Improving Diagnosis and Treatment Outcomes in Mucopolysaccharidoses

Improving Diagnosis and Treatment Outcomes in Mucopolysaccharidoses
A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy
in the Faculty of Biology, Medicine and Health
2018
Contents
1 Lysosomal disorders and Mucopolysaccharidoses 21 1.1 Lysosomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 1.2 Lysosomal storage disorders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 1.3 Mucopolysaccharidoses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 1.4 Mucopolysaccharidosis Type I . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 1.5 Mucopolysaccharidosis Type III . . . . . . . . . . . . . . . . . . . . . . . . . . . 50 1.6 Summary and research strategy . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
2 Recommendations on clinical trial design for treatment of Mucopolysaccha- ridosis Type III 57 2.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58 2.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58 2.3 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 2.4 Recommendations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 2.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 2.6 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Methods 78
3 Study designs, materials and methods 81 3.1 Outcomes of combined ERT and HSCT in MPS I . . . . . . . . . . . . . . . . . 81 3.2 Mutational profile of IDUA and genotype-phenotype relationships . . . . . . . . 83 3.3 Clinical trial of immune tolerance induction in MPS I . . . . . . . . . . . . . . . 87 3.4 Clinical trial of genistein in MPS III . . . . . . . . . . . . . . . . . . . . . . . . 104
Results 113
4 Enzyme replacement therapy prior to haematopoietic stem cell transplanta- tion in Mucopolysaccharidosis Type I: 10 year combined experience of two centres 115 4.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116 4.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116 4.3 Patients and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117 4.4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118 4.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
5 IDUA mutational profile and genotype-phenotype relationships in UK pa-
IMPROVING DIAGNOSIS AND TREATMENT OUTCOMES IN MUCOPOLYSACCHARIDOSES 3
Contents
tients with Mucopolysaccharidosis Type I 125 5.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126 5.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126 5.3 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127 5.4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131 5.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139 5.6 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144 5.7 Supplementary information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
6 Strategies for induction of immune tolerance to enzyme replacement therapy in Mucopolysaccharidosis Type I 157 6.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158 6.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158 6.3 Materials and methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160 6.4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165 6.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
7 High dose genistein in Sanfilippo syndrome: results of a randomised, double- blinded, placebo-controlled clinical trial 175 7.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176 7.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176 7.3 Patients and methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178 7.4 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184 7.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191 7.6 Supplementary information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Discussion 203
Appendices 211
A Clinical trial design recommendations for MPS III: supplementary information 213
B Genotype-phenotype relationships in MPS I: In silico analysis parameters & results 217
List of references 224
List of Tables
1.1 Clinical subtypes of MPS disorders . . . . . . . . . . . . . . . . . . . . . . . . . 23 1.2 Incidence of antibodies in MPS clinical trials . . . . . . . . . . . . . . . . . . . 40
2.1 Interventional studies in MPS III . . . . . . . . . . . . . . . . . . . . . . . . . . 61 2.2 Natural history studies in MPS III . . . . . . . . . . . . . . . . . . . . . . . . . 64
3.1 Antibodies used for T cell immunophenotyping . . . . . . . . . . . . . . . . . . 95
4.1 Patient, donor and transplant characteristics . . . . . . . . . . . . . . . . . . . . 117 4.2 Definitions of transplant outcomes . . . . . . . . . . . . . . . . . . . . . . . . . 118 4.3 Graft failures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
5.1a Geographical origin of samples and classification into phenotypic groups . . . . 129 5.1b Ethnic origin of individuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129 5.2 Novel IDUA variants identified . . . . . . . . . . . . . . . . . . . . . . . . . . . 132 5.3 Most frequently observed genotypes in UK cohort . . . . . . . . . . . . . . . . . 139 5.4 Genotype-phenotype relationships . . . . . . . . . . . . . . . . . . . . . . . . . . 142 5.5 Variants for which associations were not determined . . . . . . . . . . . . . . . 143 5.6 Prediction of phenotypic severity in a test cohort . . . . . . . . . . . . . . . . . 144 S5.1 All IDUA variants identified . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146 S5.2 IDUA genotypes observed in UK cohort . . . . . . . . . . . . . . . . . . . . . . 153 S5.3 Test cohort of 26 individuals with MPS I . . . . . . . . . . . . . . . . . . . . . . 154
6.1 Participants recruited to ITIMHS study . . . . . . . . . . . . . . . . . . . . . . 161 6.2 Treatment emergent adverse events in ITIMHS study . . . . . . . . . . . . . . . 165
7.1 Schedule of study assessments . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179 7.2 Baseline characteristics of participants in GENiSIS2013 . . . . . . . . . . . . . . 184 7.3 Biochemical outcome measures in GENiSIS2013 . . . . . . . . . . . . . . . . . . 192 7.4 Neuropsychological outcome measures in GENiSIS2013 . . . . . . . . . . . . . . 193 7.5 Behavioural outcome measures in GENiSIS2013 . . . . . . . . . . . . . . . . . . 194 7.6 Quality of life measures in GENiSIS2013 . . . . . . . . . . . . . . . . . . . . . . 195 7.7 Adverse events in GENiSIS2013 . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
IMPROVING DIAGNOSIS AND TREATMENT OUTCOMES IN MUCOPOLYSACCHARIDOSES 5
Blank page
List of Figures
2.1 Possible responses to therapy in a progressive disorder such as MPS III . . . . . 76
3.1 Physiologically based methotrexate model . . . . . . . . . . . . . . . . . . . . . 89 3.2 Subcutaneous vs. oral dosing modelled in a 1 year old . . . . . . . . . . . . . . 90 3.3 ITIMHS trial schema . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93 3.4 ITIMHS study methotrexate dosing regimen . . . . . . . . . . . . . . . . . . . . 94 3.5 Gating strategy for T cell immunophenotyping . . . . . . . . . . . . . . . . . . 97 3.6 ITIMHS study assessments (original protocol) . . . . . . . . . . . . . . . . . . . 100 3.7 ITIMHS study assessments (amended protocol) . . . . . . . . . . . . . . . . . . 102 3.8 GENiSIS2013 trial schema . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106 3.9 GENiSIS2013 study assessments . . . . . . . . . . . . . . . . . . . . . . . . . . 111
4.1 Overall and event-free survival . . . . . . . . . . . . . . . . . . . . . . . . . . . 119 4.2 Urinary GAG pre- and post-HSCT . . . . . . . . . . . . . . . . . . . . . . . . . 121
5.1 Samples received for IDUA sequencing . . . . . . . . . . . . . . . . . . . . . . . 128 5.2 Lollipop plot of IDUA variants . . . . . . . . . . . . . . . . . . . . . . . . . . . 131 5.3 Structural locations of novel missense IDUA variants . . . . . . . . . . . . . . . 137 5.4 Process for developing genotype-phenotype relationships . . . . . . . . . . . . . 141 S5.1 IDUA variants in context of whole gene . . . . . . . . . . . . . . . . . . . . . . 155 S5.2 Amino acid alignment of novel missense and in frame variants . . . . . . . . . . 156
6.1 ITIMHS study schedule and antibody responses in MPS IH patients . . . . . . 166 6.2 Biomarker responses to laronidase in MPS IH patients receiving ITI with MTX 167 6.3 MTX dose optimisation delivery schedule and antibody levels in in MPS I mice 168 6.4 Anti-laronidase antibodies in MPS I mice treated with ITI regimens . . . . . . 170 6.5 Anti-laronidase antibodies in MPS I mice treated with anti-CD4, anti-CD8 mAb 171 6.6 Cellular uptake inhibition and CD4+ cell counts . . . . . . . . . . . . . . . . . . 172
7.1 GENiSIS2013 participant flow diagram . . . . . . . . . . . . . . . . . . . . . . . 180 7.2 GENiSIS2013 biochemical outcomes . . . . . . . . . . . . . . . . . . . . . . . . 185 7.3 GENiSIS2013 neuropsychological outcomes . . . . . . . . . . . . . . . . . . . . 186 7.4 GENiSIS2013 actigraphy data . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187 7.5 GENiSIS2013 behavioural outcomes . . . . . . . . . . . . . . . . . . . . . . . . 188 7.6 GENiSIS2013 quality of life measures . . . . . . . . . . . . . . . . . . . . . . . . 189 7.7 GENiSIS2013 cytokines in plasma and CSF . . . . . . . . . . . . . .…