Departamento de Genética Humana
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- Addressing a challenging enzyme in vitro: proof of principle on the therapeutic potential of an antisense oligonucleotide approach for ML IIPublication . Matos, Liliana1. To confirm the specificity of selected ASOs to skip the GNPTAB exon 19, a scramble ASO (expected to have no effect on GNPTAB gene) was transfected in WT & ML II patient fibroblasts. RT-PCR results showed that this ASO did not changed exon 19 splicing pattern proving the specificity of GNPTAB ASOs (Fig1A). Also, the enzymatic activity of various hydrolases was analysed in the same transfected cells. Results showed that the scramble ASO seems to interfere, even if little, with hydrolases activities of treated WT & ML II fibroblasts as shown by the differences in activities observed (Fig1B). The experiments number need to be increased to confirm these results. 2. To analyse the effect of exon 19 skipping on the GlcNAc-PT, a WT construct with the full GNPTAB cDNA (pGNPTAB_WT) and a mutant without exon 19 (pGNPTAB_delEx19) were tested in HEK293T cells. RT-PCR results after transfection showed the expected transcript pattern in both constructs (Fig2A). Moreover, GNPTAB protein expression was analysed by Western Blot (WB) using an antibody (Ab) specific for a myc-His tag located in constructs downstream the GNPTAB insert. Both constructs expressed a band corresponding to the α/β precursor, with or without exon 19. However, regarding the cleaved β-subunit the results are not so clear since we observed 2 bands (~48KDa) for the WT construct and further analysis is needed to understand if any of them corresponds to the target (Fig2B). Both constructs were also transfected in ML II fibroblasts and cDNA analysis showed the expected transcript pattern. The activity of hydrolases will also be assessed to check if it increases with the delEx19 construct expression, suggesting a potential therapeutic effect. 3. We generated a novel Ab for the GlcNAc-PT β-subunit (rabbits). We expected to detect the protein in WT but not in ML II fibroblasts. However, WB results showed a band with the expected protein size in both cases (Fig3A). So, to test the Ab specificity different assays were done. The pre-bleed serum of the immunized rabbits was tested by WB and no target band was detected confirming that animals did not have Abs against the human protein (Fig3B). Also, the 2 synthetic β-subunit peptides used to immunize the animals were detected by WB confirming the specificity of the produced Abs (Fig3C). Protein sequencing (mass spectrometry) was also performed in extracts of WT & ML II fibroblasts after SDS-Page to search for the GNPTAB protein. As our Ab target has 45KDa, bands within 37-50KDa were analysed but the protein was not detected not even in the WT, suggesting that the protein amount used was insufficient for target protein detection. Finally, the Ab was tested by WB in HEK293T cells transfected with both constructs and the expected protein pattern at least for the α/β precursor was observed (Fig3D). This last experiment needs to be repeated, however results obtained in the various assays suggest that our Ab is specific for GNPTAB protein detection.
- Assessing the pro inflammatory effects of bisphenol compounds using exposure relevant in vitro co culture modelsPublication . Pereira, Gonçalo Alexandre Candeia; Jordan, Peter; Rodrigues, CecíliaInflammation has reached epidemic proportions in industrialized countries, mainly due to unhealthy habits, poor diet, environmental pollution and other factors not yet understood. If uncontrolled or prolonged, inflammation can become chronic and contribute to the development of a number of human diseases, including autoimmune diseases, intestinal diseases and, in the worst cases, tumorigenesis and tumor progression. Exposure to endocrine disrupting chemicals (EDCs) is one environmental factor contributing to inflammation, and recent studies have brought the bisphenol (BP) group of EDCs into the scientific spotlight. They have been strongly linked to various pathologies, including chronic inflammation, and their effect on human gut health is a hot topic in the scientific community. With this in mind, the aim of this work was proposed to analyze the effects of four bisphenols, BPA, BPS-MAE, BPAP and BPP, on intestinal barrier stress and associated pro-inflammatory effects. To achieve this, a co-culture system was optimized and established, consisting of an improved protocol of polarized Caco-2 epithelial cells seeded on PET insert filters in an apical compartment, together with THP-1 derived macrophages in a basolateral compartment. Subsequently, the effects of BPs exposure on barrier integrity, cellular stress and pro-inflammatory cytokine were tested in a wide range of concentrations (from 100 μM to 0.1 μM). Experimentally, we found that the model was capable of delivering BP-specific data on potential health effects. In terms of transepithelial resistance and epithelial stress, we were able to identify some clear trends that need to be consolidated with more independent experimental replicates. In particular, BPA was the least potent inducer of cellular stress responses and changes in epithelial polarization, whereas the BP analogues tested proved to be more disruptive than BPA, with BPP appearing to be the most potentially hazardous, followed by BPAP and then BPS-MAE. To access the inflammation-modulating effects of these compounds, we tested macrophages, either directly or as co-cultured cells, for expression of the pro-inflammatory marker IL-1β using a semiquantitative RT-PCR approach. An important optimization was their priming with IFN-γ to increase the sensitivity of the model and allow for more physiological relevance. Our observations showed that, once again, the BP analogues induced greater effects compared to BPA. BPP appeared to be the more potent inducer of inflammation, followed by BPS-MAE. Both showed elevated levels of the IL-1β marker at all concentrations tested. BPAP and BPA produced more attenuated effects, although significant at higher concentrations. In conclusion, this work has provided us with landmark results on these BPA analogues and their effects on gut health, adding new insights into the 'new generation' of emerging BPs and their potential adverse health effects.
- Bioquímica e Biomedicina - OncobiologyPublication . Jordan, PeterConjunto de 10 aulas da Unidade Curricular Oncobiologia no âmbito do Mestrado em Bioquímica e Biomedicina da FCUL, entre fevereiro e junho de 2025.
- BPA analogues affect intestinal barrier integrity and pro-inflammatory response in a coculture modelPublication . Pereira, Gonçalo; Barros, Patrícia; Matos, Paulo; Jordan, PeterBackground: Bisphenol (BP) A and its structural analogues are environmental pollutants with endocrine-disrupting properties and potential immune-modulating effects. Following legal restrictions on the use of BPA, structurally related compounds including BPAP, BPP, and BPS-MAE have been introduced as alternatives; however, their potential hazardous profiles remain largely unknown. Here we used a coculture cell model to investigate the effects of exposure to these BP analogues on intestinal barrier integrity, intestinal cell stress, and pro-inflammatory macrophage activation. Methods: As cellular model, Caco-2 cells were grown on filter membranes to a polarized epithelium-like layer, and cocultured with underlying basolateral THP-1 derived M0 macrophages. After apical exposure of the Caco-2 cells layer to BPs (0.1 -100 µM for 24 h), we determined transepithelial electrical resistance (TEER), polarized cell morphology by confocal microscopy, cellular stress markers (p-p38MAPK, p-JNK, p-eIF2α) by Western blot, and macrophage activation by IL-1β-transcript expression changes. In addition, M0-type macrophages were also directly incubated with BPA for comparison. Results: When M0 macrophages were directly exposed, BPA triggered IL-1β expression, an effect more evident after macrophage sensitization by the presence of interferon-γ. Apical exposure to BPA and BPS-MAE had little effect on TEER but induced some increase in epithelial stress markers, while BPAP and especially BPP clearly reduced TEER and polarized cell morphology, and showed a tendency to induce stress markers. In addition, apical cell exposure to BPP and BPS-MAE triggered clear expression of the pro-inflammatory marker IL-1β in sensitized M0 macrophages cocultured at the basolateral side, whereas BPAP and BPA were only effective at the highest concentration. Conclusion: Together, our data show that exposure of an intestinal epithelium-like layer to BPAP and BPS-MAE revealed adverse cellular effects similar to BPA, while BPP was clearly the most deleterious BP analogue. Pro-inflammatory macrophage activation was strongest after exposure to BPP followed by BPS-MAE.
- Can an Antisense Oligonucleotide Exon Skipping Rewrite the Story of N-Acetylglucosamine-1-Phosphotransferase Deficiency?Publication . Gonçalves, M.; Moreira, L.; Encarnação, M.; Gaspar, P.; Duarte, A.J.; Santos, J.I.; Coutinho, M.F.; Prata, M.J.; Omidi, M.; Pohl, S.; Silva, F.; Oliveira, P.; Matos, L.; Alves, S.Mucolipidosis II (ML II) is a Lysosomal Storage Disorder caused by N-acetylglucosamine-1-phosphotransferase (GlcNAc-PT) deficiency, which impairs the trafficking of lysosomal hydrolases. Of all ML II mutations, c.3503_3504delTC in GNPTAB exon 19 is the most frequent, making it a good target for a personalized therapy. Here, we explored an innovative therapeutic strategy based on the use of antisense oligonucleotides (ASOs). Previously, in ML II patients’ fibroblasts, we tested ASOs to induce exon 19 skipping in pre-mRNA, successfully generating an in-frame mRNA (Matos et al., 2020). Now, our aim is to determine whether this in-frame transcript leads to increased GlcNAc-PT levels improving ML II cellular phenotype.
- Can enzyme replacement therapy revert¨iNKT¨cell dysfunction in acid sphingomyelinase deficiency patients?Publication . Chaves, João; da Silva Gaspar, Paulo Jorge Miranda; Macedo, FatimaAcid sphingomyelinase deficiency (ASMD) is a lysosomal storage disease caused by deficient activity of the enzyme acid sphingomyelinase (ASM), resulting in an abnormal accumulation of sphingomyelin in lysosomes. The abnormal accumulation of sphingomyelin, a crucial cell membrane component, ultimately impairs pulmonary, hepatic, and sometimes neurological functions, with severe forms of the disease being fatal in the first years of life. Invariant Natural Killer T (iNKT) cells are lipid-reactive T cells that play a central role in a wide range of immune responses including cancer, infection and inflammation. iNKT cells are restricted to CD1d, depending on the presentation of lipids by this molecule for their function. Sphingomyelin is a lipid with affinity for CD1d and its accumulation in ASMD influences the role of iNKT cells by impairing normal lipid antigen presentation to these cells. Interestingly, ASM-/- mice have reduced number of iNKT cells and impaired iNKT cell activity, in ASMD patients a reduced frequency of iNKT cells is also observed (1). Noteworthy, enzyme replacement therapy (ERT) with recombinant ASM can prevent iNKT cell deficiency in ASM-/- mice (1). In the current study we are investigating the effect of ERT on iNKT cells in ASMD adult patients.
- Cell invasion and metastasis: role of Rho-GTPasesPublication . Matos, Paulo
- 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.
- Co-Inheritance of alpha-thalassemia and sickle cell disease in a cohort of Angolan pediatric patientsPublication . Santos, Brígida; Delgadinho, Mariana; Ginete, Catarina; Germano, Isabel; Miranda, Armandina; Arez, Ana Paula; Faustino, Paula; Brito, MiguelIntrodution: Sickle cell disease (SCD) is a recessive hereditary disease and a major global health problem, affecting over 300.000 newborn infants each year, and it is estimated that 75% of these births occur in Sub-Saharan Africa. SCD is a monogenic disease; the clinical manifestations are very heterogeneous due to environmental and genetic factors; in particular, the co-inheritance of alpha-thalassemia and an innate ability to produce fetal haemoglobin are two major modifiers that substantially impact disease pathophysiology. Objectives: This study explores the association between alpha-thalassemia, fetal haemoglobin, haematological indices, and clinical adverse events in pediatric Angolan sickle cell disease pediatric patients. Methods: A total of 200 SCD children were selected, after guardian written informed consent. None of them was treated with hydroxyurea or transfusion in the last 3 months. A venous blood sample was collected from each participant in the context of the routine medical and used for hematological analyses, fetal hemoglobin quantification, and genotyping of 3.7 kb alpha-thalassemia deletion by GAP-PCR. Mean values, standard deviation, and frequency distributions were performed to estimate the hematological, clinical, and genetic data. Results: The frequency of the 3.7 kb alpha-thalassemia deletion in homozygosity was 12.5%, and in heterozygosity was 55.0%. An increase in alpha-thalassemia frequency was observed in children older than 5 years old (11.7% vs. 13.00%). Furthermore, 3.7 kb alpha-thalassemia deletion homozygotes had a significantly higher age of the first manifestation, lower number of blood transfusions by year, higher haemoglobin, lower mean corpuscular volume, mean corpuscular haemoglobin, and lower hemolytic rate observed by a lower number of reticulocytes count. There were no differences in fetal haemoglobin between the three genotypes. Moreover, the number of stroke events, osteomyelitis, splenomegaly, splenectomy, and hepatomegaly were lower when alpha-thalassemia was co-inherited. Conclusion: The effect of alpha-thalassemia deletion in SCD was analysed, and results reinforce that this trait influences the haematological and clinical aspects and produces a milder phenotype.
- 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.