There is an unmet need to develop and test treatments for rare lysosomal disease (LD). Most LDs are present in childhood and do not currently have approved therapies. Rare diseases individually are uncommon but taken together account for a population prevalence of 3.5-5.9% worldwide. Due to their rarity, it often takes significant time and effort to diagnose rare diseases. New diagnostic tools, especially for early detection, will offer an advantage in avoiding this diagnostic odyssey. This dissertation is focused on investigating novel diagnostic and treatment methods in vitro for two neurodegenerative LDs: Gaucher disease (GD) and mucopolysaccharidosis IIIB (MPS IIIB). Mutations in NAGLU and GBA1, the genes that encode for lysosomal hydrolases required for degradation of heparan sulfate and glucocerebrosides, lead to the observed pathogenesis in MPS IIIB and GD, respectively. Since many LDs, including MPS IIIB and some forms of GD, are neurodegenerative, cell and gene-based therapeutic strategies are of significant interest. Therapeutics that offer some symptom mitigation in other LDs, such as enzyme replacement or substrate reduction therapies, do not offer appreciable disease mitigation in MPS IIIB or neurodegenerative GD. Here, a novel compound heterozygous mutation, NAGLUY140C/R297X, that results in approximately 50% residual NAGLU protein and 0.6% NAGLU enzyme activity is reported in NAGLU. Furthermore, a RFLP and site-directed mutagenesis strategy was developed to identify the presence of the relatively common p.R297X mutation in patient cell samples, in addition to two other novel molecular assays for the detection of the p.E153K mutation in NAGLU and p.N370S mutation in GBA1. MPS IIIB and GD human skin fibroblasts were reprogrammed to iPSCs using non-integrating Sendai viral vectors with a reprogramming efficiency of 0.2% and 0.3%, respectively. Resulting iPS cell lines were confirmed as being pluripotent through a barrage of analyses for markers of pluripotency and differentiation. Intriguingly, early passage MPS IIIB iPSCs were found to exhibit increased cell death and spontaneous differentiation to embryoid body-like structures, which was hypothesized to be caused by fibroblast growth factor 2 (FGF2) sequestration or degradation due to inherent heparan sulfate dysregulation. Supplemental FGF2 (100 ng/mL) was found to significantly increase confluency of MPS IIIB iPSCs after 48 hours (n = 5, p ≤ 0.05) and persisting to 96 hrs (n = 5, p ≤ 0.05), thus providing evidence for an important role of FGF2-heparan sulfate interactions in the maintenance of stem cell pluripotency. These findings highlight the importance of considering inherent disease pathology when developing disease models. Three genome editing strategies, CRISPR-Cas9, base and prime editing, are addressed throughout this dissertation. Genome editing outcomes in NAGLU and GBA1, as well as a control gene, HPRT1, are reported in HEK293 cells, human skin fibroblasts, and induced pluripotent stem cells (iPSCs). Although CRISPR-HDR failed to yield mutation correction, base editing of the common p.N370S (c.1226 A>G) in GD skin fibroblasts using with 42% efficiency is reported. Base editing of HPRT1 in HEK293 cells with an overall editing efficiency of 6 ± 0.5% (n = 3), but interestingly, when base editing at the centered nucleotide was analyzed, the editing efficiency increases to 27 ± 4.3% (n = 3). These findings align with other reports of a centered nucleotide preference for base editors and will help direct genome editing strategies in the future. This dissertation describes the first genome editing in NAGLU, and the first base editing in GBA1, and underscores the importance of optimizing genome editing strategies when targeting disease-causing mutations in patient-derived cells. The findings reported here will direct future genome editing strategies for developing cell and gene-based therapies for MPS IIIB and GD. / Graduate / 2021-12-15

Introdução: Mucopolissacaridose IVA ou Síndrome de Morquio A é uma doença autossômica recessiva causada pela deficiência da enzima lisossomal Nacetilgalactosamina- 6-sulfatase (GALNS), que resulta no acúmulo lisossomal dos glicosaminoglicanos: Queratan sulfato e Condroitin-6-sulfato nos tecidos causando as manifestações clínicas. Os fenótipos variam da forma clássica à forma atenuada, ambas sem comprometimento cognitivo. A prevalência de MPS IVA varia de 1/76.000 a 1/640.000 nascidos vivos. Objetivos: Analisar e caracterizar o genótipo de pacientes brasileiros com MPS IVA através de estudos de mutações no gene da GALNS, possibilitando a estimativa de frequência de mutações recorrentes e o estabelecimento um protocolo de rotina para triagem dessas mutações. Métodos: Análise molecular do gene da GALNS foi realizada em 26 pacientes brasileiros inicialmente através de PCR-ARMS para detecção de seis mutações recorrentes (p.G116S/ p.G139S/ p.L307P/ p.N164T/ p.R386C e p.S341R) seguidas pela amplificação de regiões codificantes por PCR e sequenciamento. Resultados: Essas mutações foram encontradas em 61,5% da nossa amostra, com uma frequência alélica de 55,8%. Destas, a mutação mais frequente foi p.S341R (26,9%), seguida de p.R386C (21,1%) e p.G116S (7,7%). As mutações p.N164T, p.G139S, p.L307P não foram encontradas em nossa amostra. Além destas, foi encontrada por sequenciamento do éxon 5 uma mutação nova p.C165Y. Conclusão: O protocolo usado para detecção de mutações comuns mostrou-se adequado como um screening inicial de mutações no gene da GALNS, identificando mutações em 61,5% dos pacientes e permitiu a caracterização de 55,8% dos alelos. A mutação p.S341R foi encontrada apenas em pacientes do Nordeste. A identificação de indivíduos heterozigotos nessas famílias será importante para aconselhamento genético e para estimar a prevalência da doença nessa região. Estudos adicionais para identificação da origem dessa mutação, incluindo análises de segregação e haplótipo estão em andamento, e serão avaliadas em conjunto com dados epidemiológicos. / Background: Mucopolysaccharidosis IVA or Morquio A syndrome, is an autosomal recessive disorder caused by deficiency of lysosomal enzyme Nacetylgalactosamine- 6-sulfatase (GALNS), which results in lysosomal storage of glycosaminoglycans: Keratan sulfate and Chondroitin-6-sulfate in tissues causing clinical manifestations. The phenotypes vary from the classical to attenuated form, both without cognitive impairment. The prevalence of MPS IVA ranges from 1/76.000 to 1/640.000 live births. Objective: To analyze and characterize the genotype of Brazilian patients with MPS IVA, through molecular study of mutations in the GALNS gene, enabling the estimative of frequency of recurrent mutations and the establishment of a protocol for routine screening of these mutations. Methods: Molecular analysis of GALNS gene was performed in 26 Brazilian patients initially by ARMS-PCR to detect six recurrent mutations (p.G116S/ p.G139S/ p.L307P/ p.N164T/ p.R386C and p.S341R) followed by amplification of coding regions by PCR and sequencing. Results: These mutations were found in 61.5% of our sample, which were present in 55.8% of the alleles. The most frequent mutation was p.RS341R (26.9%), followed by p.R386C (21.1%) and p.G116S (7.7%). Mutations p.N164T, p.G139S, p.L307P were not found in our sample. A novel mutation p.C165Y was found after sequencing of exon 5. Conclusion: The protocol used for detection of common mutations was shown to be adequate for a first screening of mutations at the GALNS gene, once it identified the genotype in 61.5% of patients and allowed the characterization of 55.8% of alleles. The p.S341R was found only in patients from the Northeast. The identification of heterozygous individuals within these families will be important for genetic counseling and for estimating the disease prevalence in this region. Further studies to identify the origin of this mutation, including haplotype and segregation analyses are in progress, and will be evaluated in conjunction with epidemiological data.

Introdução: Mucopolissacaridose IVA ou Síndrome de Morquio A é uma doença autossômica recessiva causada pela deficiência da enzima lisossomal Nacetilgalactosamina- 6-sulfatase (GALNS), que resulta no acúmulo lisossomal dos glicosaminoglicanos: Queratan sulfato e Condroitin-6-sulfato nos tecidos causando as manifestações clínicas. Os fenótipos variam da forma clássica à forma atenuada, ambas sem comprometimento cognitivo. A prevalência de MPS IVA varia de 1/76.000 a 1/640.000 nascidos vivos. Objetivos: Analisar e caracterizar o genótipo de pacientes brasileiros com MPS IVA através de estudos de mutações no gene da GALNS, possibilitando a estimativa de frequência de mutações recorrentes e o estabelecimento um protocolo de rotina para triagem dessas mutações. Métodos: Análise molecular do gene da GALNS foi realizada em 26 pacientes brasileiros inicialmente através de PCR-ARMS para detecção de seis mutações recorrentes (p.G116S/ p.G139S/ p.L307P/ p.N164T/ p.R386C e p.S341R) seguidas pela amplificação de regiões codificantes por PCR e sequenciamento. Resultados: Essas mutações foram encontradas em 61,5% da nossa amostra, com uma frequência alélica de 55,8%. Destas, a mutação mais frequente foi p.S341R (26,9%), seguida de p.R386C (21,1%) e p.G116S (7,7%). As mutações p.N164T, p.G139S, p.L307P não foram encontradas em nossa amostra. Além destas, foi encontrada por sequenciamento do éxon 5 uma mutação nova p.C165Y. Conclusão: O protocolo usado para detecção de mutações comuns mostrou-se adequado como um screening inicial de mutações no gene da GALNS, identificando mutações em 61,5% dos pacientes e permitiu a caracterização de 55,8% dos alelos. A mutação p.S341R foi encontrada apenas em pacientes do Nordeste. A identificação de indivíduos heterozigotos nessas famílias será importante para aconselhamento genético e para estimar a prevalência da doença nessa região. Estudos adicionais para identificação da origem dessa mutação, incluindo análises de segregação e haplótipo estão em andamento, e serão avaliadas em conjunto com dados epidemiológicos. / Background: Mucopolysaccharidosis IVA or Morquio A syndrome, is an autosomal recessive disorder caused by deficiency of lysosomal enzyme Nacetylgalactosamine- 6-sulfatase (GALNS), which results in lysosomal storage of glycosaminoglycans: Keratan sulfate and Chondroitin-6-sulfate in tissues causing clinical manifestations. The phenotypes vary from the classical to attenuated form, both without cognitive impairment. The prevalence of MPS IVA ranges from 1/76.000 to 1/640.000 live births. Objective: To analyze and characterize the genotype of Brazilian patients with MPS IVA, through molecular study of mutations in the GALNS gene, enabling the estimative of frequency of recurrent mutations and the establishment of a protocol for routine screening of these mutations. Methods: Molecular analysis of GALNS gene was performed in 26 Brazilian patients initially by ARMS-PCR to detect six recurrent mutations (p.G116S/ p.G139S/ p.L307P/ p.N164T/ p.R386C and p.S341R) followed by amplification of coding regions by PCR and sequencing. Results: These mutations were found in 61.5% of our sample, which were present in 55.8% of the alleles. The most frequent mutation was p.RS341R (26.9%), followed by p.R386C (21.1%) and p.G116S (7.7%). Mutations p.N164T, p.G139S, p.L307P were not found in our sample. A novel mutation p.C165Y was found after sequencing of exon 5. Conclusion: The protocol used for detection of common mutations was shown to be adequate for a first screening of mutations at the GALNS gene, once it identified the genotype in 61.5% of patients and allowed the characterization of 55.8% of alleles. The p.S341R was found only in patients from the Northeast. The identification of heterozygous individuals within these families will be important for genetic counseling and for estimating the disease prevalence in this region. Further studies to identify the origin of this mutation, including haplotype and segregation analyses are in progress, and will be evaluated in conjunction with epidemiological data.

Introdução: Mucopolissacaridose IVA ou Síndrome de Morquio A é uma doença autossômica recessiva causada pela deficiência da enzima lisossomal Nacetilgalactosamina- 6-sulfatase (GALNS), que resulta no acúmulo lisossomal dos glicosaminoglicanos: Queratan sulfato e Condroitin-6-sulfato nos tecidos causando as manifestações clínicas. Os fenótipos variam da forma clássica à forma atenuada, ambas sem comprometimento cognitivo. A prevalência de MPS IVA varia de 1/76.000 a 1/640.000 nascidos vivos. Objetivos: Analisar e caracterizar o genótipo de pacientes brasileiros com MPS IVA através de estudos de mutações no gene da GALNS, possibilitando a estimativa de frequência de mutações recorrentes e o estabelecimento um protocolo de rotina para triagem dessas mutações. Métodos: Análise molecular do gene da GALNS foi realizada em 26 pacientes brasileiros inicialmente através de PCR-ARMS para detecção de seis mutações recorrentes (p.G116S/ p.G139S/ p.L307P/ p.N164T/ p.R386C e p.S341R) seguidas pela amplificação de regiões codificantes por PCR e sequenciamento. Resultados: Essas mutações foram encontradas em 61,5% da nossa amostra, com uma frequência alélica de 55,8%. Destas, a mutação mais frequente foi p.S341R (26,9%), seguida de p.R386C (21,1%) e p.G116S (7,7%). As mutações p.N164T, p.G139S, p.L307P não foram encontradas em nossa amostra. Além destas, foi encontrada por sequenciamento do éxon 5 uma mutação nova p.C165Y. Conclusão: O protocolo usado para detecção de mutações comuns mostrou-se adequado como um screening inicial de mutações no gene da GALNS, identificando mutações em 61,5% dos pacientes e permitiu a caracterização de 55,8% dos alelos. A mutação p.S341R foi encontrada apenas em pacientes do Nordeste. A identificação de indivíduos heterozigotos nessas famílias será importante para aconselhamento genético e para estimar a prevalência da doença nessa região. Estudos adicionais para identificação da origem dessa mutação, incluindo análises de segregação e haplótipo estão em andamento, e serão avaliadas em conjunto com dados epidemiológicos. / Background: Mucopolysaccharidosis IVA or Morquio A syndrome, is an autosomal recessive disorder caused by deficiency of lysosomal enzyme Nacetylgalactosamine- 6-sulfatase (GALNS), which results in lysosomal storage of glycosaminoglycans: Keratan sulfate and Chondroitin-6-sulfate in tissues causing clinical manifestations. The phenotypes vary from the classical to attenuated form, both without cognitive impairment. The prevalence of MPS IVA ranges from 1/76.000 to 1/640.000 live births. Objective: To analyze and characterize the genotype of Brazilian patients with MPS IVA, through molecular study of mutations in the GALNS gene, enabling the estimative of frequency of recurrent mutations and the establishment of a protocol for routine screening of these mutations. Methods: Molecular analysis of GALNS gene was performed in 26 Brazilian patients initially by ARMS-PCR to detect six recurrent mutations (p.G116S/ p.G139S/ p.L307P/ p.N164T/ p.R386C and p.S341R) followed by amplification of coding regions by PCR and sequencing. Results: These mutations were found in 61.5% of our sample, which were present in 55.8% of the alleles. The most frequent mutation was p.RS341R (26.9%), followed by p.R386C (21.1%) and p.G116S (7.7%). Mutations p.N164T, p.G139S, p.L307P were not found in our sample. A novel mutation p.C165Y was found after sequencing of exon 5. Conclusion: The protocol used for detection of common mutations was shown to be adequate for a first screening of mutations at the GALNS gene, once it identified the genotype in 61.5% of patients and allowed the characterization of 55.8% of alleles. The p.S341R was found only in patients from the Northeast. The identification of heterozygous individuals within these families will be important for genetic counseling and for estimating the disease prevalence in this region. Further studies to identify the origin of this mutation, including haplotype and segregation analyses are in progress, and will be evaluated in conjunction with epidemiological data.