYSIS OF THE T4826I MUTATION ........................................................................ 138 FIGURE 5-8 SSCP DETECTION OF THE THR4826ILE MUTATION ...................................................................... 139 FIGURE 5-9 PCR PRODUCTS ENCOMPASSlNG RYR1 MUTATION-RICH REGIONS ......................................... 140 FIGURE 5-10 SSCP DETECTION OF THE ARG2452TRP MUTATION 1N FAMILY 36 ............................................ 141 FIGURE 5-11 IDENTIFICATION OF THE ARG401CYS MUTATION ....................................................................... 143 FIGURE 5-12 SEGREGATION OF THEARG401CYS MUTATION lN FAMILY 70 .................................................. 143 FIGURE 5-13 SSCP ANALYSIS OF THE G1021A (GLY341ARG) MUTATION IN FAMILY 24 ............................... 145 FIGURE 5-14 DETECTION OF THE G1021A (GLY341ARG) MUTATION .............................................................. 146 FIGURE 5-15 SEGREGATION OF THE GL Y341ARG MUTATION WITH MH lN FAMILY 24 ................................ 147 FIGURE 5-16 SSCP DETECTION OF THE HIS4833TYR MUTATION ...................................................................... 149 FIGURE 5-17 CHARACTERISATION OF THE HIS4833TYR MUTATION ............................................................... 149 FIGURE 5-18 PROXIMITY OF NOVEL C-TERMINAL RYR1 MUTATIONS ........................................................... 150 FIGURE 5-19 SEGREGATION OF THE HIS4833TYR MUTATION lN FAMILY 1... ................................................. 150 FIGURE 5-20 IDENTIFICATION OF THE ARG2454HIS AND ARG2452TRP MUTATIONS .................................... 152 FIGURE 6-1 DISTRIBUTION OF IVCT DATA FOR SUBJECTS WITH AND WITHOUT THR4826ILE ............... 164 FIGURE 6-2 DOSE RESPONSE CURVES FOR PATIENTS WITH AND WITHOUT THR4826ILE ...................... 166 FIGURE 6-3 DISTRIBUTION OF IVCT DATA ........................................................................................................ 167 FIGURE 6-4 CORRELATION BETWEEN IVCT RESPONSE AND THE THR4826ILE MUTATION ....................... l71 FIGURE 6-5 DISCORDANCE BETWEEN THR4826ILE AND MHS IN THE CHES FAMILY ............................... 174 FIGtJR? 6-6 COMPARISON OF IVCT DATA FOR DIFFERENT RYR1 MUTATIONS ........................................... 178 FIGURE 6-7 CONSERVATION OF AMINO ACIDS SURROUNDING MHS MUTATIONS ...................................... 91 FIGURE 6-8 GLUTAMlNE 3756 IN THE HUMAN RYR1 SEQUENCE IS NOT CONSERVED .............................. 192 FIGURE 6-9 CONSERVATION OF THR4826 AND HIS4833 AMONG RYR ISOFORMS ........................................ 193 FIGURE 6-10 RELATIVE POSffiONS OF RYR1 CHANNEL MUTATIONS ACCORDING TO MODELS FOR RYR1 TRANSMEMBRANE TOPOLOGY ...................................................................................................... 196 V