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- Analysis and evaluation of genotoxicity and carcinogenicity assessment in EU legislation to improve regulatory implementation of NAMs: A focus on in silico approachesPublication . Bossa, Cecília; Raitano, Giuseppa; Benfenati, Emilio; Alivernini, Silvia; Andreoli, Cristina; Aquilina, G.; Attias, L.; Dusinska, Maria; El Yamani, N.; Louro, Henriqueta; Marcon, Francesca; Rundèn-Pran, E.; Russo, Maria Teresa; Silva, Maria João; Battistelli, Chiara LauraGenotoxicity and carcinogenicity are key endpoints for the risk assessment of all types of substances. Research on alternatives to animal testing for these endpoints has been active for decades, leading to the development of short-term in vitro tests that are integrated into current testing strategies. Nevertheless, high relevance is still devoted to data from in vivo studies. In parallel, progress in the comprehension of mechanisms underpinning genotoxicity and genotoxic carcinogenicity processes, together with the analysis of the great wealth of experimental data produced, allowed the discovery of structural determinants utilized in quantitative and qualitative structure-activity relationships and enabling in silico predictions of these endpoints. Presented here is a case study part of the collective effort carried out within the European Partnership for the Assessment of Risks from Chemicals (PARC) to address the challenges associated with innovation in chemical risk assessment, including the phasing out of animal testing through the introduction of New Approach Methodologies (NAMs) [1,2]. The case study aims to analyze current practices of the regulatory evaluation of genotoxicity and carcinogenicity hazard in several EU frameworks, in order to highlight needs and challenges in the actual or potential use of NAMs as well as short-and long- term goals towards the overcoming of animal testing. Among other NAMs, we are focusing on the role of in silico approaches highlighting strategies to increase the regulatory application and acceptance of QSAR based approaches. To this aim, the OECD QSAR Assessment Framework [3,4] has been identified as a suitable tool for evaluating the models and their predictions and will be applied to selected case studies. Moreover, a list of human relevant carcinogens has been developed as reference chemicals to evaluate and possibly refine in silico methodologies supporting a human-centric paradigm shift in toxicology.
- Forty-four years of newborn screening in Portugal: new challenges, the same commitment to the communityPublication . Marcão, Ana; Sousa, Carmen; Pinho, Conceição; Ribeiro, Diogo; Rodrigues, Diogo; Guimarães, Fábio; Fonseca, Helena; Rocha, Hugo; Carvalho, Ivone; Lopes, Lurdes; Vilarinho, LauraIntrodução: O Programa Nacional de Rastreio Neonatal (PNRN) é um programa sistemático destinado a todos os recém-nascidos (RN) com nascimento em Portugal, e que atualmente inclui 28 patologias, das quais uma em estudo piloto. O aumento do número de patologias rastreadas, a implementação de novas e mais complexas técnicas de rastreio, o aumento da diversidade genética da população Portuguesa, os novos hábitos dietéticos e a exigência crescente da sociedade atual, trouxeram desafios que exigiram uma adaptação permanente do programa ao longo destes anos. Material e métodos: Mais de 4, 200 000 RN foram rastreados desde 1979. Diferentes métodos e estratégias de rastreio foram utilizados ao longo destes 44 anos. Atualmente, utilizam-se técnicas imunológicas (HC e CF), espectrometria de massa em tandem (IEM), eletroforese capilar (SCD) e estudo genético (FQ e SMA). Resultados: A antecipação da data de colheita (3º-6º dia), e a publicação de resultados na internet foram importantes mudanças organizacionais do programa. A alteração do protocolo de colheitas nos RN grandes prematuros veio responder à necessidade de evitar resultados falsos negativos no rastreio do CH. A performance do rastreio das 24 IEM foi claramente melhorada com a introdução de vários testes de segunda linha na estratégia de rastreio. A alteração recente da estratégia de rastreio da CF (2023), passando a incluir o estudo genético, trouxe uma melhoria extraordinária na performance deste rastreio, esperando-se ainda uma melhoria acrescida com uma nova alteração introduzida em 2024. As alterações efetuadas permitiram aumentar a sensibilidade e especificidade de deteção das várias patologias rastreadas e melhorar a resposta do PNRN à comunidade. Conclusão: O PNRN é um programa dinâmico que se mantém em constante atualização, quer em termos organizacionais e comunicacionais, quer em termos de patologias rastreadas e estratégias de rastreio. Desde 1979, mais de 2,700 casos positivos foram identificados e referenciados para CR, permitindo uma intervenção terapêutica adequada, com benefício dos RN e das famílias. A atualização permanente dos programas de rastreio, com adaptação constante aos novos desafios tecnológicos e às mudanças emergentes na comunidade a que se dirigem é fundamental para o seu sucesso.
- Transcriptomic response of Mytilus galloprovincialis to emerging contaminants: Data analysis workflowPublication . Copeto, Sandra; Ferreira, Inês; Duarte, Silvia; Vieira, Luís; Ferrão, José; Silva, Marco; Diniz, Mário; Motta, CarlaIntroduction: Environmental pollutants such as tetrabromobisphenol A (TBBPA), perfluoroalkyl substances (PFASs) like perfluorooctanoic acid (PFOA), and endocrine-disrupting compounds (EDCs) as 17α-ethinylestradiol (EE2) are commonly detected in coastal ecosystems. The Mediterranean mussel, Mytilus galloprovincialis, is a species of significant ecological and economic importance. Recent genomic studies have revealed an open pan-genome structure, with approximately 25–30% of protein-coding genes varying among individuals due to presence/absence variation (PAV). Assessing their molecular effects on marine organisms requires robust experimental models that reflect realistic exposure scenarios. Aim: Investigate transcriptomic alterations in M. galloprovincialis following exposure to environmentally relevant concentrations of TBBPA, PFOA, and EE2 under controlled laboratory conditions. Methods: Adult mussels were collected from Guincho coast (Portugal) and acclimated for 5 days under laboratory conditions (20 ± 1°C; salinity 33 ± 1 g·L⁻¹; pH 8.1). Mussels were then exposed for 28 days to TBBPA (1, 10, 100 µg/L), PFOA (1, 100 µg/L), or EE2 (10, 1000 ng/L), with and unexposed group (control). Each treatment consisted of four biological replicates (two males and two females). At the end of the exposure period, mussels were dissected, and soft tissues were preserved at −80°C. RNA was extracted from whole-body homogenates, and only samples with an RNA Integrity Number (RIN) > 9.0 were selected for sequencing. Results: RNA libraries were prepared using the Illumina TruSeq Stranded mRNA protocol and sequenced on a NextSeq 2000 platform (2×100 bp paired-end), generating over 85 Gbp of high-quality data (>84% bases with Q30). Raw reads underwent quality control using FastQC and MultiQC. Reads were aligned to the M. galloprovincialis reference genome using the splice-aware aligner STAR. Differential gene expression analysis was performed with DESeq2, and functional interpretation was based on Gene Ontology (GO) and KEGG pathway enrichment. Conclusion: This approach demonstrates the utility of mussel transcriptomics for ecotoxicogenomic assessment of marine pollution.
- Is Antisense Oligonucleotide-Mediated Exon Skipping a Potential Therapeutic Approach for Mucolipidosis II?Publication . Gonçalves, Mariana; Moreira, Luciana; Encarnação, Marisa; Duarte, Ana Joana; Gaspar, Paulo; Santos, Juliana Inês; Coutinho Maria Francisca; Prata, Maria João; Omidi, Maryam; Pohl, Sandra; Silva, Frederico; Oliveira, Paula; Matos, Liliana; Alves, SandraIntridution: Mucolipidosis II (ML II) is a Lysosomal Storage Disorder caused by N-acetylglucosamine-1-phosphotransferase (GlcNAc-PT) deficiency, which impairs lysosomal hydrolases trafficking. Here, we explored an innovative therapeutic strategy based on the use of antisense oligonucleotides (ASOs) to promote targeted skipping of GNPTAB exon 19, which harbors c.3503_3504del, the most frequent disease-causing variant. Previously, in ML II patients’ fibroblasts, we tested ASOs to induce exon 19 skipping, successfully generating an in-frame mRNA1. Now, our aim is to determine if this in-frame transcript leads to increased GlcNAc-PT levels. Methodology: First, the GlcNAc-PT activity was measured in fibroblasts, but activity levels were similar in ML II and control fibroblasts (treated/non-treated) showing that the assay is not proper to measure endogenous levels. To overcome this, we designed 3 constructs: a WT (full GNPTAB cDNA), a del_ex19 (without exon 19) and a mutant (with the mutation c.3503_3504del) that were transfected in HEK293T cells. Then GlcNAc-PT expression was analyzed by Western Blot (WB). Also, we measured the activity of several hydrolases and evaluated the expression of α-galactosidase A (α-Gal) by WB after ASO treatment. To further validate this therapy we also generated a novel GlcNAc-PT antibody in rabbits. Results: Our results showed that HEK293T cells were able to express all the constructs. The WB of both WT and del_ex19 constructs showed bands corresponding to the α/β precursor. However, only the WT construct expressed the β-subunit, suggesting that there is no GlcNAc-PT activity in the absence of exon 19. As expected, in the delTC construct WB no α/β precursor band was detected. We also observed a slight increase in the activity of various lysosomal hydrolases in ML II fibroblasts after treatment. However, only the α-Gal values were statistically significant, but the WB analysis for this enzyme did not reveal any band in ASO-treated ML II cells. We also developed a novel antibody for GlcNAc-PT. Preliminary results showed a β-subunit band both in control and patient fibroblasts (unexpected), but in overexpression both WT and del_ex19 constructs presented α/β precursor bands. So, further assays are needed to assess its specificity. Conclusion: Our ASO-based approach effectively promotes exon 19 skipping. However, this strategy, as far as we have been able to prove, is not able to restore any GlcNAc-PT enzymatic activity. Further validation, including co-localization studies are planned to clarify these findings.
- Early diagnosis of acid sphingomyelinase deficiency (ASMD) through biomarkers analysisPublication . Neiva, Raquel; da Silva Gaspar, Paulo Jorge Miranda; Sousa e Silva, Lisbeth Elena; Gonçalves, I.; Ferreira, S.; Diogo, Luisa; Vilarinho, LauraIntroduction: Acid sphingomyelinase deficiency (ASMD), historically known as Niemann–Pick disease (NPD) types A, A/B, and B, is a rare, progressive, potentially fatal lysosomal storage disease caused by pathogenic variants in SMPD1 gene. It presents a wide spectrum of symptoms, age of onset, and degree and type of organ effected. The disease manifestations frequently involve hepatosplenomegaly with progressive organ dysfunction, interstitial lung disease, and bleeding. In this work, we will present a patient whose lysosomal biomarkers study allowed the diagnosis of ASMD. Methods: This patient had hepatosplenomegaly, elevated transaminases in which the primary clinical suspicion was an acid lipase deficiency. By the analysis of our multiplex biomarker panel by LC-MS/MS analysis, we were able to do a differential diagnosis. Results/Case report: The lysosphingomyelin (lysoSM) and lysosphingomyelin-509 (lysoSm-509) were approximately 100 a 150x than normal, suggestive of Niemann–Pick disease. The diagnosis of ASMD was confirmed by reduced acid sphingomyelinase enzyme activity measured in peripheral blood leukocytes and the presence of a pathogenic variant in both alleles in the SMPD1 gene. Conclusion: ASMD can be underestimate and the diagnostic odissey arise from an overlap in symptomology with other diseases, including primary hepatic disease, Gaucher disease, Niemann–Pick disease, and lysosomal acid lipase deficiency. The multiplex biomarker panel, with different lysolipids, allows simultaneously diagnosis of different LSDs, in a timely manner, leading to an early intervention, before the appearance of more deleterious symtpoms.
- Diagnóstico pré-natal num feto com deleção intersticial na região 6p25.3, restrição de crescimento fetal e artéria subclávia direita aberrantePublication .A restrição de crescimento fetal (RCF) é uma das complicações mais frequentes no período fetal, associando-se a um aumento da morbilidade e mortalidade perinatais. Deleções na região 6p25.3 estão associadas a síndromes específicos, com poucos dados pré-natais. Apresentamos o caso de uma grávida, referenciada por RCF e artéria subclávia direita aberrante (ARSA) no feto. Fez-se amniocentese às 23 semanas. Pretende-se identificar condições genéticas associadas e um melhor conhecimento em DPN. Realizou-se o estudo por microarray (CytoScan 750K) e, posteriormente, estudos do cariotipo e microarray nos progenitores. O microarray identificou uma deleção intersticial, com 1,30 Mb, em 6p25.3, num perfil do sexo feminino. Esta alteração inclui o gene FOXC1, integrando-se na região de síndrome de deleção 6pter-p24. Os estudos no pai revelaram uma deleção semelhante à do feto. Atendendo à gravidade das síndromes associadas à deleção encontrada, à fase da gestação, ao contexto de RCF e ARSA, o casal optou pela interrupção médica da gravidez. A síndrome de deleção 6pter-p24 caracteriza-se pela presença de anomalias do sistema nervoso central, dismorfias faciais, atraso de desenvolvimento, malformações oculares, anomalias esqueléticas e cardíacas. Geralmente, origina-se de novo. Apresenta considerável sobreposição clínica com a síndrome de Axenfeld-Rieger, também relacionada com alterações no gene FOXC1. Alterações semelhantes são classificadas com significado clínico provavelmente patogénico. Em DPN, os raros casos descritos com deleções semelhantes apresentam sobretudo malformação de Dandy-Walker e anomalias cardíacas. O facto de a alteração fetal ser semelhante à do pai constituiu um achado relevante pois, do nosso conhecimento, esta herança da deleção não está descrita. O pai apresentou problemas de crescimento e tem algumas anomalias esqueléticas referidas na literatura, sem as patologias mais graves associadas às síndromes nesta região. Alguns autores referem uma penetrância e expressividade elevadas, mas não completas. Salienta-se a importância do microarray na identificação de alterações genéticas em casos com RCF.
- Reverse phenotyping after ngs panel of x-linked intellectual disability unravels creatine transporter (SLC6A8) deficiencyPublication . Padeira, Gonçalo; Jacinto, Sandra; Venâncio, Margarida; Marcão, Ana; Conceição, Carla; Ferreira, Ana CristinaX-linked intellectual disability (XLID) is characterized by extensive genetic heterogeneity. Next-generation sequencing (NGS) have been used in these cases as a cost-effective diagnosis approach. Genetic findings often reveal variants unforeseen during clinical investigation, prompting the need for reevaluation of specific features designated as reverse phenotyping (RP). X-linked creatine transporter deficiency (CTD) is a potentially treatable intellectual disability caused by pathogenic variants in the SLC6A8 gene leading to impaired creatine transport into the brain. A 7-year-old boy with intellectual disability, speech delay, hyperactivity and epilepsy was referred to Metabolic and Neuropediatric Clinic. Family history identified a mother with learning difficulties and a maternal uncle with intellectual disability, indicating a possible X-linked inheritance. NGS intellectual disability panel identified a variant classified as probably pathogenic (c.880_881del (p(Lys294Alafs*2)) in the SLC6A8 gene, in hemizygosity which prompted referral to Metabolic and Neuropediatric Clinic. Reverse phenotyping was carried out with biochemical and imaging assessment that showed: high urinary Creatine-Creatinine ratio (2.17; RV 0.04-1.07) with normal guanidinoacetate acid and absence of creatine peak in brain MRI spectroscopy, confirming the diagnosis. Genetic studies on female family members are ongoing. He started treatment with creatine, arginine and glycine in the last appointment. CTD is a rare disease that has been reported in more than 150 individuals worldwide. We present a case in which the diagnostic approach was reverse phenotyping, through biochemical and imaging studies, after the identification of pathogenic variants in SLC6A8 by NGS panel. The efficacy of its treatment remains controversial with variable results, and a close evaluation will be needed.
- Upstream Open Reading Frames Regulate PERK Translation InitiationPublication . Fernandes, Rafael; Silvestre, Samuel; Ponte, João; Lacerda, Rafaela; Romão, LuísaIntroduction: Upstream open reading frames (uORFs) are cis-acting elements located within the 5’ leader sequence (5’UTR) of transcripts, which can regulate translation of the correspondent main open reading frame (mORF). During endoplasmic reticulum (ER) stress, the accumulation of unfolded proteins activates the ER-resident PKR-like ER kinase (PERK), which results in phosphorylation of eIF2α to inhibit global mRNA translation, while allowing the selective uORF-mediated translation of downstream effectors responsible for stress resolution or, ultimately, cell death. The dual role of PERK in regulating cell fate was implicated in human diseases, like diabetes, neurodegenerative disorders and cancer. Moreover, mutations in the EIF2AK3 gene (encoding PERK) were associated to the rare genetic disease, Wolcott-Rallison Syndrome (WRS).
- The potential function of alternative translation initiation of Argonaute 1 in cancerPublication . Vieira da Silva, Verónica; Lacerda, Rafaela; Romão, LuísaTranslation is one of the most regulated and energy-consuming cellular processes crucial for proper cell function. Translation is initiated by the canonical cap-dependent mechanism. However, under stress conditions, the initiation of canonical translation is inhibited, which allows the translation of specific proteins via alternative mechanisms. This project aims to understand the biological relevance of alternative protein synthesis mechanisms in Argonaute 1 (AGO1) expression. The AGO1 protein is involved in microRNA regulation, gene expression modulation and inhibition. AGO1 is also involved in the regulation of gene expression by RNA interference (RNAi), and its deregulation can lead to the activation of oncogenes or the suppression of tumor suppressor genes, contributing to the development and progression of cancer. Our work has shown that AGO1 mRNA can be translated through a cap-independent initiation mechanism. An upstream open reading frame (uORF) has also been identified in its 5’ untranslated region (5’UTR), which may play a role in the initiation of AGO1 translation. The results showed that the 5’UTR of human AGO1 supports a cap-independent mechanism of translation initiation, which is maintained under stress conditions. However, our analyses did not provide conclusive evidence for a regulatory role of the uORF in this initiation process. To this end, the 5’UTR of human AGO1 was cloned into a bicistronic vector containing Renilla (RLuc) and Firefly luciferase (FLuc), with FLuc positioned downstream of the 5’UTR. Luminometry assays will be used to evaluate the relative FLuc/RLuc translation efficiency under the control of the AGO1 5’UTR. The same approach will be used with monocistronistic reporter vectors, contaning only FLuc. This project aims to understand how these alternative mechanisms of mRNA translation initiation can influence AGO1 expression and help explain their potential roles in certain pathologies and cancer progression, such as colorectal cancer.
- Olipudase alfa enzyme replacement therapy. One-year outcomes in an adult patient with acid sphingomyelinase deficiency type BPublication . Cardoso, M.; Chaves, P.C.; Pintalhão, M.; da Silva Gaspar, Paulo Jorge Miranda; Castro, R.; Bastos, J.; Silva, A.; Campos, T.; Macedo, Fatima; Rodrigues, E.; Leão Teles, ElisaIntroduction: Acid Sphingomyelinase Deficiency (ASMD) is a rare autosomal recessive lysosomal storage disorder caused by variants in the SMPD1 gene, leading to a deficiency in the activity of sphingomyelinase (ASM) that catabolizes sphingomyelin (SPM). ASMD Type B is a late-onset, severe disease characterized by progressive hepatosplenomegaly, gradual deterioration of liver and pulmonary function, osteopenia and an atherogenic lipid profile. Olipudase alfa is a recombinant human ASM enzyme replacement therapy indicated for the treatment of non-C-NS manifestations of ASMD.