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- Next Generation Sequencing and Lysosomal Dysfunction: Novel mutations associated with Neurodegenerative disorders.Publication . Encarnação, Marisa; Coutinho, Maria Francisca; Matos, Liliana; Silva, Lisbeth; Ribeiro, Diogo; Nogueira, Célia; Vilarinho, Laura; Alves, SandraLysosomal Storage Disorders (LSD) are a group of inherited metabolic diseases characterized by a wide range in phenotypes and clinical variability. The diagnosis is often difficult and time consuming, with multiple tests/samples being required before a definitive diagnosis is reached. Next Generation Sequencing (NGS) is changing this scenario by allowing variant assessment at a large scale in a single run. The aim of this work was to develop an NGS-based workflow for the identification of LSD-causing variants. We designed a panel including exons and intronic flanking regions from 96 genes involved in lysosome homeostasis and function. The workflow was performed using a Sureselect protocol followed by sequencing in an Illumina MiSeq® platform. For alignment and variant anotation softwares Surecall and wANNOVAR were used. Validation of this custom-targeted panel was performed in 5 blind controls. For the studied cases, we could reach molecular diagnosis consistent with the clinical and biochemical diagnosis in 7 patients, corresponding to a diagnostic rate of 67% (7/11). For the undiagnosed patients, an extended custom panel composed also of autophagy modulators and other genes involved in lysosome biogenesis will be tested. From our first results we would like to highlight the detection of a novel frameshift mutation in the GM2A gene, which is associated with the extremely rare AB variant of Gangliosidosis, biochemically and clinically undistinguishable from the other two (Tay Sachs and Sandhoff Diseases). Also noteworthy, we were able to find out the molecular defect of a patient with a general clinical suspicion of Neuronal Ceroid Lipofuscinosis (CLN). From the 14 possible genes associated to these disorders, we detected the molecular defect in a single analysis. In fact, we identified a novel missense variant in the MFSD8 gene, reaching the diagnosis of a CLN7. Additionally, novel mutations in GLA, GALC, and NAGLU genes were found. We have also started a functional analysis to investigate the impact of two novel splicing mutations (GNPTAB and ARSB) and two novel missense mutations in NPC1 gene.
- Genomics and transcriptomics approach - diagnosis of a challenging case of Niemann-Pick type C (NP-C)Publication . Encarnação, Marisa; Coutinho, Maria Francisca; Cho, Soo-Min; Cardoso, Maria Teresa; Chaves, Paulo; Gaspar, Paulo; Santos, Juliana Inês; Ribeiro, Isaura; Quelhas, Dulce; Lacerda, Lúcia; Leão-Teles, Elisa; Futerman, Anthony H.; Vilarinho, Laura; Alves, SandraNP-C is a neurodegenerative Inherited Metabolic Disease with a heterogeneous clinical presentation, and due to mutations in either the NPC1 or NPC2 genes.We have studied a patient with clinical diagnosis of NP-C but presenting inconclusive results regarding molecular analysis.To better characterize this patient, we have performed NGS-based technologies (targeted DNA sequencing and single cell-RNA sequencing).For the molecular diagnosis we used a NGS gene panel followed by the analysis of cDNA.Latter, we used massively parallel single cell RNA-seq (MARS-Seq) to address gene profiling changes and characterize the pathomechanisms related to specific disease-causing mutations. Using our targeted NGS panel we identified two novel mutations in NPC1 gene.Next, through cDNA analysis of one of the patient parents we were able to understand the impact of the silent mutation.This mutation leads to exon skipping giving origin to an out-of-frame transcript and eliciting the nonsense-mediated decay pathway.Thus, we were not able to easily detect the mutant transcript which turned the molecular diagnosis more challenging. Apparently the presence of the other mutation (a missense mutation) impairs the NPC protein folding leading to its ER retention.The MARS-Seq analysis of this patient showed that a number of upregulated genes are related to the unfold protein response (UPR) and ER stress, which deserves further studies.
- Assessing Niemann-Pick Type C (NP-C) through a multi-omics approach genomic and transcriptomic profile of challenging casesPublication . Encarnação, Marisa; Coutinho, Maria Francisca; Cho, Soo-Min; Cardoso, Maria Teresa; Chaves, Paulo; Ribeiro, Isaura; Santos, Juliana Inês; Gaspar, Paulo; Quelhas, Dulce; Lacerda, Lúcia; Leão-Teles, Elisa; Futerman, Anthony H.; Vilarinho, Laura; Alves, SandraNiemann-Pick type C (NP-C) is a neurodegenerative Inherited Metabolic Disease with a heterogeneous clinical presentation, due to mutations in either the NPC1 or NPC2 genes. We studied patients with clinical diagnosis of NP-C but presenting inconclusive results regarding biomarkers testing and molecular analysis. Using NGS- targeted DNA sequencing we have identified some novel putative mutations and subsequent cDNA analysis allowed us to stablish the functional effect of a silent mutation (previously reported as a polymorphism) in the NPC1 splicing process. We demonstrated that this mutation leads to exon skipping, frameshift and premature stop codon and identified it in two NP-C patients from two unrelated Portuguese families. This mutation most likelly leads to a very unstable transcript that was overlooked. Also, to better characterize the pathomechanisms related to specific disease-causing mutations in NP-C patients, we analysed gene expression profiles in cultured skin fibroblasts and compared them to control individuals using Massively Parallel RNA Single-Cell Sequencing (MARS-Seq). The most prominent hits from this transcriptomics analysis were validated by qRT-PCR. The MARS-Seq analysis showed that a number of genes were upregulated and a significant number of the highly enriched genes are related to the unfold protein response (UPR) and Endoplasmic Reticulum (ER) stress, in a specific patient, which deserves further studies. ER stress is a hallmark of many neurodegenerative diseases, including LSD and can be due to misfolded/unfolded proteins as result of a specific missense mutation. Our preliminary results suggest that UPR activation is variable among NP-C patients, and this is likely to depend on the mutation type. Several other factors may contribute to this though, which could explain the heterogeneous presentation of this pathology. Additionally, we have investigated the same patients studied in MARS-Seq at the protein and celular levels. Interestingly, and according to recently published work, we observed that, for the analyzed mutations a significant part of the mutated NPC1 protein was retained/ delayed in the ER.
- Transcriptomics profiling of Niemann-Pick type C patients: activation of the unfold protein response in a specific casePublication . Encarnação, Marisa; Coutinho, Maria Francisca; Cho, Soo-Min; Cardoso, Maria Teresa; Chaves, Paulo; Gaspar, Paulo; Santos, Juliana Inês; Ribeiro, Isaura; Quelhas, Dulce; Lacerda, Lúcia; Leão-Teles, Elisa; Futerman, Anthony H.; Vilarinho, Laura; Alves, SandraBackground: Niemann-Pick type C (NP-C) is a neurodegenerative Lysosomal Storage Disease (LSD) with a heterogeneous clinical presentation secondary to abnormal intracellular accumulation of cholesterol. We have studied a patient with clinical diagnosis of NP-C but presenting inconclusive results regarding biomarkers testing and molecular analysis. To better characterize this patient, we have performed NGS-based technologies (targeted DNA sequencing and single cell-RNA sequencing). Methods: For the molecular diagnosis we used a NGS gene panel followed by the analysis of cDNA (in the patient and both parents). Latter, we have used massively parallel single cell RNA-seq (MARS-Seq) to address gene profiling changes and better characterize the pathomechanisms related to specific disease-causing mutations in this patient as well as in two NPC patients. The most prominent hits from this transcriptomics analysis were validated by qRT-PCR. Results and Discussion: Using our targeted NGS panel we identified two novel mutations in NPC1 gene (p.V505G; p.V562V). Next, through cDNA analysis of one of the patient parents we were able to understand the impact of the V562V silent mutation located in the middle of the exon 11. This mutation leads to exon 11 skipping giving origin to an out-of-frame transcript and eliciting the nonsense-mediated decay pathway. This mechanism contributed to the almost absence of the mutant transcript in the patient. Thus, we were not able to easily detect it in the sequencing electropherogram of the patient which turned the molecular diagnosis more challenging. By its turns, apparently the presence of the other mutation (the missense V505G) impairs the proper NPC protein folding leading to its ER retention. In fact, the MARS-Seq analysis of this patient showed that a number of genes were upregulated and a significant number of the highly enriched genes are related to the unfold protein response (UPR).
- The p.Ala1035Val variant in Niemann–Pick type C1: Clinical and molecular characterization in Brazilian and Portuguese patients suggests a shared founder effectPublication . Alegretti, Ana Paula; Hammerschmidt, Tatiane; Ribeiro, Isaura; Quelhas, Dulce; Polese-Bonato, Márcia; Saraiva-Pereira, Maria Luiza; Martins, Esmeralda; Guigliani, Roberto; Encarnação, Marisa; Alves Sandra; Regla Vargas, CarmenIntroduction: Niemann–Pick disease type C1 (NPC1, OMIM 257220) is a rare, progressive, and fatal autosomal recessive lysosomal storage disorder caused by pathogenic variants in the NPC1 gene. These variants disrupt intracellular lipid trafficking, leading to the accumulation of cholesterol and glycosphingolipids and resulting in severe, multisystem dysfunction for which no cure currently exists. Materials and methods: To investigate the potential founder effect and shared ancestry of the p.Ala1035Val variant, we analyzed 30 genetically confirmed NPC1 cases, comprising 18 Brazilian (12 of whom were homozygous) and 12 Portuguese participants (3 of whom were homozygous), each carrying at least one p.Ala1035Val allele. Diagnosis was established by clinical evaluation, biochemical assays, and filipin staining, with molecular confirmation by NPC1 genotyping. Results: All analyzed individuals exhibited a conserved haplotype across the SNVs in exons 6 (c.644 A > G, p.His215Arg), 12 (c.1926G > C, p.Ile642Met), 17 (c.2572 A > G, p.Ile858Val), and 18 (c.2793C > T, p.Asn931=), strongly supporting a shared founder effect consistent with an Iberian-associated ancestral background. Among Brazilian (n = 14), visceral involvement occurred in 10/14 (71.4%), predominantly hepatosplenomegaly (6/14, 42.9%), and developmental/cognitive alterations in 10/14 (71.4%), followed by ataxia or gait disturbance in 4/14 (28.6%). Among the Portuguese (n = 3), all presented with visceral involvement, characterized by hepatosplenomegaly (3/3, 100%); one had developmental delay (1/3, 33.3%), and none exhibited ataxia/gait disturbance. Despite the small sample size, clinical patterns appeared similar between the two groups, with differences likely reflecting sampling variability. Discussion: These findings expand the known variant spectrum of NPC1 in Brazilian and Portuguese populations, supporting a possible founder effect resulting from Portuguese colonisation. They also highlight the clinical value of haplotype analysis as a tool for tracing disease origin and improving stratification in medical settings. Furthermore, they emphasise the importance of refining early diagnostic strategies to optimise patient management and improve outcomes in NPC, while highlighting the need for larger, multicenter studies to corroborate this hypothesis and refine its clinical and genetic implications.