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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.
- Dysregulated gene expression in colorectal cancer upon exposure to bisphenol A alternatives - a new approachPublication . Lacerda, Rafaela; Ventura, Célia; Louro, Henriqueta; Silva, Maria João; Romão, LuísaBisphenol A (BPA) has been widely used in plastics and resins since the 1950s, making it a common part of everyday products like food containers and bottle linings. Alternative substances are increasingly replacing BPA, but they are raising health and environmental concerns. Some mimic BPA’s endocrine-disrupting effects, while others affect different biological pathways. Substitutions in bisphenols can alter their biological properties, including nuclear receptor activation. Some BPA alternatives, like BPS, BPF and BPZ, may also pose cancer risks by activating oestrogen receptors, potentially even more than BPA itself. They may also contribute to colorectal cancer (CRC). Research suggests that BPA and its substitutes can influence cancer progression by altering cellular pathways, promoting metastasis and affecting gene expression. One of the key steps in gene expression regulation is translation initiation, whose canonical pathway is globally impaired under stress conditions, like exposure to BPA alternatives. Thus, we will subject NCM460 (normal intestinal mucosa) and HCT116 (colorectal carcinoma) cells to BPS, BPF and BPZ exposure and identify the transcripts actively being translated in such conditions, using ribosome profiling. We will analyse data with the R package anota2seq and evaluate the positively identified targets (compared to total RNA sequencing) for the existence of alternative mechanisms of translation initiation regulating their expression. The accurate characterisation of such mechanisms will be crucial for designing antisense RNA oligomers (ASOs) for potential therapeutic approaches. We will evaluate the cytotoxic effects of BPS, BPF and BPZ in the presence or absence of the selected alternatively translated transcripts (functional or targeted with the designed ASOs). Cytotoxic effects will be assessed through in vitro assays, analysing metabolic activity, membrane integrity, and cell proliferation. Thus, our research explores protein synthesis dysregulation to reduce CRC risks from BPS, BPF and BPZ exposure — an emerging public health issue.
- 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.
- 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.