Departamento de Genética Humana
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Browsing Departamento de Genética Humana by Field of Science and Technology (FOS) "Ciências Médicas"
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- Changes in environmental exposures over decades may influence the genetic architecture of severe spermatogenic failurePublication . Cerván-Martín, Miriam; González-Muñoz, Sara; Guzmán-Jiménez, Andrea; Higueras-Serrano, Inmaculada; Castilla, José A.; Garrido, Nicolás; Luján, Saturnino; Bassas, Lluís; Seixas, Susana; Gonçalves, João; Lopes, Alexandra M; Larriba, Sara; Palomino-Morales, Rogelio J.; Bossini-Castillo, Lara; Carmona, F. DavidStudy question: Do the genetic determinants of idiopathic severe spermatogenic failure (SPGF) differ between generations? Summary answer: Our data support that the genetic component of idiopathic SPGF is impacted by dynamic changes in environmental exposures over decades. What is known already: The idiopathic form of SPGF has a multifactorial etiology wherein an interaction between genetic, epigenetic, and environmental factors leads to the disease onset and progression. At the genetic level, genome-wide association studies (GWASs) allow the analysis of millions of genetic variants across the genome in a hypothesis-free manner, as a valuable tool for identifying susceptibility risk loci. However, little is known about the specific role of non-genetic factors and their influence on the genetic determinants in this type of conditions. Study design, size, duration: Case-control genetic association analyses were performed including a total of 912 SPGF cases and 1360 unaffected controls. Participants/materials, setting, methods: All participants had European ancestry (Iberian and German). SPGF cases were diagnosed during the last decade either with idiopathic non-obstructive azoospermia (n = 547) or with idiopathic non-obstructive oligozoospermia (n = 365). Case-control genetic association analyses were performed by logistic regression models considering the generation as a covariate and by in silico functional characterization of the susceptibility genomic regions. Main results and the role of chance: This analysis revealed 13 novel genetic association signals with SPGF, with eight of them being independent. The observed associations were mostly explained by the interaction between each lead variant and the age-group. Additionally, we established links between these loci and diverse non-genetic factors, such as toxic or dietary habits, respiratory disorders, and autoimmune diseases, which might potentially influence the genetic architecture of idiopathic SPGF. Large scale data: GWAS data are available from the authors upon reasonable request. Limitations, reasons for caution: Additional independent studies involving large cohorts in ethnically diverse populations are warranted to confirm our findings. Wider implications of the findings: Overall, this study proposes an innovative strategy to achieve a more precise understanding of conditions such as SPGF by considering the interactions between a variable exposome through different generations and genetic predisposition to complex diseases.
- Comparison of the ABC and ACMG systems for variant classificationPublication . Houge, Gunnar; Bratland, Eirik; Aukrust, Ingvild; Tveten, Kristian; Žukauskaitė, Gabrielė; Sansovic, Ivona; rea-Fernández, Alejandro J.B; Mayer, Karin; Paakkola, Teija; McKenna, Caoimhe; Wright, William; Markovic, Milica Keckarevic; Lildballe, Dorte L.; Konecny, Michal; Smol, Thomas; Alhopuro, Pia; Gouttenoire, Estelle Arnaud; Obeid, Katharina; Todorova, Albena; Jankovic, Milena; Lubieniecka, Joanna M.; Stojiljkovic, Maja; Buisine, Marie-Pierre; Haukanes, Bjørn Ivar; Lorans, Marie; Roomere, Hanno; Petit, François M.; Haanpää, Maria K.; Beneteau, Claire; Pérez, Belén; Plaseska-Karanfilska, Dijana; Rath, Matthias; Fuhrmann, Nico; Ferreira, Bibiana I.; Stephanou, Coralea; Sjursen, Wenche; Maver, Aleš; Rouzier, Cécile; Chirita-Emandi, Adela; Gonçalves, João; Kuek, Wei Cheng David; Broly, Martin; Haer-Wigman, Lonneke; Thong, Meow-Keong; Tae, Sok-Kun; Hyblova, Michaela; Dunnen, Johan T. den; Laner, AndreasThe ABC and ACMG variant classification systems were compared by asking mainly European clinical laboratories to classify variants in 10 challenging cases using both systems, and to state if the variant in question would be reported as a relevant result or not as a measure of clinical utility. In contrast to the ABC system, the ACMG system was not made to guide variant reporting but to determine the likelihood of pathogenicity. Nevertheless, this comparison is justified since the ACMG class determines variant reporting in many laboratories. Forty-three laboratories participated in the survey. In seven cases, the classification system used did not influence the reporting likelihood when variants labeled as “maybe report” after ACMG-based classification were included. In three cases of population frequent but disease-associated variants, there was a difference in favor of reporting after ABC classification. A possible reason is that ABC step C (standard variant comments) allows a variant to be reported in one clinical setting but not another, e.g., based on Bayesian-based likelihood calculation of clinical relevance. Finally, the selection of ACMG criteria was compared between 36 laboratories. When excluding criteria used by less than four laboratories (<10%), the average concordance rate was 46%. Taken together, ABC-based classification is more clear-cut than ACMG-based classification since molecular and clinical information is handled separately, and variant reporting can be adapted to the clinical question and phenotype. Furthermore, variants do not get a clinically inappropriate label, like pathogenic when not pathogenic in a clinical context, or variant of unknown significance when the significance is known.
- Newborn Screening for Sickle Cell Disease: Results from a Pilot Study in the Portuguese PopulationPublication . Rodrigues, Diogo; Marcão, Ana; Lopes, Lurdes; Ventura, Ana; Faria, Teresa; Ferrão, Anabela; Gonçalves, Carolina; Kjöllerström, Paula; Castro, Ana; Fraga, Sofia; Almeida, Marta; Maia, Tabita; Gomes, João; Lachado, Ana; Guerra, Isabel; Ferreira, Fátima; Trigo, Fernanda; Bento, Celeste; Vilarinho, LauraThe Portuguese Newborn Screening Program currently includes 28 pathologies: congenital hypothyroidism, cystic fibrosis, 24 inborn errors of metabolism, sickle cell disease and spinal muscular atrophy. This pilot study for sickle cell disease newborn screening, including 188,217 samples, was performed between May 2021 and December 2023, with phase I, including 24,130 newborns, in the Lisbon and Setubal districts and phase II, including 164,087 newborns, in the whole country. DBS samples were analyzed through capillary electrophoresis. In phase I, a high birth incidence of sickle cell disease was found (1:928 NBs), resulting from the identification of 24 HbSS and 2 HbSC patients. This birth incidence decreased but remained significant when the pilot study for sickle cell disease newborn screening was expanded to a national level, with the identification of 67 sickle cell disease patients (59 HbSS and 8 HbSC), revealing a birth incidence of 1:2449 NBs. These data suggest that this condition is becoming increasingly relevant in Portugal, thus reflecting a general European trend, where sickle cell disease is already recognized as a public health problem. Therefore, it highlights the importance of its integration into the Portuguese National Newborn Screening Program panel in January 2024, thus allowing the early identification and clinical follow-up of these patients.
- Pesquisa de Deleções/Duplicações em Genes Associados a Cancro Hereditário por MLPA DigitalPublication . Alves, Beatriz Correia; Gonçalves, João; Melo, Maria Joana Lima BarbosaA presença, na linha germinativa, de Variações do Número de Cópias (CNV) em genes de predisposição para cancro hereditário pode aumentar a suscetibilidade a esta doença. A identificação de uma CNV patogénica ou provavelmente patogénica num doente oncológico tem um impacto significativo na gestão clínica do indivíduo afetado e dos seus familiares. Tradicionalmente, a pesquisa de CNV no diagnóstico molecular de cancro hereditário é realizada apenas para alguns genes através do MLPA (Multiplex Ligation-dependent Probe Amplification) convencional. Nos últimos anos, o desenvolvimento de softwares de análise in silico de CNV com base em dados de NGS (Next-Generation Sequencing) representou um avanço significativo, ao possibilitar a pesquisa de deleções e duplicações em múltiplos genes em simultâneo. No entanto, estas ferramentas apresentam ainda limitações. Dada a relevância de uma análise abrangente que integre o maior número possível de genes relevantes no âmbito da patologia em causa, este trabalho teve como principal objetivo implementar uma nova metodologia de pesquisa de CNV em genes associados a cancro hereditário, que combina os princípios do MLPA convencional com a capacidade da NGS de analisar vários genes em simultâneo: o MLPA digital. Neste estudo, foi realizada a pesquisa de CNV por MLPA digital em amostras de doentes com história clínica e familiar de cancro, seguida de validação dos resultados utilizando outras metodologias de genética molecular e classificação das variantes identificadas segundo as recomendações da CanVIG-UK. O MLPA digital demonstrou ser eficaz na deteção de deleções e duplicações em genes associados a cancro hereditário, apresentando um desempenho adequado para a utilização em laboratórios clínicos, com sensibilidade de 100% e especificidade de 98%. A eficácia dos softwares de pesquisa in silico panelcn.MOPS e DRAGEN Enrichment foi confirmada através da concordância entre os resultados destas ferramentas e do MLPA digital. Foram identificadas cinco variantes patogénicas ou provavelmente patogénicas nos genes APC, BRCA1, BRCA2 e CHEK2, que justificam os fenótipos dos doentes. Este estudo demonstra que o MLPA digital é uma alternativa ao MLPA convencional na primeira fase de pesquisa molecular de CNV germinativas em genes associados a cancro hereditário, permitindo a análise de múltiplos genes em várias amostras em simultâneo.
- Sitosterolemia In iberoamerican countries: 16 new cases and phenotype genotype analysisPublication . Alves, Ana Catarina; Chora, Joana Rita; Miranda, Beatriz; Medeiros, Ana Margarida; Graça, Rafael; Bañares, Virginia G.; Araujo, Maria Beatriz; Vilagut, Ferrán Trías; Soler, Cristina; Meavilla, Silvia; Toledo, Maria J. Benitez; Volpe, Camila Garcia; Reyes, Ximena; Dell'Oca, Nicolás; Martins, Paula; Marado, Diana; Vilarinho, Laura; Dias, Aureliano Jorge; Ferreira, Ana Cristina; Padeira, Gonçalo; Casañas, Marta; Alegre-González, Diana; Lozano, José Mosquera; Aguiar, Patrício; Gonçalves, Filipa Sousa; Ernaga, Ander; Apellaniz-Ruiz, Maria; Rubi, Rodrigo; Figueroa, Nahún Muñoz; Vasquez, Norma Alejandra; Valdivielso, Pedro; Bourbon, Mafalda; ElsevierBackground: Sitosterolemia is a rare autosomal recessive lipid disorder caused by biallelic pathogenic variants in ABCG5 or ABCG8 genes. It is characterized by elevated plasma plant sterol concentrations, xanthomas, and an increased risk of premature cardiovascular disease. As happens with familial hypercholesterolemia (FH), sitosterolemia is subdiagnosed and is frequently confounded with FH, resulting in inappropriate management. This study aims to describe newly identified cases across Iberoamerican countries and to highlight the need for improved diagnostic strategies. Methods: We report 16 cases of molecularly confirmed sitosterolemia from 5 Iberoamerican countries (Argentina, Mexico, Portugal, Spain, and Uruguay), including 12 index cases and 4 relatives identified by cascade screening. Clinical, biochemical, and molecular data were collected and analyzed. β-sitosterol levels were measured when possible, and variant classification followed American College of Medical Genetics and Genomics (ACMG) guidelines with disease-specific adaptations. Results: Fifteen individuals had biallelic variants in ABCG8 and 1 had a homozygous frameshift variant in ABCG5. Ten distinct ABCG8 variants were identified, including 7 nonsense and 3 missense variants. Xanthomas were observed in 56% of cases. Most cases were initially diagnosed as FH, with a diagnostic delay of up to 30 years. Treatment with ezetimibe, alone or combined with statins, led to biochemical and clinical improvement, including xanthoma regression in some cases. Conclusion: Sitosterolemia remains underdiagnosed due to lack of systematic screening and clinical overlap with FH. Our findings highlight the importance of including ABCG5/8 in genetic testing panels and of recognizing clinical clues for early diagnosis, enabling targeted treatment and prevention of adverse outcomes. Adapted ACMG variant classification improves interpretability for ABCG5/8-related sitosterolemia.
- The role of UPF1 cap-independent translation in colorectal cancerPublication . Lacerda, Rafaela; Menezes,Juliane; Elias, Adriana; Sousa, Sofia de; Romão, LuísaColorectal cancer (CRC) is one of the deadliest diseases worldwide with projections pointing towards an increase for the next two decades. Translation dysregulation of many genes contributes to CRC development, and here we are studying the role of translation dysregulation of up-frameshift 1 (UPF1) in CRC. This protein is involved in many cellular mechanisms such as nonsense-mediated mRNA decay, cell cycle progression, or telomere maintenance and homeostasis. It also works as a tumour suppressor protein in most cancers but not in CRC, in which UPF1 plays an oncogenic role. We used the Xena platform to perform in silico analyses that revealed UPF1 protein overexpressed in CRC, contrary to several other analysed cancers. Besides, UPF1 protein levels are increased in CRC compared to the counterpart normal tissues. Experimentally, we confirmed that UPF1 protein expression is maintained in different CRC cell lines under normal conditions or endoplasmic reticulum (ER) stress. To understand the mechanism underlying such maintenance, we used a bicistronic reporter construct to test whether UPF1 5’ untranslated region (UTR) can mediate alternative translation initiation and we concluded that such sequence drives cap-independent translation initiation, in both normal and stress conditions. Deletional and mutational analyses of UPF1 5’UTR showed that nucleotides 1–100 [stem-loop (SL) I] and 151–275 (SL III) — out of 275 nucleotides — are the minimal required sequences for the cap-independent translation initiation mechanism to work properly. Using RNA antisense oligonucleotides (ASOs) targeting UPF1 SL I and III, we observed a reduced UPF1 expression in HCT116 (CRC) cells, supporting the functional role of SL I and SL III in mediating cap-independent translation. Altogether, these results highlight the importance of cap-independent translation initiation in UPF1 expression regulation, in conditions that mimic the tumour microenvironment, and this might be used as a therapeutic target.